Mon Nov 17 12:31:15 EST 2025 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR /usr/local/freesurfer/stable5_3_0/bin/recon-all -subjid PBRHOPE_HOPE086_PETMR -i /autofs/space/hope_002/users/PBR28_HOPE/data/PBRHOPE_HOPE086_PETMR/mprage/mprage.nii.gz subjid PBRHOPE_HOPE086_PETMR setenv SUBJECTS_DIR /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Actual FREESURFER_HOME /autofs/vast/freesurfer/centos6_x86_64/stable5_3_0 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux r440-30.nmr.mgh.harvard.edu 4.18.0-553.79.1.el8_10.x86_64 #1 SMP Wed Oct 15 12:48:32 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize unlimited memoryuse 134217728 kbytes vmemoryuse unlimited descriptors 131072 memorylocked unlimited maxproc 1539494 maxlocks unlimited maxsignal 1539494 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 394168604 73429476 66107348 111656 254631780 318000008 Swap: 33554428 102084 33452344 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:31:15-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:31:15-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:31:16-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:31:16-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:31:16-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:31:16-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:31:16-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:31:16-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:31:16-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:31:16-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:31:16-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:31:16-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:31:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:31:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:31:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:31:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:31:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:31:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:31:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:31:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:31:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:31:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:31:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:31:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:31:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:31:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:31:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:31:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:31:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:31:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:31:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:31:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:31:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:31:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:31:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:31:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:31:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:31:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/stable5_3_0/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/freesurfer/stable5_3_0/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR mri_convert /autofs/space/hope_002/users/PBR28_HOPE/data/PBRHOPE_HOPE086_PETMR/mprage/mprage.nii.gz /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/orig/001.mgz mri_convert /autofs/space/hope_002/users/PBR28_HOPE/data/PBRHOPE_HOPE086_PETMR/mprage/mprage.nii.gz /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/space/hope_002/users/PBR28_HOPE/data/PBRHOPE_HOPE086_PETMR/mprage/mprage.nii.gz... TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0593086, -0.99824, 6.27738e-09) j_ras = (-0.00869582, -0.000516653, -0.999962) k_ras = (-0.998202, -0.0593064, 0.00871118) writing to /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/orig/001.mgz... #------------------------------------------ Started at Mon Nov 17 12:31:15 EST 2025 Ended at Mon Nov 17 12:31:23 EST 2025 #@#%# recon-all-run-time-hours 0.002 recon-all -s PBRHOPE_HOPE086_PETMR finished without error at Mon Nov 17 12:31:23 EST 2025 New invocation of recon-all Mon Nov 17 12:32:23 EST 2025 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR /usr/local/freesurfer/stable5_3_0/bin/recon-all -subjid PBRHOPE_HOPE086_PETMR -autorecon-all subjid PBRHOPE_HOPE086_PETMR setenv SUBJECTS_DIR /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Actual FREESURFER_HOME /autofs/vast/freesurfer/centos6_x86_64/stable5_3_0 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux r440-30.nmr.mgh.harvard.edu 4.18.0-553.79.1.el8_10.x86_64 #1 SMP Wed Oct 15 12:48:32 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize unlimited memoryuse 134217728 kbytes vmemoryuse unlimited descriptors 131072 memorylocked unlimited maxproc 1539494 maxlocks unlimited maxsignal 1539494 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 394168604 68328152 71043636 111664 254796816 323104196 Swap: 33554428 102084 33452344 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:32:23-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:32:23-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:32:24-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:32:24-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:32:24-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:32:24-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:32:24-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:32:24-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:32:24-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:32:24-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:32:24-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:32:24-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:32:24-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:32:24-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:32:24-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:32:24-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:32:24-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:32:25-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:32:25-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:32:25-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:32:25-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:32:25-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:32:25-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:32:25-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:32:25-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:32:25-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:32:25-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:32:25-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:32:25-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:32:25-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:32:25-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:32:26-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:32:26-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:32:26-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:32:26-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:32:26-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:32:26-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2025/11/17-17:32:26-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: ek657 Machine: r440-30.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 4.18.0-553.79.1.el8_10.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/stable5_3_0/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/freesurfer/stable5_3_0/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# MotionCor Mon Nov 17 12:32:26 EST 2025 Found 1 runs /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/orig/001.mgz /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/rawavg.mgz /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR mri_convert /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/rawavg.mgz /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/orig.mgz --conform mri_convert /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/rawavg.mgz /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/rawavg.mgz... TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0593086, -0.99824, 6.27738e-09) j_ras = (-0.00869582, -0.000516653, -0.999962) k_ras = (-0.998202, -0.0593064, 0.00871118) Original Data has (1, 1, 1) mm size and (280, 280, 208) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/orig.mgz... mri_add_xform_to_header -c /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/transforms/talairach.xfm /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/orig.mgz /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Mon Nov 17 12:32:35 EST 2025 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Mon Nov 17 12:34:16 EST 2025 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.2498, pval=0.0169 >= threshold=0.0050) awk -f /usr/local/freesurfer/stable5_3_0/bin/extract_talairach_avi_QA.awk /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/transforms/talairach_avi.log tal_QC_AZS /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/transforms/talairach_avi.log TalAviQA: 0.97836 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Mon Nov 17 12:34:16 EST 2025 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri /usr/local/freesurfer/stable5_3_0/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux r440-30.nmr.mgh.harvard.edu 4.18.0-553.79.1.el8_10.x86_64 #1 SMP Wed Oct 15 12:48:32 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux Mon Nov 17 12:34:16 EST 2025 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 tmpdir is ./tmp.mri_nu_correct.mni.2066796 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.2066796/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.2066796/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig.mgz... TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 2.6077e-08, -5.96046e-08) j_ras = (6.33299e-08, 1.97906e-09, -1) k_ras = (-1.11759e-08, 1, 2.96859e-09) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.2066796/nu0.mnc... -------------------------------------------------------- Iteration 1 Mon Nov 17 12:34:18 EST 2025 nu_correct -clobber ./tmp.mri_nu_correct.mni.2066796/nu0.mnc ./tmp.mri_nu_correct.mni.2066796/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.2066796/0/ defined(@array) is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/nu_estimate_np_and_em line 165. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/nu_estimate_np_and_em line 170. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/nu_estimate_np_and_em line 211. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/nu_estimate_np_and_em line 1051. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/nu_estimate_np_and_em line 1054. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/nu_estimate_np_and_em line 1449. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/nu_estimate_np_and_em line 1455. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/nu_estimate_np_and_em line 1457. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/nu_estimate_np_and_em line 1481. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/nu_estimate_np_and_em line 1631. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/nu_estimate_np_and_em line 1633. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/nu_estimate_np_and_em line 1635. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/nu_estimate_np_and_em line 1637. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/nu_estimate_np_and_em line 1639. (Maybe you should just omit the defined()?) [ek657@r440-30.nmr.mgh.harvard.edu:/autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/] [2025-11-17 12:34:19] running: /usr/local/freesurfer/stable5_3_0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.2066796/0/ ./tmp.mri_nu_correct.mni.2066796/nu0.mnc ./tmp.mri_nu_correct.mni.2066796/nu1.imp Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Number of iterations: 50 CV of field change: 0.00166609 [ek657@r440-30.nmr.mgh.harvard.edu:/autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/] [2025-11-17 12:34:54] running: /usr/local/freesurfer/stable5_3_0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.2066796/nu0.mnc ./tmp.mri_nu_correct.mni.2066796/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Mon Nov 17 12:35:00 EST 2025 nu_correct -clobber ./tmp.mri_nu_correct.mni.2066796/nu1.mnc ./tmp.mri_nu_correct.mni.2066796/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.2066796/1/ defined(@array) is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/nu_estimate_np_and_em line 165. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/nu_estimate_np_and_em line 170. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/nu_estimate_np_and_em line 211. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/nu_estimate_np_and_em line 1051. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/nu_estimate_np_and_em line 1054. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/nu_estimate_np_and_em line 1449. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/nu_estimate_np_and_em line 1455. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/nu_estimate_np_and_em line 1457. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/nu_estimate_np_and_em line 1481. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/nu_estimate_np_and_em line 1631. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/nu_estimate_np_and_em line 1633. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/nu_estimate_np_and_em line 1635. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/nu_estimate_np_and_em line 1637. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/nu_estimate_np_and_em line 1639. (Maybe you should just omit the defined()?) [ek657@r440-30.nmr.mgh.harvard.edu:/autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/] [2025-11-17 12:35:00] running: /usr/local/freesurfer/stable5_3_0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.2066796/1/ ./tmp.mri_nu_correct.mni.2066796/nu1.mnc ./tmp.mri_nu_correct.mni.2066796/nu2.imp Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/stable5_3_0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Number of iterations: 48 CV of field change: 0.000975525 [ek657@r440-30.nmr.mgh.harvard.edu:/autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/] [2025-11-17 12:35:38] running: /usr/local/freesurfer/stable5_3_0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.2066796/nu1.mnc ./tmp.mri_nu_correct.mni.2066796/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.2066796/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.2066796/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.2066796/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.2066796/ones.mgz sysname Linux hostname r440-30.nmr.mgh.harvard.edu machine x86_64 user ek657 input ./tmp.mri_nu_correct.mni.2066796/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.2066796/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 Found 16777216 values in range Counting number of voxels Found 16777216 voxels in final mask mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.2066796/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.2066796/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2066796/input.mean.dat $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.2066796/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.2066796/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2066796/input.mean.dat sysname Linux hostname r440-30.nmr.mgh.harvard.edu machine x86_64 user ek657 UseRobust 0 Loading ./tmp.mri_nu_correct.mni.2066796/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 16777216.000 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.2066796/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.2066796/ones.mgz --i ./tmp.mri_nu_correct.mni.2066796/nu2.mnc --sum ./tmp.mri_nu_correct.mni.2066796/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2066796/output.mean.dat $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.2066796/ones.mgz --i ./tmp.mri_nu_correct.mni.2066796/nu2.mnc --sum ./tmp.mri_nu_correct.mni.2066796/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2066796/output.mean.dat sysname Linux hostname r440-30.nmr.mgh.harvard.edu machine x86_64 user ek657 UseRobust 0 Loading ./tmp.mri_nu_correct.mni.2066796/ones.mgz Loading ./tmp.mri_nu_correct.mni.2066796/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 16777216.000 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.2066796/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.2066796/nu2.mnc ./tmp.mri_nu_correct.mni.2066796/nu2.mnc mul .84477633474731773627 Saving result to './tmp.mri_nu_correct.mni.2066796/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.2066796/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.2066796/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.2066796/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 2.6077e-08, -5.96046e-08) j_ras = (6.33299e-08, 1.97906e-09, -1) k_ras = (-1.11759e-08, 1, 2.96859e-09) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 4 seconds. mapping (25, 120) to ( 3, 110) Mon Nov 17 12:36:10 EST 2025 mri_nu_correct.mni done mri_add_xform_to_header -c /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Mon Nov 17 12:36:10 EST 2025 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.086 0.122 -0.018 2.579; -0.084 0.815 0.593 -5.657; 0.065 -0.571 0.941 -14.180; 0.000 0.000 0.000 1.000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 11 Starting OpenSpline(): npoints = 11 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 91 gm peak at 72 (72), valley at 57 (57) csf peak at 36, setting threshold to 60 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 91 gm peak at 71 (71), valley at 57 (57) csf peak at 35, setting threshold to 59 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 34 seconds. #-------------------------------------------- #@# Skull Stripping Mon Nov 17 12:37:45 EST 2025 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri mri_em_register -skull nu.mgz /usr/local/freesurfer/stable5_3_0/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta ======= NUMBER OF OPENMP THREADS = 1 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 5 reading 1 input volumes... logging results to talairach_with_skull.log reading '/usr/local/freesurfer/stable5_3_0/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=28.0 skull bounding box = (41, 24, 0) --> (208, 255, 219) using (97, 101, 110) as brain centroid... mean wm in atlas = 126, using box (76,72,83) --> (117, 129,137) to find MRI wm before smoothing, mri peak at 106 after smoothing, mri peak at 107, scaling input intensities by 1.178 scaling channel 0 by 1.17757 initial log_p = -4.6 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.609656 @ (9.091, 9.091, 9.091) max log p = -4.609656 @ (0.000, 0.000, 0.000) max log p = -4.524116 @ (-11.364, -6.818, 2.273) max log p = -4.524116 @ (0.000, 0.000, 0.000) max log p = -4.487876 @ (-0.568, 0.568, 0.568) max log p = -4.487876 @ (0.000, 0.000, 0.000) Found translation: (-2.8, 2.8, 11.9): log p = -4.488 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.2, old_max_log_p =-4.5 (thresh=-4.5) 1.226 0.081 -0.140 -20.755; 0.000 1.071 0.618 -40.055; 0.161 -0.613 1.061 65.376; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.2, old_max_log_p =-4.2 (thresh=-4.2) 1.134 0.075 -0.129 -9.766; -0.023 1.227 0.510 -44.955; 0.160 -0.468 1.133 44.688; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.2, old_max_log_p =-4.2 (thresh=-4.2) 1.134 0.075 -0.129 -9.766; -0.023 1.227 0.510 -44.955; 0.160 -0.468 1.133 44.688; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.1, old_max_log_p =-4.2 (thresh=-4.2) 1.095 0.016 -0.112 -4.214; 0.035 1.133 0.640 -54.366; 0.120 -0.605 1.019 74.762; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 1.095 0.016 -0.112 -4.214; 0.035 1.112 0.628 -51.075; 0.120 -0.605 1.019 74.762; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 1.092 0.007 -0.117 -2.491; 0.045 1.111 0.637 -52.989; 0.120 -0.615 1.015 75.668; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 1.094 0.016 -0.111 -4.065; 0.037 1.107 0.647 -52.848; 0.119 -0.623 1.009 77.596; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3481 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.09392 0.01571 -0.11137 -4.06468; 0.03668 1.10673 0.64714 -52.84793; 0.11899 -0.62315 1.00896 77.59627; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.09392 0.01571 -0.11137 -4.06468; 0.03668 1.10673 0.64714 -52.84793; 0.11899 -0.62315 1.00896 77.59627; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.094 0.016 -0.111 -4.065; 0.037 1.107 0.647 -52.848; 0.119 -0.623 1.009 77.596; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -4.1 (old=-4.6) transform before final EM align: 1.094 0.016 -0.111 -4.065; 0.037 1.107 0.647 -52.848; 0.119 -0.623 1.009 77.596; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 382743 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.09392 0.01571 -0.11137 -4.06468; 0.03668 1.10673 0.64714 -52.84793; 0.11899 -0.62315 1.00896 77.59627; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.09392 0.01571 -0.11137 -4.06468; 0.03668 1.10673 0.64714 -52.84793; 0.11899 -0.62315 1.00896 77.59627; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = 4.5 tol 0.000000 final transform: 1.094 0.016 -0.111 -4.065; 0.037 1.107 0.647 -52.848; 0.119 -0.623 1.009 77.596; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 17 minutes and 50 seconds. mri_watershed -T1 -brain_atlas /usr/local/freesurfer/stable5_3_0/average/RB_all_withskull_2008-03-26.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=123 y=105 z=84 r=104 first estimation of the main basin volume: 4784007 voxels Looking for seedpoints 2 found in the cerebellum 11 found in the rest of the brain global maximum in x=96, y=99, z=55, 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=14875628464 voxels, voxel volume =1.000 = 14875628464 mmm3 = 14875628.544 cm3 done. PostAnalyze...Basin Prior 14 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=123,y=110, z=73, r=9655 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=5 , nb = 45226 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=5 , nb = -1031259066 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=12 , nb = -1044318067 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1037801211 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=5 , nb = -1076827658 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1079323624 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 5, 7, 37, 69 after analyzing : 5, 27, 37, 37 RIGHT_CER before analyzing : 5, 12, 52, 69 after analyzing : 5, 38, 52, 45 LEFT_CER before analyzing : 12, 19, 42, 74 after analyzing : 12, 34, 42, 44 RIGHT_BRAIN before analyzing : 4, 5, 35, 69 after analyzing : 4, 25, 35, 36 LEFT_BRAIN before analyzing : 5, 7, 37, 68 after analyzing : 5, 27, 37, 37 OTHER before analyzing : 4, 14, 82, 95 after analyzing : 4, 59, 82, 68 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...64 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.011 curvature mean = 68.267, std = 7.400 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 8.76, sigma = 21.26 after rotation: sse = 8.76, sigma = 21.26 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 16.39, its var is 34.61 before Erosion-Dilatation 16.61% of inacurate vertices after Erosion-Dilatation 25.63% of inacurate vertices 59.58% of 'positive' inacurate vertices 40.42% 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...41 iterations mri_strip_skull: done peeling brain Brain Size = 1544704 voxels, voxel volume = 1.000 mm3 = 1544704 mmm3 = 1544.704 cm3 ****************************** Saving brainmask.auto.mgz done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Mon Nov 17 12:55:51 EST 2025 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /usr/local/freesurfer/stable5_3_0/average/RB_all_2008-03-26.gca transforms/talairach.lta ======= NUMBER OF OPENMP THREADS = 1 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/usr/local/freesurfer/stable5_3_0/average/RB_all_2008-03-26.gca'... average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 14.9 or > 790.2 total sample mean = 84.4 (994 zeros) ************************************************ spacing=8, using 2772 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2772, passno 0, spacing 8 resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=23.9 skull bounding box = (60, 48, 0) --> (187, 183, 133) using (102, 93, 67) as brain centroid... mean wm in atlas = 107, using box (86,76,51) --> (117, 109,83) to find MRI wm before smoothing, mri peak at 104 after smoothing, mri peak at 104, scaling input intensities by 1.029 scaling channel 0 by 1.02885 initial log_p = -4.4 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.385551 @ (9.091, 9.091, 9.091) max log p = -4.235786 @ (-4.545, -4.545, 4.545) max log p = -4.176949 @ (-2.273, -2.273, 2.273) max log p = -4.150449 @ (1.136, -1.136, 1.136) max log p = -4.138612 @ (-0.568, -0.568, -0.568) max log p = -4.138612 @ (0.000, 0.000, 0.000) Found translation: (2.8, 0.6, 16.5): log p = -4.139 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 1.075 0.000 0.000 -6.457; 0.000 1.066 0.140 -12.183; 0.000 -0.131 0.991 32.678; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 1.075 0.000 0.000 -6.457; 0.000 1.066 0.140 -12.183; 0.000 -0.131 0.991 32.678; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.1 (thresh=-4.1) 1.084 0.143 -0.052 -22.801; -0.133 1.016 0.145 11.499; 0.076 -0.130 1.008 21.764; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 1.070 0.096 0.006 -19.010; -0.090 0.990 0.207 1.606; 0.014 -0.209 1.016 39.543; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 1.050 0.048 -0.075 -2.292; -0.019 0.980 0.268 -9.579; 0.091 -0.271 1.017 36.677; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-4.0 (thresh=-4.0) 1.067 -0.013 -0.103 2.931; 0.072 0.961 0.482 -34.914; 0.094 -0.484 1.000 66.897; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.8, old_max_log_p =-3.9 (thresh=-3.9) 1.049 0.017 -0.079 -0.053; 0.056 0.920 0.677 -43.907; 0.079 -0.623 0.890 96.569; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 7 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.068 0.017 -0.080 -2.342; 0.061 0.877 0.733 -44.131; 0.074 -0.669 0.828 107.197; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 8 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.088 0.018 -0.082 -4.764; 0.060 0.860 0.720 -42.950; 0.072 -0.656 0.813 107.162; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 9 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.088 0.018 -0.082 -4.764; 0.057 0.865 0.680 -39.890; 0.076 -0.640 0.851 101.802; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 10 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.088 0.018 -0.082 -4.764; 0.057 0.865 0.680 -39.890; 0.076 -0.640 0.851 101.802; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 11 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.084 0.037 -0.077 -6.372; 0.039 0.866 0.683 -37.147; 0.085 -0.641 0.853 100.723; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 12 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.7, old_max_log_p =-3.8 (thresh=-3.8) 1.085 0.023 -0.089 -4.423; 0.057 0.868 0.682 -39.959; 0.085 -0.640 0.852 100.729; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 13 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.7, old_max_log_p =-3.7 (thresh=-3.7) 1.087 0.023 -0.089 -4.731; 0.057 0.867 0.681 -39.773; 0.085 -0.640 0.851 100.734; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 14 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.7, old_max_log_p =-3.7 (thresh=-3.7) 1.087 0.023 -0.089 -4.731; 0.057 0.867 0.681 -39.773; 0.085 -0.640 0.851 100.734; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2772 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.08725 0.02286 -0.08891 -4.73085; 0.05681 0.86688 0.68135 -39.77274; 0.08476 -0.63953 0.85057 100.73400; 0.00000 0.00000 0.00000 1.00000; nsamples 2772 Quasinewton: input matrix 1.08725 0.02286 -0.08891 -4.73085; 0.05681 0.86688 0.68135 -39.77274; 0.08476 -0.63953 0.85057 100.73400; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 017: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.087 0.023 -0.089 -4.731; 0.057 0.867 0.681 -39.773; 0.085 -0.640 0.851 100.734; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.7 (old=-4.4) transform before final EM align: 1.087 0.023 -0.089 -4.731; 0.057 0.867 0.681 -39.773; 0.085 -0.640 0.851 100.734; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 312841 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.08725 0.02286 -0.08891 -4.73085; 0.05681 0.86688 0.68135 -39.77274; 0.08476 -0.63953 0.85057 100.73400; 0.00000 0.00000 0.00000 1.00000; nsamples 312841 Quasinewton: input matrix 1.08725 0.02286 -0.08891 -4.73085; 0.05681 0.86688 0.68135 -39.77274; 0.08476 -0.63953 0.85057 100.73400; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 018: -log(p) = 4.1 after pass:transform: ( 1.09, 0.02, -0.09, -4.73) ( 0.06, 0.87, 0.68, -39.77) ( 0.08, -0.64, 0.85, 100.73) IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 020: -log(p) = 4.1 tol 0.000000 final transform: 1.087 0.023 -0.089 -4.731; 0.057 0.867 0.681 -39.773; 0.085 -0.640 0.851 100.734; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 30 minutes and 14 seconds. #-------------------------------------- #@# CA Normalize Mon Nov 17 13:26:05 EST 2025 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/stable5_3_0/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/usr/local/freesurfer/stable5_3_0/average/RB_all_2008-03-26.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=21.9 skull bounding box = (60, 48, 0) --> (187, 184, 133) using (102, 93, 67) as brain centroid... mean wm in atlas = 107, using box (86,76,51) --> (117, 109,83) to find MRI wm before smoothing, mri peak at 104 after smoothing, mri peak at 104, scaling input intensities by 1.029 scaling channel 0 by 1.02885 using 244171 sample points... INFO: compute sample coordinates transform 1.087 0.023 -0.089 -4.731; 0.057 0.867 0.681 -39.773; 0.085 -0.640 0.851 100.734; 0.000 0.000 0.000 1.000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (117, 47, 14) --> (184, 178, 154) Left_Cerebral_White_Matter: limiting intensities to 109.0 --> 166.0 7 of 32 (21.9%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (64, 47, 19) --> (128, 171, 154) Right_Cerebral_White_Matter: limiting intensities to 101.0 --> 166.0 0 of 113 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (124, 141, 56) --> (169, 184, 102) Left_Cerebellum_White_Matter: limiting intensities to 94.0 --> 166.0 0 of 18 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (81, 141, 56) --> (123, 184, 104) Right_Cerebellum_White_Matter: limiting intensities to 96.0 --> 166.0 0 of 10 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (110, 123, 76) --> (140, 182, 111) using 173 total control points for intensity normalization... bias field = 0.942 +- 0.061 0 of 166 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (117, 47, 14) --> (184, 178, 154) Left_Cerebral_White_Matter: limiting intensities to 90.0 --> 157.0 1 of 75 (1.3%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (64, 47, 19) --> (128, 171, 154) Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 157.0 0 of 153 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (124, 141, 56) --> (169, 184, 102) Left_Cerebellum_White_Matter: limiting intensities to 86.0 --> 157.0 8 of 28 (28.6%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (81, 141, 56) --> (123, 184, 104) Right_Cerebellum_White_Matter: limiting intensities to 81.0 --> 157.0 0 of 25 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (110, 123, 76) --> (140, 182, 111) Brain_Stem: limiting intensities to 79.0 --> 157.0 0 of 45 (0.0%) samples deleted using 326 total control points for intensity normalization... bias field = 1.001 +- 0.056 0 of 317 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (117, 47, 14) --> (184, 178, 154) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 158.0 0 of 190 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (64, 47, 19) --> (128, 171, 154) Right_Cerebral_White_Matter: limiting intensities to 89.0 --> 158.0 0 of 254 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (124, 141, 56) --> (169, 184, 102) Left_Cerebellum_White_Matter: limiting intensities to 84.0 --> 158.0 6 of 35 (17.1%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (81, 141, 56) --> (123, 184, 104) Right_Cerebellum_White_Matter: limiting intensities to 77.0 --> 158.0 0 of 26 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (110, 123, 76) --> (140, 182, 111) Brain_Stem: limiting intensities to 77.0 --> 158.0 0 of 91 (0.0%) samples deleted using 596 total control points for intensity normalization... bias field = 1.006 +- 0.055 1 of 590 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 15 seconds. #-------------------------------------- #@# CA Reg Mon Nov 17 13:27:20 EST 2025 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer/stable5_3_0/average/RB_all_2008-03-26.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log ======= NUMBER OF OPENMP THREADS = 1 ======= reading input volume 'norm.mgz'... reading GCA '/usr/local/freesurfer/stable5_3_0/average/RB_all_2008-03-26.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.29 (predicted orig area = 6.2) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=1.010, neg=0, invalid=96777 0001: dt=129.472000, rms=0.889 (11.950%), neg=0, invalid=96777 0002: dt=295.936000, rms=0.829 (6.793%), neg=0, invalid=96777 0003: dt=110.976000, rms=0.798 (3.760%), neg=0, invalid=96777 0004: dt=129.472000, rms=0.791 (0.813%), neg=0, invalid=96777 0005: dt=129.472000, rms=0.781 (1.327%), neg=0, invalid=96777 0006: dt=129.472000, rms=0.776 (0.548%), neg=0, invalid=96777 0007: dt=221.952000, rms=0.767 (1.211%), neg=0, invalid=96777 0008: dt=73.984000, rms=0.764 (0.375%), neg=0, invalid=96777 0009: dt=887.808000, rms=0.750 (1.895%), neg=0, invalid=96777 0010: dt=73.984000, rms=0.748 (0.242%), neg=0, invalid=96777 0011: dt=73.984000, rms=0.746 (0.202%), neg=0, invalid=96777 0012: dt=73.984000, rms=0.744 (0.314%), neg=0, invalid=96777 0013: dt=73.984000, rms=0.741 (0.365%), neg=0, invalid=96777 0014: dt=73.984000, rms=0.738 (0.416%), neg=0, invalid=96777 0015: dt=73.984000, rms=0.735 (0.444%), neg=0, invalid=96777 0016: dt=73.984000, rms=0.732 (0.443%), neg=0, invalid=96777 0017: dt=73.984000, rms=0.729 (0.435%), neg=0, invalid=96777 0018: dt=73.984000, rms=0.726 (0.385%), neg=0, invalid=96777 0019: dt=73.984000, rms=0.723 (0.329%), neg=0, invalid=96777 0020: dt=73.984000, rms=0.721 (0.324%), neg=0, invalid=96777 0021: dt=73.984000, rms=0.719 (0.300%), neg=0, invalid=96777 0022: dt=73.984000, rms=0.717 (0.259%), neg=0, invalid=96777 0023: dt=73.984000, rms=0.715 (0.249%), neg=0, invalid=96777 0024: dt=73.984000, rms=0.713 (0.261%), neg=0, invalid=96777 0025: dt=73.984000, rms=0.711 (0.275%), neg=0, invalid=96777 0026: dt=73.984000, rms=0.709 (0.314%), neg=0, invalid=96777 0027: dt=73.984000, rms=0.707 (0.330%), neg=0, invalid=96777 0028: dt=73.984000, rms=0.705 (0.306%), neg=0, invalid=96777 0029: dt=73.984000, rms=0.703 (0.252%), neg=0, invalid=96777 0030: dt=73.984000, rms=0.701 (0.199%), neg=0, invalid=96777 0031: dt=73.984000, rms=0.700 (0.164%), neg=0, invalid=96777 0032: dt=73.984000, rms=0.699 (0.169%), neg=0, invalid=96777 0033: dt=73.984000, rms=0.698 (0.153%), neg=0, invalid=96777 0034: dt=73.984000, rms=0.697 (0.125%), neg=0, invalid=96777 0035: dt=73.984000, rms=0.696 (0.098%), neg=0, invalid=96777 0036: dt=73.984000, rms=0.696 (0.099%), neg=0, invalid=96777 0037: dt=73.984000, rms=0.695 (0.121%), neg=0, invalid=96777 0038: dt=73.984000, rms=0.694 (0.143%), neg=0, invalid=96777 0039: dt=73.984000, rms=0.693 (0.150%), neg=0, invalid=96777 0040: dt=73.984000, rms=0.692 (0.136%), neg=0, invalid=96777 0041: dt=73.984000, rms=0.691 (0.132%), neg=0, invalid=96777 0042: dt=73.984000, rms=0.690 (0.112%), neg=0, invalid=96777 0043: dt=73.984000, rms=0.689 (0.118%), neg=0, invalid=96777 0044: dt=73.984000, rms=0.689 (0.096%), neg=0, invalid=96777 0045: dt=0.000000, rms=0.689 (0.002%), neg=0, invalid=96777 0046: dt=0.850000, rms=0.689 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.689, neg=0, invalid=96777 0047: dt=295.936000, rms=0.687 (0.263%), neg=0, invalid=96777 0048: dt=369.920000, rms=0.686 (0.189%), neg=0, invalid=96777 0049: dt=369.920000, rms=0.686 (-0.466%), neg=0, invalid=96777 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.694, neg=0, invalid=96777 0050: dt=82.944000, rms=0.690 (0.571%), neg=0, invalid=96777 0051: dt=82.944000, rms=0.684 (0.943%), neg=0, invalid=96777 0052: dt=31.104000, rms=0.681 (0.362%), neg=0, invalid=96777 0053: dt=145.152000, rms=0.674 (1.073%), neg=0, invalid=96777 0054: dt=25.920000, rms=0.672 (0.331%), neg=0, invalid=96777 0055: dt=331.776000, rms=0.663 (1.233%), neg=0, invalid=96777 0056: dt=25.920000, rms=0.659 (0.733%), neg=0, invalid=96777 0057: dt=36.288000, rms=0.657 (0.219%), neg=0, invalid=96777 0058: dt=36.288000, rms=0.656 (0.199%), neg=0, invalid=96777 0059: dt=36.288000, rms=0.654 (0.248%), neg=0, invalid=96777 0060: dt=36.288000, rms=0.652 (0.307%), neg=0, invalid=96777 0061: dt=36.288000, rms=0.650 (0.374%), neg=0, invalid=96777 0062: dt=36.288000, rms=0.647 (0.473%), neg=0, invalid=96777 0063: dt=36.288000, rms=0.644 (0.476%), neg=0, invalid=96777 0064: dt=36.288000, rms=0.641 (0.441%), neg=0, invalid=96777 0065: dt=36.288000, rms=0.638 (0.384%), neg=0, invalid=96777 0066: dt=36.288000, rms=0.636 (0.392%), neg=0, invalid=96777 0067: dt=36.288000, rms=0.633 (0.382%), neg=0, invalid=96777 0068: dt=36.288000, rms=0.631 (0.326%), neg=0, invalid=96777 0069: dt=36.288000, rms=0.630 (0.268%), neg=0, invalid=96777 0070: dt=36.288000, rms=0.628 (0.229%), neg=0, invalid=96777 0071: dt=36.288000, rms=0.627 (0.261%), neg=0, invalid=96777 0072: dt=36.288000, rms=0.625 (0.220%), neg=0, invalid=96777 0073: dt=36.288000, rms=0.624 (0.187%), neg=0, invalid=96777 0074: dt=36.288000, rms=0.623 (0.149%), neg=0, invalid=96777 0075: dt=36.288000, rms=0.622 (0.164%), neg=0, invalid=96777 0076: dt=36.288000, rms=0.621 (0.170%), neg=0, invalid=96777 0077: dt=36.288000, rms=0.620 (0.161%), neg=0, invalid=96777 0078: dt=36.288000, rms=0.619 (0.130%), neg=0, invalid=96777 0079: dt=36.288000, rms=0.618 (0.116%), neg=0, invalid=96777 0080: dt=36.288000, rms=0.618 (0.114%), neg=0, invalid=96777 0081: dt=124.416000, rms=0.617 (0.052%), neg=0, invalid=96777 0082: dt=124.416000, rms=0.617 (-0.266%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.617, neg=0, invalid=96777 0083: dt=36.288000, rms=0.616 (0.163%), neg=0, invalid=96777 0084: dt=82.944000, rms=0.616 (0.113%), neg=0, invalid=96777 0085: dt=82.944000, rms=0.616 (-0.010%), neg=0, invalid=96777 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.649, neg=0, invalid=96777 0086: dt=2.800000, rms=0.649 (0.029%), neg=0, invalid=96777 0087: dt=2.000000, rms=0.649 (0.008%), neg=0, invalid=96777 0088: dt=2.000000, rms=0.649 (-0.006%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.649, neg=0, invalid=96777 0089: dt=1.600000, rms=0.649 (0.004%), neg=0, invalid=96777 0090: dt=0.400000, rms=0.649 (0.001%), neg=0, invalid=96777 0091: dt=0.400000, rms=0.649 (-0.001%), neg=0, invalid=96777 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.738, neg=0, invalid=96777 0092: dt=5.031250, rms=0.717 (2.950%), neg=0, invalid=96777 0093: dt=3.432099, rms=0.715 (0.253%), neg=0, invalid=96777 0094: dt=1.008000, rms=0.715 (0.012%), neg=0, invalid=96777 0095: dt=1.008000, rms=0.715 (-0.002%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.715, neg=0, invalid=96777 0096: dt=0.000000, rms=0.715 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.800, neg=0, invalid=96777 0097: dt=0.594595, rms=0.798 (0.217%), neg=0, invalid=96777 0098: dt=1.203791, rms=0.796 (0.286%), neg=0, invalid=96777 0099: dt=1.979592, rms=0.793 (0.387%), neg=0, invalid=96777 0100: dt=0.448000, rms=0.793 (0.019%), neg=0, invalid=96777 0101: dt=0.448000, rms=0.792 (0.027%), neg=0, invalid=96777 0102: dt=0.448000, rms=0.792 (0.031%), neg=0, invalid=96777 0103: dt=0.448000, rms=0.792 (0.000%), neg=0, invalid=96777 0104: dt=0.448000, rms=0.792 (-0.059%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.792, neg=0, invalid=96777 0105: dt=1.280000, rms=0.791 (0.132%), neg=0, invalid=96777 0106: dt=0.000000, rms=0.791 (0.000%), neg=0, invalid=96777 0107: dt=0.100000, rms=0.791 (-0.008%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.719, neg=0, invalid=96777 0108: dt=0.320000, rms=0.703 (2.205%), neg=0, invalid=96777 0109: dt=0.000000, rms=0.703 (0.006%), neg=0, invalid=96777 0110: dt=0.050000, rms=0.703 (-0.292%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.703, neg=0, invalid=96777 0111: dt=0.000000, rms=0.703 (0.000%), neg=0, invalid=96777 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.10350 (15) Left_Lateral_Ventricle (4): linear fit = 0.47 x + 0.0 (1307 voxels, overlap=0.007) Left_Lateral_Ventricle (4): linear fit = 0.47 x + 0.0 (1307 voxels, peak = 11), gca=11.2 gca peak = 0.14022 (22) mri peak = 0.09502 (12) Right_Lateral_Ventricle (43): linear fit = 0.46 x + 0.0 (961 voxels, overlap=0.008) Right_Lateral_Ventricle (43): linear fit = 0.46 x + 0.0 (961 voxels, peak = 10), gca=10.0 gca peak = 0.24234 (100) mri peak = 0.04361 (96) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (313 voxels, overlap=0.693) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (313 voxels, peak = 100), gca=100.5 gca peak = 0.19192 (97) mri peak = 0.06078 (90) Left_Pallidum (13): linear fit = 0.94 x + 0.0 (216 voxels, overlap=0.716) Left_Pallidum (13): linear fit = 0.94 x + 0.0 (216 voxels, peak = 91), gca=90.7 gca peak = 0.24007 (63) mri peak = 0.04880 (73) Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (608 voxels, overlap=0.028) Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (608 voxels, peak = 72), gca=71.5 gca peak = 0.29892 (64) mri peak = 0.06470 (78) Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (484 voxels, overlap=0.561) Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (484 voxels, peak = 71), gca=71.4 gca peak = 0.12541 (104) mri peak = 0.07971 (108) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (61680 voxels, overlap=0.760) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (61680 voxels, peak = 109), gca=108.7 gca peak = 0.13686 (104) mri peak = 0.06357 (106) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (61717 voxels, overlap=0.866) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (61717 voxels, peak = 107), gca=106.6 gca peak = 0.11691 (63) mri peak = 0.03382 (80) Left_Cerebral_Cortex (3): linear fit = 1.24 x + 0.0 (17803 voxels, overlap=0.162) Left_Cerebral_Cortex (3): linear fit = 1.24 x + 0.0 (17803 voxels, peak = 78), gca=77.8 gca peak = 0.13270 (63) mri peak = 0.03496 (75) Right_Cerebral_Cortex (42): linear fit = 1.20 x + 0.0 (19834 voxels, overlap=0.014) Right_Cerebral_Cortex (42): linear fit = 1.20 x + 0.0 (19834 voxels, peak = 75), gca=75.3 gca peak = 0.15182 (70) mri peak = 0.08527 (85) Right_Caudate (50): linear fit = 1.15 x + 0.0 (374 voxels, overlap=0.207) Right_Caudate (50): linear fit = 1.15 x + 0.0 (374 voxels, peak = 81), gca=80.8 gca peak = 0.14251 (76) mri peak = 0.08036 (90) Left_Caudate (11): linear fit = 1.16 x + 0.0 (639 voxels, overlap=0.206) Left_Caudate (11): linear fit = 1.16 x + 0.0 (639 voxels, peak = 89), gca=88.5 gca peak = 0.12116 (60) mri peak = 0.02567 (85) Left_Cerebellum_Cortex (8): linear fit = 1.58 x + 0.0 (13440 voxels, overlap=0.000) Left_Cerebellum_Cortex (8): linear fit = 1.58 x + 0.0 (13440 voxels, peak = 94), gca=94.5 gca peak = 0.12723 (61) mri peak = 0.03476 (90) Right_Cerebellum_Cortex (47): linear fit = 1.48 x + 0.0 (15734 voxels, overlap=0.001) Right_Cerebellum_Cortex (47): linear fit = 1.48 x + 0.0 (15734 voxels, peak = 90), gca=90.0 gca peak = 0.22684 (88) mri peak = 0.03453 (80) Left_Cerebellum_White_Matter (7): linear fit = 0.94 x + 0.0 (5942 voxels, overlap=0.404) Left_Cerebellum_White_Matter (7): linear fit = 0.94 x + 0.0 (5942 voxels, peak = 82), gca=82.3 gca peak = 0.21067 (87) mri peak = 0.03378 (75) Right_Cerebellum_White_Matter (46): linear fit = 0.90 x + 0.0 (5590 voxels, overlap=0.189) Right_Cerebellum_White_Matter (46): linear fit = 0.90 x + 0.0 (5590 voxels, peak = 79), gca=78.7 gca peak = 0.25455 (62) mri peak = 0.07695 (76) Left_Amygdala (18): linear fit = 1.18 x + 0.0 (222 voxels, overlap=0.189) Left_Amygdala (18): linear fit = 1.18 x + 0.0 (222 voxels, peak = 73), gca=73.5 gca peak = 0.39668 (62) mri peak = 0.10860 (78) Right_Amygdala (54): linear fit = 1.24 x + 0.0 (223 voxels, overlap=0.068) Right_Amygdala (54): linear fit = 1.24 x + 0.0 (223 voxels, peak = 77), gca=76.6 gca peak = 0.10129 (93) mri peak = 0.05783 (107) Left_Thalamus_Proper (10): linear fit = 1.12 x + 0.0 (4723 voxels, overlap=0.324) Left_Thalamus_Proper (10): linear fit = 1.12 x + 0.0 (4723 voxels, peak = 105), gca=104.6 gca peak = 0.12071 (89) mri peak = 0.05597 (103) Right_Thalamus_Proper (49): linear fit = 1.15 x + 0.0 (3812 voxels, overlap=0.265) Right_Thalamus_Proper (49): linear fit = 1.15 x + 0.0 (3812 voxels, peak = 103), gca=102.8 gca peak = 0.13716 (82) mri peak = 0.05246 (95) Left_Putamen (12): linear fit = 1.13 x + 0.0 (2122 voxels, overlap=0.260) Left_Putamen (12): linear fit = 1.13 x + 0.0 (2122 voxels, peak = 93), gca=93.1 gca peak = 0.15214 (84) mri peak = 0.06524 (93) Right_Putamen (51): linear fit = 1.12 x + 0.0 (2068 voxels, overlap=0.374) Right_Putamen (51): linear fit = 1.12 x + 0.0 (2068 voxels, peak = 94), gca=94.5 gca peak = 0.08983 (85) mri peak = 0.07515 (90) Brain_Stem (16): linear fit = 1.08 x + 0.0 (8589 voxels, overlap=0.592) Brain_Stem (16): linear fit = 1.08 x + 0.0 (8589 voxels, peak = 91), gca=91.4 gca peak = 0.11809 (92) mri peak = 0.06928 (95) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (636 voxels, overlap=0.470) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (636 voxels, peak = 103), gca=102.6 gca peak = 0.12914 (94) mri peak = 0.05822 (101) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (633 voxels, overlap=0.353) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (633 voxels, peak = 102), gca=102.0 gca peak = 0.21100 (36) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13542 (27) uniform distribution in MR - rejecting arbitrary fit gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21802 (40) gca peak Left_Cerebellum_Cortex = 0.12116 (60) gca peak Third_Ventricle = 0.21100 (36) gca peak Fourth_Ventricle = 0.13542 (27) gca peak CSF = 0.17123 (45) gca peak Left_Accumbens_area = 0.25875 (69) gca peak Left_undetermined = 0.96240 (36) gca peak Left_vessel = 0.33262 (65) gca peak Left_choroid_plexus = 0.09846 (46) gca peak Right_Inf_Lat_Vent = 0.28113 (34) gca peak Right_Accumbens_area = 0.27120 (72) gca peak Right_vessel = 0.61915 (60) gca peak Right_choroid_plexus = 0.12775 (51) gca peak Fifth_Ventricle = 0.45329 (44) gca peak WM_hypointensities = 0.11729 (81) gca peak non_WM_hypointensities = 0.10912 (56) gca peak Optic_Chiasm = 0.33287 (75) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means setting label Left_Cerebellum_Cortex based on Right_Cerebellum_Cortex = 1.48 x + 0: 90 estimating mean gm scale to be 1.18 x + 0.0 estimating mean wm scale to be 1.03 x + 0.0 estimating mean csf scale to be 0.46 x + 0.0 saving intensity scales to talairach.label_intensities.txt **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.759, neg=0, invalid=96777 0112: dt=92.480000, rms=0.739 (2.575%), neg=0, invalid=96777 0113: dt=129.472000, rms=0.733 (0.843%), neg=0, invalid=96777 0114: dt=221.952000, rms=0.725 (1.137%), neg=0, invalid=96777 0115: dt=32.368000, rms=0.723 (0.198%), neg=0, invalid=96777 0116: dt=92.480000, rms=0.722 (0.159%), neg=0, invalid=96777 0117: dt=369.920000, rms=0.715 (0.902%), neg=0, invalid=96777 0118: dt=32.368000, rms=0.714 (0.172%), neg=0, invalid=96777 0119: dt=32.368000, rms=0.714 (0.056%), neg=0, invalid=96777 0120: dt=129.472000, rms=0.713 (0.089%), neg=0, invalid=96777 0121: dt=369.920000, rms=0.709 (0.607%), neg=0, invalid=96777 0122: dt=32.368000, rms=0.708 (0.177%), neg=0, invalid=96777 0123: dt=32.368000, rms=0.707 (0.048%), neg=0, invalid=96777 0124: dt=32.368000, rms=0.707 (0.017%), neg=0, invalid=96777 0125: dt=32.368000, rms=0.707 (0.019%), neg=0, invalid=96777 0126: dt=32.368000, rms=0.707 (0.047%), neg=0, invalid=96777 0127: dt=32.368000, rms=0.706 (0.118%), neg=0, invalid=96777 0128: dt=32.368000, rms=0.704 (0.194%), neg=0, invalid=96777 0129: dt=32.368000, rms=0.703 (0.230%), neg=0, invalid=96777 0130: dt=32.368000, rms=0.701 (0.218%), neg=0, invalid=96777 0131: dt=32.368000, rms=0.700 (0.200%), neg=0, invalid=96777 0132: dt=32.368000, rms=0.699 (0.179%), neg=0, invalid=96777 0133: dt=32.368000, rms=0.698 (0.160%), neg=0, invalid=96777 0134: dt=32.368000, rms=0.697 (0.148%), neg=0, invalid=96777 0135: dt=32.368000, rms=0.695 (0.168%), neg=0, invalid=96777 0136: dt=32.368000, rms=0.694 (0.195%), neg=0, invalid=96777 0137: dt=32.368000, rms=0.693 (0.208%), neg=0, invalid=96777 0138: dt=32.368000, rms=0.691 (0.197%), neg=0, invalid=96777 0139: dt=32.368000, rms=0.690 (0.177%), neg=0, invalid=96777 0140: dt=32.368000, rms=0.689 (0.157%), neg=0, invalid=96777 0141: dt=32.368000, rms=0.688 (0.138%), neg=0, invalid=96777 0142: dt=32.368000, rms=0.687 (0.126%), neg=0, invalid=96777 0143: dt=32.368000, rms=0.686 (0.130%), neg=0, invalid=96777 0144: dt=32.368000, rms=0.685 (0.140%), neg=0, invalid=96777 0145: dt=32.368000, rms=0.684 (0.144%), neg=0, invalid=96777 0146: dt=32.368000, rms=0.683 (0.141%), neg=0, invalid=96777 0147: dt=32.368000, rms=0.682 (0.126%), neg=0, invalid=96777 0148: dt=32.368000, rms=0.682 (0.119%), neg=0, invalid=96777 0149: dt=32.368000, rms=0.681 (0.110%), neg=0, invalid=96777 0150: dt=32.368000, rms=0.680 (0.104%), neg=0, invalid=96777 0151: dt=32.368000, rms=0.679 (0.105%), neg=0, invalid=96777 0152: dt=32.368000, rms=0.679 (0.116%), neg=0, invalid=96777 0153: dt=32.368000, rms=0.678 (0.123%), neg=0, invalid=96777 0154: dt=32.368000, rms=0.677 (0.119%), neg=0, invalid=96777 0155: dt=32.368000, rms=0.676 (0.111%), neg=0, invalid=96777 0156: dt=32.368000, rms=0.676 (0.103%), neg=0, invalid=96777 0157: dt=32.368000, rms=0.675 (0.092%), neg=0, invalid=96777 0158: dt=32.368000, rms=0.674 (0.088%), neg=0, invalid=96777 0159: dt=32.368000, rms=0.674 (0.088%), neg=0, invalid=96777 0160: dt=32.368000, rms=0.673 (0.087%), neg=0, invalid=96777 0161: dt=32.368000, rms=0.673 (0.089%), neg=0, invalid=96777 0162: dt=32.368000, rms=0.672 (0.089%), neg=0, invalid=96777 0163: dt=32.368000, rms=0.671 (0.089%), neg=0, invalid=96777 0164: dt=32.368000, rms=0.671 (0.082%), neg=0, invalid=96777 0165: dt=32.368000, rms=0.670 (0.076%), neg=0, invalid=96777 0166: dt=32.368000, rms=0.670 (0.073%), neg=0, invalid=96777 0167: dt=32.368000, rms=0.669 (0.072%), neg=0, invalid=96777 0168: dt=32.368000, rms=0.669 (0.072%), neg=0, invalid=96777 0169: dt=32.368000, rms=0.668 (0.071%), neg=0, invalid=96777 0170: dt=32.368000, rms=0.668 (0.070%), neg=0, invalid=96777 0171: dt=32.368000, rms=0.667 (0.069%), neg=0, invalid=96777 0172: dt=32.368000, rms=0.667 (0.064%), neg=0, invalid=96777 0173: dt=32.368000, rms=0.667 (0.060%), neg=0, invalid=96777 0174: dt=32.368000, rms=0.666 (0.057%), neg=0, invalid=96777 0175: dt=32.368000, rms=0.666 (0.057%), neg=0, invalid=96777 0176: dt=32.368000, rms=0.665 (0.058%), neg=0, invalid=96777 0177: dt=32.368000, rms=0.665 (0.058%), neg=0, invalid=96777 0178: dt=32.368000, rms=0.665 (0.057%), neg=0, invalid=96777 0179: dt=32.368000, rms=0.664 (0.056%), neg=0, invalid=96777 0180: dt=32.368000, rms=0.664 (0.053%), neg=0, invalid=96777 0181: dt=32.368000, rms=0.664 (0.053%), neg=0, invalid=96777 0182: dt=32.368000, rms=0.663 (0.049%), neg=0, invalid=96777 0183: dt=32.368000, rms=0.663 (0.046%), neg=0, invalid=96777 0184: dt=32.368000, rms=0.663 (0.041%), neg=0, invalid=96777 0185: dt=32.368000, rms=0.662 (0.038%), neg=0, invalid=96777 0186: dt=32.368000, rms=0.662 (0.042%), neg=0, invalid=96777 0187: dt=32.368000, rms=0.662 (0.046%), neg=0, invalid=96777 0188: dt=32.368000, rms=0.662 (0.046%), neg=0, invalid=96777 0189: dt=32.368000, rms=0.661 (0.042%), neg=0, invalid=96777 0190: dt=32.368000, rms=0.661 (0.039%), neg=0, invalid=96777 0191: dt=32.368000, rms=0.661 (0.036%), neg=0, invalid=96777 0192: dt=32.368000, rms=0.661 (0.036%), neg=0, invalid=96777 0193: dt=32.368000, rms=0.660 (0.037%), neg=0, invalid=96777 0194: dt=32.368000, rms=0.660 (0.039%), neg=0, invalid=96777 0195: dt=32.368000, rms=0.660 (0.037%), neg=0, invalid=96777 0196: dt=32.368000, rms=0.660 (0.036%), neg=0, invalid=96777 0197: dt=32.368000, rms=0.659 (0.033%), neg=0, invalid=96777 0198: dt=32.368000, rms=0.659 (0.030%), neg=0, invalid=96777 0199: dt=32.368000, rms=0.659 (0.032%), neg=0, invalid=96777 0200: dt=32.368000, rms=0.659 (0.034%), neg=0, invalid=96777 0201: dt=32.368000, rms=0.658 (0.036%), neg=0, invalid=96777 0202: dt=32.368000, rms=0.658 (0.033%), neg=0, invalid=96777 0203: dt=32.368000, rms=0.658 (0.035%), neg=0, invalid=96777 0204: dt=32.368000, rms=0.658 (0.032%), neg=0, invalid=96777 0205: dt=32.368000, rms=0.658 (0.031%), neg=0, invalid=96777 0206: dt=32.368000, rms=0.657 (0.031%), neg=0, invalid=96777 0207: dt=32.368000, rms=0.657 (0.034%), neg=0, invalid=96777 0208: dt=32.368000, rms=0.657 (0.033%), neg=0, invalid=96777 0209: dt=32.368000, rms=0.657 (0.030%), neg=0, invalid=96777 0210: dt=32.368000, rms=0.657 (0.028%), neg=0, invalid=96777 0211: dt=32.368000, rms=0.656 (0.026%), neg=0, invalid=96777 0212: dt=32.368000, rms=0.656 (0.028%), neg=0, invalid=96777 0213: dt=32.368000, rms=0.656 (0.031%), neg=0, invalid=96777 0214: dt=32.368000, rms=0.656 (0.028%), neg=0, invalid=96777 0215: dt=32.368000, rms=0.656 (0.026%), neg=0, invalid=96777 0216: dt=32.368000, rms=0.656 (0.026%), neg=0, invalid=96777 0217: dt=32.368000, rms=0.655 (0.025%), neg=0, invalid=96777 0218: dt=32.368000, rms=0.655 (0.027%), neg=0, invalid=96777 0219: dt=32.368000, rms=0.655 (0.023%), neg=0, invalid=96777 0220: dt=32.368000, rms=0.655 (0.020%), neg=0, invalid=96777 0221: dt=517.888000, rms=0.655 (0.041%), neg=0, invalid=96777 0222: dt=110.976000, rms=0.655 (0.014%), neg=0, invalid=96777 0223: dt=110.976000, rms=0.655 (-0.004%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.655, neg=0, invalid=96777 0224: dt=443.904000, rms=0.652 (0.422%), neg=0, invalid=96777 0225: dt=129.472000, rms=0.651 (0.073%), neg=0, invalid=96777 0226: dt=129.472000, rms=0.651 (0.034%), neg=0, invalid=96777 0227: dt=129.472000, rms=0.651 (0.029%), neg=0, invalid=96777 0228: dt=129.472000, rms=0.650 (0.069%), neg=0, invalid=96777 0229: dt=129.472000, rms=0.650 (0.066%), neg=0, invalid=96777 0230: dt=129.472000, rms=0.650 (0.066%), neg=0, invalid=96777 0231: dt=129.472000, rms=0.649 (0.084%), neg=0, invalid=96777 0232: dt=129.472000, rms=0.648 (0.089%), neg=0, invalid=96777 0233: dt=129.472000, rms=0.648 (0.067%), neg=0, invalid=96777 0234: dt=129.472000, rms=0.648 (0.064%), neg=0, invalid=96777 0235: dt=129.472000, rms=0.647 (0.095%), neg=0, invalid=96777 0236: dt=129.472000, rms=0.647 (0.073%), neg=0, invalid=96777 0237: dt=129.472000, rms=0.646 (0.030%), neg=0, invalid=96777 0238: dt=129.472000, rms=0.646 (0.052%), neg=0, invalid=96777 0239: dt=129.472000, rms=0.645 (0.090%), neg=0, invalid=96777 0240: dt=129.472000, rms=0.645 (0.043%), neg=0, invalid=96777 0241: dt=129.472000, rms=0.645 (0.012%), neg=0, invalid=96777 0242: dt=129.472000, rms=0.645 (0.084%), neg=0, invalid=96777 0243: dt=129.472000, rms=0.644 (0.069%), neg=0, invalid=96777 0244: dt=129.472000, rms=0.644 (0.030%), neg=0, invalid=96777 0245: dt=129.472000, rms=0.644 (0.020%), neg=0, invalid=96777 0246: dt=129.472000, rms=0.643 (0.071%), neg=0, invalid=96777 0247: dt=129.472000, rms=0.643 (0.063%), neg=0, invalid=96777 0248: dt=129.472000, rms=0.643 (0.036%), neg=0, invalid=96777 0249: dt=129.472000, rms=0.642 (0.028%), neg=0, invalid=96777 0250: dt=129.472000, rms=0.642 (0.082%), neg=0, invalid=96777 0251: dt=129.472000, rms=0.642 (0.062%), neg=0, invalid=96777 0252: dt=129.472000, rms=0.641 (0.040%), neg=0, invalid=96777 0253: dt=129.472000, rms=0.641 (0.028%), neg=0, invalid=96777 0254: dt=129.472000, rms=0.641 (0.055%), neg=0, invalid=96777 0255: dt=129.472000, rms=0.640 (0.073%), neg=0, invalid=96777 0256: dt=129.472000, rms=0.640 (0.031%), neg=0, invalid=96777 0257: dt=129.472000, rms=0.640 (0.015%), neg=0, invalid=96777 0258: dt=129.472000, rms=0.640 (0.076%), neg=0, invalid=96777 0259: dt=129.472000, rms=0.639 (0.069%), neg=0, invalid=96777 0260: dt=129.472000, rms=0.639 (0.034%), neg=0, invalid=96777 0261: dt=129.472000, rms=0.639 (0.031%), neg=0, invalid=96777 0262: dt=129.472000, rms=0.638 (0.049%), neg=0, invalid=96777 0263: dt=129.472000, rms=0.638 (0.052%), neg=0, invalid=96777 0264: dt=129.472000, rms=0.638 (0.027%), neg=0, invalid=96777 0265: dt=129.472000, rms=0.638 (0.025%), neg=0, invalid=96777 0266: dt=129.472000, rms=0.637 (0.055%), neg=0, invalid=96777 0267: dt=129.472000, rms=0.637 (0.042%), neg=0, invalid=96777 0268: dt=129.472000, rms=0.637 (0.028%), neg=0, invalid=96777 0269: dt=129.472000, rms=0.637 (0.033%), neg=0, invalid=96777 0270: dt=129.472000, rms=0.636 (0.042%), neg=0, invalid=96777 0271: dt=129.472000, rms=0.636 (0.029%), neg=0, invalid=96777 0272: dt=129.472000, rms=0.636 (0.032%), neg=0, invalid=96777 0273: dt=129.472000, rms=0.636 (0.037%), neg=0, invalid=96777 0274: dt=129.472000, rms=0.636 (0.031%), neg=0, invalid=96777 0275: dt=129.472000, rms=0.635 (0.034%), neg=0, invalid=96777 0276: dt=129.472000, rms=0.635 (0.031%), neg=0, invalid=96777 0277: dt=129.472000, rms=0.635 (0.038%), neg=0, invalid=96777 0278: dt=129.472000, rms=0.635 (0.041%), neg=0, invalid=96777 0279: dt=129.472000, rms=0.635 (0.029%), neg=0, invalid=96777 0280: dt=129.472000, rms=0.634 (0.021%), neg=0, invalid=96777 0281: dt=129.472000, rms=0.634 (0.034%), neg=0, invalid=96777 0282: dt=129.472000, rms=0.634 (0.029%), neg=0, invalid=96777 0283: dt=129.472000, rms=0.634 (0.027%), neg=0, invalid=96777 0284: dt=129.472000, rms=0.634 (0.030%), neg=0, invalid=96777 0285: dt=129.472000, rms=0.634 (0.019%), neg=0, invalid=96777 0286: dt=129.472000, rms=0.633 (0.021%), neg=0, invalid=96777 0287: dt=129.472000, rms=0.633 (0.036%), neg=0, invalid=96777 0288: dt=129.472000, rms=0.633 (0.033%), neg=0, invalid=96777 0289: dt=129.472000, rms=0.633 (0.017%), neg=0, invalid=96777 0290: dt=129.472000, rms=0.633 (0.019%), neg=0, invalid=96777 0291: dt=129.472000, rms=0.633 (0.020%), neg=0, invalid=96777 0292: dt=129.472000, rms=0.632 (0.026%), neg=0, invalid=96777 0293: dt=129.472000, rms=0.632 (0.015%), neg=0, invalid=96777 0294: dt=129.472000, rms=0.632 (0.027%), neg=0, invalid=96777 0295: dt=129.472000, rms=0.632 (0.020%), neg=0, invalid=96777 0296: dt=129.472000, rms=0.632 (0.032%), neg=0, invalid=96777 0297: dt=129.472000, rms=0.632 (0.018%), neg=0, invalid=96777 0298: dt=129.472000, rms=0.632 (0.001%), neg=0, invalid=96777 0299: dt=369.920000, rms=0.631 (0.046%), neg=0, invalid=96777 0300: dt=2.023000, rms=0.631 (-0.001%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.634, neg=0, invalid=96777 0301: dt=36.288000, rms=0.632 (0.211%), neg=0, invalid=96777 0302: dt=145.152000, rms=0.628 (0.650%), neg=0, invalid=96777 0303: dt=20.736000, rms=0.627 (0.176%), neg=0, invalid=96777 0304: dt=497.664000, rms=0.611 (2.652%), neg=0, invalid=96777 0305: dt=25.920000, rms=0.609 (0.243%), neg=0, invalid=96777 0306: dt=36.288000, rms=0.608 (0.183%), neg=0, invalid=96777 0307: dt=36.288000, rms=0.608 (0.048%), neg=0, invalid=96777 0308: dt=36.288000, rms=0.607 (0.100%), neg=0, invalid=96777 0309: dt=36.288000, rms=0.606 (0.144%), neg=0, invalid=96777 0310: dt=36.288000, rms=0.605 (0.212%), neg=0, invalid=96777 0311: dt=36.288000, rms=0.603 (0.318%), neg=0, invalid=96777 0312: dt=36.288000, rms=0.600 (0.442%), neg=0, invalid=96777 0313: dt=36.288000, rms=0.597 (0.511%), neg=0, invalid=96777 0314: dt=36.288000, rms=0.594 (0.484%), neg=0, invalid=96777 0315: dt=36.288000, rms=0.592 (0.448%), neg=0, invalid=96777 0316: dt=36.288000, rms=0.589 (0.426%), neg=0, invalid=96777 0317: dt=36.288000, rms=0.587 (0.373%), neg=0, invalid=96777 0318: dt=36.288000, rms=0.585 (0.301%), neg=0, invalid=96777 0319: dt=36.288000, rms=0.584 (0.269%), neg=0, invalid=96777 0320: dt=36.288000, rms=0.582 (0.294%), neg=0, invalid=96777 0321: dt=36.288000, rms=0.580 (0.276%), neg=0, invalid=96777 0322: dt=36.288000, rms=0.579 (0.254%), neg=0, invalid=96777 0323: dt=36.288000, rms=0.578 (0.227%), neg=0, invalid=96777 0324: dt=36.288000, rms=0.576 (0.210%), neg=0, invalid=96777 0325: dt=36.288000, rms=0.575 (0.193%), neg=0, invalid=96777 0326: dt=36.288000, rms=0.574 (0.174%), neg=0, invalid=96777 0327: dt=36.288000, rms=0.573 (0.146%), neg=0, invalid=96777 0328: dt=36.288000, rms=0.573 (0.148%), neg=0, invalid=96777 0329: dt=36.288000, rms=0.572 (0.154%), neg=0, invalid=96777 0330: dt=36.288000, rms=0.571 (0.152%), neg=0, invalid=96777 0331: dt=36.288000, rms=0.570 (0.147%), neg=0, invalid=96777 0332: dt=36.288000, rms=0.569 (0.141%), neg=0, invalid=96777 0333: dt=36.288000, rms=0.568 (0.144%), neg=0, invalid=96777 0334: dt=36.288000, rms=0.568 (0.123%), neg=0, invalid=96777 0335: dt=36.288000, rms=0.567 (0.118%), neg=0, invalid=96777 0336: dt=36.288000, rms=0.566 (0.118%), neg=0, invalid=96777 0337: dt=36.288000, rms=0.566 (0.119%), neg=0, invalid=96777 0338: dt=36.288000, rms=0.565 (0.102%), neg=0, invalid=96777 0339: dt=36.288000, rms=0.565 (0.097%), neg=0, invalid=96777 0340: dt=36.288000, rms=0.564 (0.103%), neg=0, invalid=96777 0341: dt=36.288000, rms=0.563 (0.086%), neg=0, invalid=96777 0342: dt=36.288000, rms=0.563 (0.088%), neg=0, invalid=96777 0343: dt=36.288000, rms=0.562 (0.088%), neg=0, invalid=96777 0344: dt=36.288000, rms=0.562 (0.086%), neg=0, invalid=96777 0345: dt=36.288000, rms=0.562 (0.067%), neg=0, invalid=96777 0346: dt=36.288000, rms=0.561 (0.074%), neg=0, invalid=96777 0347: dt=36.288000, rms=0.561 (0.070%), neg=0, invalid=96777 0348: dt=36.288000, rms=0.560 (0.062%), neg=0, invalid=96777 0349: dt=36.288000, rms=0.560 (0.051%), neg=0, invalid=96777 0350: dt=36.288000, rms=0.560 (0.055%), neg=0, invalid=96777 0351: dt=36.288000, rms=0.559 (0.080%), neg=0, invalid=96777 0352: dt=36.288000, rms=0.559 (0.070%), neg=0, invalid=96777 0353: dt=36.288000, rms=0.559 (0.055%), neg=0, invalid=96777 0354: dt=36.288000, rms=0.558 (0.047%), neg=0, invalid=96777 0355: dt=36.288000, rms=0.558 (0.061%), neg=0, invalid=96777 0356: dt=36.288000, rms=0.558 (0.045%), neg=0, invalid=96777 0357: dt=36.288000, rms=0.558 (0.048%), neg=0, invalid=96777 0358: dt=36.288000, rms=0.557 (0.036%), neg=0, invalid=96777 0359: dt=36.288000, rms=0.557 (0.059%), neg=0, invalid=96777 0360: dt=36.288000, rms=0.557 (0.075%), neg=0, invalid=96777 0361: dt=36.288000, rms=0.556 (0.049%), neg=0, invalid=96777 0362: dt=36.288000, rms=0.556 (0.026%), neg=0, invalid=96777 0363: dt=36.288000, rms=0.556 (0.046%), neg=0, invalid=96777 0364: dt=36.288000, rms=0.556 (0.073%), neg=0, invalid=96777 0365: dt=36.288000, rms=0.555 (0.044%), neg=0, invalid=96777 0366: dt=36.288000, rms=0.555 (0.021%), neg=0, invalid=96777 0367: dt=36.288000, rms=0.555 (0.001%), neg=0, invalid=96777 0368: dt=82.944000, rms=0.555 (0.084%), neg=0, invalid=96777 0369: dt=1.944000, rms=0.555 (-0.003%), neg=0, invalid=96777 0370: dt=1.944000, rms=0.555 (0.000%), neg=0, invalid=96777 0371: dt=1.944000, rms=0.555 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.555, neg=0, invalid=96777 0372: dt=36.288000, rms=0.554 (0.165%), neg=0, invalid=96777 0373: dt=36.288000, rms=0.553 (0.159%), neg=0, invalid=96777 0374: dt=124.416000, rms=0.552 (0.201%), neg=0, invalid=96777 0375: dt=9.072000, rms=0.552 (0.020%), neg=0, invalid=96777 0376: dt=0.141750, rms=0.552 (0.001%), neg=0, invalid=96777 0377: dt=0.070875, rms=0.552 (-0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.565, neg=0, invalid=96777 0378: dt=44.800000, rms=0.561 (0.579%), neg=0, invalid=96777 0379: dt=11.200000, rms=0.560 (0.301%), neg=0, invalid=96777 0380: dt=11.200000, rms=0.558 (0.323%), neg=0, invalid=96777 0381: dt=44.800000, rms=0.555 (0.595%), neg=0, invalid=96777 0382: dt=9.043478, rms=0.552 (0.391%), neg=0, invalid=96777 0383: dt=8.000000, rms=0.552 (0.109%), neg=0, invalid=96777 0384: dt=11.200000, rms=0.551 (0.222%), neg=0, invalid=96777 0385: dt=44.800000, rms=0.548 (0.400%), neg=0, invalid=96777 0386: dt=10.569343, rms=0.547 (0.302%), neg=0, invalid=96777 0387: dt=8.000000, rms=0.546 (0.090%), neg=0, invalid=96777 0388: dt=44.800000, rms=0.544 (0.405%), neg=0, invalid=96777 0389: dt=5.905579, rms=0.543 (0.156%), neg=0, invalid=96777 0390: dt=44.800000, rms=0.541 (0.425%), neg=0, invalid=96777 0391: dt=19.200000, rms=0.540 (0.154%), neg=0, invalid=96777 0392: dt=8.000000, rms=0.540 (0.082%), neg=0, invalid=96777 0393: dt=44.800000, rms=0.538 (0.316%), neg=0, invalid=96777 0394: dt=5.633803, rms=0.537 (0.080%), neg=0, invalid=96777 0395: dt=179.200000, rms=0.535 (0.511%), neg=0, invalid=96777 0396: dt=9.600000, rms=0.532 (0.551%), neg=0, invalid=96777 0397: dt=11.200000, rms=0.531 (0.191%), neg=0, invalid=96777 0398: dt=11.200000, rms=0.530 (0.076%), neg=0, invalid=96777 0399: dt=102.400000, rms=0.529 (0.206%), neg=0, invalid=96777 0400: dt=2.800000, rms=0.529 (0.061%), neg=0, invalid=96777 0401: dt=2.800000, rms=0.529 (0.058%), neg=0, invalid=96777 0402: dt=9.600000, rms=0.528 (0.114%), neg=0, invalid=96777 0403: dt=25.600000, rms=0.528 (0.096%), neg=0, invalid=96777 0404: dt=6.400000, rms=0.527 (0.033%), neg=0, invalid=96777 0405: dt=6.400000, rms=0.527 (0.030%), neg=0, invalid=96777 0406: dt=6.400000, rms=0.527 (0.042%), neg=0, invalid=96777 0407: dt=6.400000, rms=0.527 (0.049%), neg=0, invalid=96777 0408: dt=6.400000, rms=0.526 (0.067%), neg=0, invalid=96777 0409: dt=6.400000, rms=0.526 (0.078%), neg=0, invalid=96777 0410: dt=6.400000, rms=0.525 (0.091%), neg=0, invalid=96777 0411: dt=6.400000, rms=0.525 (0.105%), neg=0, invalid=96777 0412: dt=6.400000, rms=0.524 (0.110%), neg=0, invalid=96777 0413: dt=6.400000, rms=0.524 (0.108%), neg=0, invalid=96777 0414: dt=6.400000, rms=0.523 (0.107%), neg=0, invalid=96777 0415: dt=6.400000, rms=0.523 (0.110%), neg=0, invalid=96777 0416: dt=6.400000, rms=0.522 (0.109%), neg=0, invalid=96777 0417: dt=6.400000, rms=0.521 (0.109%), neg=0, invalid=96777 0418: dt=6.400000, rms=0.521 (0.109%), neg=0, invalid=96777 0419: dt=6.400000, rms=0.520 (0.112%), neg=0, invalid=96777 0420: dt=6.400000, rms=0.520 (0.107%), neg=0, invalid=96777 0421: dt=6.400000, rms=0.519 (0.102%), neg=0, invalid=96777 0422: dt=6.400000, rms=0.519 (0.100%), neg=0, invalid=96777 0423: dt=6.400000, rms=0.518 (0.099%), neg=0, invalid=96777 0424: dt=6.400000, rms=0.518 (0.096%), neg=0, invalid=96777 0425: dt=6.400000, rms=0.517 (0.079%), neg=0, invalid=96777 0426: dt=6.400000, rms=0.517 (0.081%), neg=0, invalid=96777 0427: dt=6.400000, rms=0.516 (0.079%), neg=0, invalid=96777 0428: dt=6.400000, rms=0.516 (0.077%), neg=0, invalid=96777 0429: dt=6.400000, rms=0.516 (0.072%), neg=0, invalid=96777 0430: dt=6.400000, rms=0.515 (0.069%), neg=0, invalid=96777 0431: dt=6.400000, rms=0.515 (0.070%), neg=0, invalid=96777 0432: dt=6.400000, rms=0.515 (0.070%), neg=0, invalid=96777 0433: dt=6.400000, rms=0.514 (0.062%), neg=0, invalid=96777 0434: dt=6.400000, rms=0.514 (0.060%), neg=0, invalid=96777 0435: dt=6.400000, rms=0.514 (0.051%), neg=0, invalid=96777 0436: dt=6.400000, rms=0.513 (0.058%), neg=0, invalid=96777 0437: dt=6.400000, rms=0.513 (0.054%), neg=0, invalid=96777 0438: dt=6.400000, rms=0.513 (0.046%), neg=0, invalid=96777 0439: dt=6.400000, rms=0.513 (0.045%), neg=0, invalid=96777 0440: dt=6.400000, rms=0.513 (0.040%), neg=0, invalid=96777 0441: dt=6.400000, rms=0.512 (0.040%), neg=0, invalid=96777 0442: dt=6.400000, rms=0.512 (0.042%), neg=0, invalid=96777 0443: dt=6.400000, rms=0.512 (0.041%), neg=0, invalid=96777 0444: dt=6.400000, rms=0.512 (0.036%), neg=0, invalid=96777 0445: dt=6.400000, rms=0.512 (0.034%), neg=0, invalid=96777 0446: dt=6.400000, rms=0.511 (0.039%), neg=0, invalid=96777 0447: dt=6.400000, rms=0.511 (0.035%), neg=0, invalid=96777 0448: dt=6.400000, rms=0.511 (0.044%), neg=0, invalid=96777 0449: dt=6.400000, rms=0.511 (0.041%), neg=0, invalid=96777 0450: dt=6.400000, rms=0.511 (0.036%), neg=0, invalid=96777 0451: dt=6.400000, rms=0.510 (0.029%), neg=0, invalid=96777 0452: dt=6.400000, rms=0.510 (0.031%), neg=0, invalid=96777 0453: dt=6.400000, rms=0.510 (0.031%), neg=0, invalid=96777 0454: dt=6.400000, rms=0.510 (0.031%), neg=0, invalid=96777 0455: dt=6.400000, rms=0.510 (0.023%), neg=0, invalid=96777 0456: dt=6.400000, rms=0.510 (0.021%), neg=0, invalid=96777 0457: dt=11.200000, rms=0.510 (0.014%), neg=0, invalid=96777 0458: dt=11.200000, rms=0.510 (0.003%), neg=0, invalid=96777 0459: dt=11.200000, rms=0.510 (0.005%), neg=0, invalid=96777 0460: dt=11.200000, rms=0.510 (0.007%), neg=0, invalid=96777 0461: dt=11.200000, rms=0.509 (0.018%), neg=0, invalid=96777 0462: dt=11.200000, rms=0.509 (0.019%), neg=0, invalid=96777 0463: dt=11.200000, rms=0.509 (0.010%), neg=0, invalid=96777 0464: dt=11.200000, rms=0.509 (0.019%), neg=0, invalid=96777 0465: dt=11.200000, rms=0.509 (0.017%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.509, neg=0, invalid=96777 0466: dt=44.800000, rms=0.507 (0.414%), neg=0, invalid=96777 0467: dt=11.200000, rms=0.507 (0.042%), neg=0, invalid=96777 0468: dt=11.200000, rms=0.507 (0.042%), neg=0, invalid=96777 0469: dt=11.200000, rms=0.506 (0.027%), neg=0, invalid=96777 0470: dt=11.200000, rms=0.506 (0.008%), neg=0, invalid=96777 0471: dt=11.200000, rms=0.506 (-0.001%), neg=0, invalid=96777 0472: dt=25.600000, rms=0.506 (0.027%), neg=0, invalid=96777 0473: dt=9.600000, rms=0.506 (0.006%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.535, neg=0, invalid=96777 0474: dt=0.000000, rms=0.535 (0.002%), neg=0, invalid=96777 0475: dt=0.000000, rms=0.535 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.535, neg=0, invalid=96777 0476: dt=0.000000, rms=0.535 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.590, neg=0, invalid=96777 0477: dt=1.580357, rms=0.584 (1.107%), neg=0, invalid=96777 0478: dt=0.448000, rms=0.583 (0.049%), neg=0, invalid=96777 0479: dt=0.448000, rms=0.583 (-0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.583, neg=0, invalid=96777 0480: dt=1.088710, rms=0.582 (0.191%), neg=0, invalid=96777 0481: dt=0.384000, rms=0.582 (0.016%), neg=0, invalid=96777 0482: dt=0.384000, rms=0.582 (-0.003%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.527, neg=0, invalid=96777 0483: dt=0.320000, rms=0.514 (2.567%), neg=0, invalid=96777 0484: dt=0.028000, rms=0.513 (0.093%), neg=0, invalid=96777 0485: dt=0.384000, rms=0.507 (1.237%), neg=0, invalid=96777 0486: dt=0.028000, rms=0.507 (0.045%), neg=0, invalid=96777 0487: dt=0.028000, rms=0.506 (0.040%), neg=0, invalid=96777 0488: dt=0.028000, rms=0.506 (0.077%), neg=0, invalid=96777 0489: dt=0.028000, rms=0.505 (0.104%), neg=0, invalid=96777 0490: dt=0.028000, rms=0.505 (0.128%), neg=0, invalid=96777 0491: dt=0.028000, rms=0.505 (0.031%), neg=0, invalid=96777 0492: dt=0.028000, rms=0.504 (0.058%), neg=0, invalid=96777 0493: dt=0.028000, rms=0.504 (0.080%), neg=0, invalid=96777 0494: dt=0.028000, rms=0.503 (0.099%), neg=0, invalid=96777 0495: dt=0.028000, rms=0.503 (0.114%), neg=0, invalid=96777 0496: dt=0.028000, rms=0.502 (0.124%), neg=0, invalid=96777 0497: dt=0.028000, rms=0.502 (0.131%), neg=0, invalid=96777 0498: dt=0.028000, rms=0.501 (0.133%), neg=0, invalid=96777 0499: dt=0.028000, rms=0.500 (0.131%), neg=0, invalid=96777 0500: dt=0.028000, rms=0.500 (0.129%), neg=0, invalid=96777 0501: dt=0.028000, rms=0.499 (0.123%), neg=0, invalid=96777 0502: dt=0.028000, rms=0.498 (0.115%), neg=0, invalid=96777 0503: dt=0.028000, rms=0.498 (0.109%), neg=0, invalid=96777 0504: dt=0.028000, rms=0.497 (0.100%), neg=0, invalid=96777 0505: dt=0.028000, rms=0.497 (0.088%), neg=0, invalid=96777 0506: dt=0.028000, rms=0.497 (0.077%), neg=0, invalid=96777 0507: dt=0.028000, rms=0.496 (0.071%), neg=0, invalid=96777 0508: dt=0.028000, rms=0.496 (0.063%), neg=0, invalid=96777 0509: dt=0.028000, rms=0.496 (0.055%), neg=0, invalid=96777 0510: dt=0.028000, rms=0.495 (0.044%), neg=0, invalid=96777 0511: dt=0.028000, rms=0.495 (0.039%), neg=0, invalid=96777 0512: dt=0.028000, rms=0.495 (0.033%), neg=0, invalid=96777 0513: dt=0.028000, rms=0.495 (0.027%), neg=0, invalid=96777 0514: dt=0.028000, rms=0.495 (0.024%), neg=0, invalid=96777 0515: dt=0.028000, rms=0.495 (0.019%), neg=0, invalid=96777 0516: dt=0.000000, rms=0.495 (-0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.495, neg=0, invalid=96777 0517: dt=0.448000, rms=0.490 (1.006%), neg=0, invalid=96777 0518: dt=0.001750, rms=0.490 (0.002%), neg=0, invalid=96777 0519: dt=0.001750, rms=0.490 (0.000%), neg=0, invalid=96777 0520: dt=0.001750, rms=0.490 (-0.001%), neg=0, invalid=96777 label assignment complete, 0 changed (0.00%) ********************************************************************************************* ********************************************************************************************* ********************************************************************************************* ********************* ALLOWING NEGATIVE NODES IN DEFORMATION ******************************** ********************************************************************************************* ********************************************************************************************* ********************************************************************************************* **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.487, neg=0, invalid=96777 0521: dt=0.000000, rms=0.487 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.487, neg=0, invalid=96777 0522: dt=129.472000, rms=0.486 (0.114%), neg=0, invalid=96777 0523: dt=55.488000, rms=0.486 (0.030%), neg=0, invalid=96777 0524: dt=55.488000, rms=0.486 (0.019%), neg=0, invalid=96777 0525: dt=55.488000, rms=0.486 (0.031%), neg=0, invalid=96777 0526: dt=55.488000, rms=0.486 (0.038%), neg=0, invalid=96777 0527: dt=55.488000, rms=0.486 (0.037%), neg=0, invalid=96777 0528: dt=55.488000, rms=0.486 (0.037%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.486, neg=0, invalid=96777 0529: dt=15.552000, rms=0.485 (0.031%), neg=0, invalid=96777 0530: dt=9.072000, rms=0.485 (0.010%), neg=0, invalid=96777 0531: dt=9.072000, rms=0.485 (0.008%), neg=0, invalid=96777 0532: dt=9.072000, rms=0.485 (-0.003%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.485, neg=0, invalid=96777 0533: dt=145.152000, rms=0.481 (0.822%), neg=0, invalid=96777 0534: dt=15.552000, rms=0.481 (0.082%), neg=0, invalid=96777 0535: dt=15.552000, rms=0.481 (0.045%), neg=0, invalid=96777 0536: dt=15.552000, rms=0.480 (0.059%), neg=0, invalid=96777 0537: dt=15.552000, rms=0.480 (0.059%), neg=0, invalid=96777 0538: dt=15.552000, rms=0.480 (0.079%), neg=0, invalid=96777 0539: dt=15.552000, rms=0.479 (0.102%), neg=0, invalid=96777 0540: dt=15.552000, rms=0.479 (0.128%), neg=0, invalid=96777 0541: dt=15.552000, rms=0.478 (0.138%), neg=0, invalid=96777 0542: dt=15.552000, rms=0.477 (0.145%), neg=0, invalid=96777 0543: dt=15.552000, rms=0.477 (0.141%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0544: dt=15.552000, rms=0.476 (0.134%), neg=0, invalid=96777 0545: dt=15.552000, rms=0.475 (0.121%), neg=0, invalid=96777 0546: dt=15.552000, rms=0.475 (0.097%), neg=0, invalid=96777 0547: dt=82.944000, rms=0.475 (0.041%), neg=0, invalid=96777 0548: dt=82.944000, rms=0.475 (-0.010%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.475, neg=0, invalid=96777 iter 0, gcam->neg = 51 after 16 iterations, nbhd size=1, neg = 0 0549: dt=32.000000, rms=0.473 (0.503%), neg=0, invalid=96777 0550: dt=11.200000, rms=0.472 (0.199%), neg=0, invalid=96777 0551: dt=11.200000, rms=0.471 (0.202%), neg=0, invalid=96777 iter 0, gcam->neg = 14 after 10 iterations, nbhd size=1, neg = 0 0552: dt=11.200000, rms=0.469 (0.306%), neg=0, invalid=96777 iter 0, gcam->neg = 60 after 12 iterations, nbhd size=1, neg = 0 0553: dt=11.200000, rms=0.468 (0.334%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0554: dt=11.200000, rms=0.467 (0.253%), neg=0, invalid=96777 iter 0, gcam->neg = 13 after 7 iterations, nbhd size=1, neg = 0 0555: dt=11.200000, rms=0.466 (0.227%), neg=0, invalid=96777 iter 0, gcam->neg = 13 after 12 iterations, nbhd size=1, neg = 0 0556: dt=11.200000, rms=0.465 (0.245%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 15 iterations, nbhd size=2, neg = 0 0557: dt=11.200000, rms=0.463 (0.287%), neg=0, invalid=96777 iter 0, gcam->neg = 13 after 15 iterations, nbhd size=1, neg = 0 0558: dt=11.200000, rms=0.462 (0.264%), neg=0, invalid=96777 iter 0, gcam->neg = 6 after 7 iterations, nbhd size=1, neg = 0 0559: dt=11.200000, rms=0.461 (0.230%), neg=0, invalid=96777 iter 0, gcam->neg = 5 after 7 iterations, nbhd size=1, neg = 0 0560: dt=11.200000, rms=0.460 (0.216%), neg=0, invalid=96777 iter 0, gcam->neg = 10 after 8 iterations, nbhd size=1, neg = 0 0561: dt=11.200000, rms=0.459 (0.249%), neg=0, invalid=96777 iter 0, gcam->neg = 46 after 13 iterations, nbhd size=1, neg = 0 0562: dt=11.200000, rms=0.458 (0.192%), neg=0, invalid=96777 iter 0, gcam->neg = 9 after 32 iterations, nbhd size=3, neg = 0 0563: dt=11.200000, rms=0.458 (0.063%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 0 iterations, nbhd size=0, neg = 0 0564: dt=11.200000, rms=0.457 (0.055%), neg=0, invalid=96777 0565: dt=11.200000, rms=0.457 (0.125%), neg=0, invalid=96777 0566: dt=11.200000, rms=0.456 (0.078%), neg=0, invalid=96777 0567: dt=11.200000, rms=0.456 (0.049%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 12 iterations, nbhd size=2, neg = 0 0568: dt=11.200000, rms=0.456 (0.048%), neg=0, invalid=96777 0569: dt=11.200000, rms=0.456 (0.021%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.456, neg=0, invalid=96777 iter 0, gcam->neg = 45 after 49 iterations, nbhd size=3, neg = 0 0570: dt=38.400000, rms=0.453 (0.619%), neg=0, invalid=96777 0571: dt=6.939227, rms=0.452 (0.229%), neg=0, invalid=96777 0572: dt=6.939227, rms=0.451 (0.116%), neg=0, invalid=96777 0573: dt=6.939227, rms=0.451 (0.127%), neg=0, invalid=96777 0574: dt=6.939227, rms=0.450 (0.141%), neg=0, invalid=96777 iter 0, gcam->neg = 10 after 41 iterations, nbhd size=4, neg = 0 0575: dt=6.939227, rms=0.450 (0.106%), neg=0, invalid=96777 0576: dt=6.939227, rms=0.449 (0.122%), neg=0, invalid=96777 0577: dt=6.939227, rms=0.449 (0.107%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0578: dt=32.000000, rms=0.448 (0.087%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 16 iterations, nbhd size=2, neg = 0 0579: dt=32.000000, rms=0.448 (-0.299%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.456, neg=0, invalid=96777 0580: dt=0.720000, rms=0.456 (0.006%), neg=0, invalid=96777 0581: dt=1.008000, rms=0.455 (0.011%), neg=0, invalid=96777 0582: dt=2.304000, rms=0.455 (0.027%), neg=0, invalid=96777 0583: dt=0.576000, rms=0.455 (-0.004%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.455, neg=0, invalid=96777 iter 0, gcam->neg = 4 after 5 iterations, nbhd size=1, neg = 0 0584: dt=4.521739, rms=0.455 (0.111%), neg=0, invalid=96777 0585: dt=1.008000, rms=0.455 (0.015%), neg=0, invalid=96777 0586: dt=1.008000, rms=0.455 (0.022%), neg=0, invalid=96777 0587: dt=1.008000, rms=0.455 (0.041%), neg=0, invalid=96777 0588: dt=1.008000, rms=0.454 (0.037%), neg=0, invalid=96777 0589: dt=1.008000, rms=0.454 (0.010%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.463, neg=0, invalid=96777 0590: dt=0.000000, rms=0.463 (0.001%), neg=0, invalid=96777 0591: dt=0.000000, rms=0.463 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.463, neg=0, invalid=96777 0592: dt=0.001750, rms=0.463 (0.000%), neg=0, invalid=96777 0593: dt=0.001250, rms=0.463 (0.000%), neg=0, invalid=96777 0594: dt=0.001250, rms=0.463 (-0.001%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.449, neg=0, invalid=96777 iter 0, gcam->neg = 750 after 42 iterations, nbhd size=3, neg = 0 0595: dt=1.760977, rms=0.412 (8.131%), neg=0, invalid=96777 0596: dt=0.000188, rms=0.412 (-0.004%), neg=0, invalid=96777 0597: dt=0.000188, rms=0.412 (0.002%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0598: dt=0.000188, rms=0.412 (-0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.412, neg=0, invalid=96777 0599: dt=0.000313, rms=0.412 (0.000%), neg=0, invalid=96777 0600: dt=0.000000, rms=0.412 (0.000%), neg=0, invalid=96777 iter 0, gcam->neg = 139 after 8 iterations, nbhd size=1, neg = 0 0601: dt=0.050000, rms=0.412 (-0.251%), neg=0, invalid=96777 label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.399, neg=0, invalid=96777 0602: dt=0.000000, rms=0.400 (-0.180%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.400, neg=0, invalid=96777 0603: dt=32.368000, rms=0.400 (0.008%), neg=0, invalid=96777 0604: dt=32.368000, rms=0.400 (0.002%), neg=0, invalid=96777 0605: dt=32.368000, rms=0.400 (0.001%), neg=0, invalid=96777 0606: dt=32.368000, rms=0.400 (-0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.400, neg=0, invalid=96777 0607: dt=0.000000, rms=0.400 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.400, neg=0, invalid=96777 0608: dt=36.288000, rms=0.400 (0.025%), neg=0, invalid=96777 0609: dt=82.944000, rms=0.400 (0.020%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 13 iterations, nbhd size=2, neg = 0 0610: dt=82.944000, rms=0.400 (0.013%), neg=0, invalid=96777 0611: dt=82.944000, rms=0.400 (0.020%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 54 iterations, nbhd size=4, neg = 0 0612: dt=82.944000, rms=0.400 (-0.008%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.400, neg=0, invalid=96777 iter 0, gcam->neg = 9 after 48 iterations, nbhd size=2, neg = 0 0613: dt=6.400000, rms=0.400 (-0.030%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.400, neg=0, invalid=96777 iter 0, gcam->neg = 70 after 200 iterations, nbhd size=4, neg = 2 starting rms=0.004, neg=2, removing folds in lattice.... iter 1, dt=0.000125: new neg 0, old_neg 2, delta 2, rms=0.003 (20.895%) 0614: dt=25.600000, rms=0.399 (0.246%), neg=0, invalid=96777 iter 0, gcam->neg = 51 after 200 iterations, nbhd size=2, neg = 1 starting rms=0.003, neg=1, removing folds in lattice.... iter 1, dt=0.000156: new neg 0, old_neg 1, delta 1, rms=0.003 (12.136%) 0615: dt=32.000000, rms=0.399 (0.099%), neg=0, invalid=96777 iter 0, gcam->neg = 42 after 200 iterations, nbhd size=1, neg = 4 starting rms=0.005, neg=4, removing folds in lattice.... iter 1, dt=0.000120: new neg 0, old_neg 4, delta 4, rms=0.003 (39.102%) 0616: dt=32.000000, rms=0.398 (0.174%), neg=0, invalid=96777 iter 0, gcam->neg = 13 after 200 iterations, nbhd size=4, neg = 1 starting rms=0.003, neg=1, removing folds in lattice.... iter 1, dt=0.000125: new neg 0, old_neg 1, delta 1, rms=0.003 (13.358%) 0617: dt=32.000000, rms=0.398 (0.183%), neg=0, invalid=96777 iter 0, gcam->neg = 14 after 200 iterations, nbhd size=4, neg = 2 starting rms=0.004, neg=2, removing folds in lattice.... iter 1, dt=0.000120: new neg 0, old_neg 2, delta 2, rms=0.003 (29.727%) 0618: dt=32.000000, rms=0.397 (0.109%), neg=0, invalid=96777 iter 0, gcam->neg = 27 after 200 iterations, nbhd size=2, neg = 1 starting rms=0.003, neg=1, removing folds in lattice.... iter 1, dt=0.000188: new neg 0, old_neg 1, delta 1, rms=0.003 (17.656%) 0619: dt=32.000000, rms=0.397 (0.043%), neg=0, invalid=96777 iter 0, gcam->neg = 28 after 200 iterations, nbhd size=2, neg = 2 starting rms=0.004, neg=2, removing folds in lattice.... iter 1, dt=0.000120: new neg 0, old_neg 2, delta 2, rms=0.003 (30.437%) 0620: dt=25.600000, rms=0.397 (0.094%), neg=0, invalid=96777 iter 0, gcam->neg = 44 after 200 iterations, nbhd size=3, neg = 3 starting rms=0.005, neg=3, removing folds in lattice.... iter 1, dt=0.000100: new neg 0, old_neg 3, delta 3, rms=0.003 (33.203%) 0621: dt=32.000000, rms=0.396 (0.084%), neg=0, invalid=96777 iter 0, gcam->neg = 9 after 200 iterations, nbhd size=4, neg = 4 starting rms=0.004, neg=4, removing folds in lattice.... iter 1, dt=0.000100: new neg 0, old_neg 4, delta 4, rms=0.003 (35.013%) 0622: dt=32.000000, rms=0.396 (-0.023%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.399, neg=0, invalid=96777 iter 0, gcam->neg = 6 after 6 iterations, nbhd size=1, neg = 0 0623: dt=1.008000, rms=0.399 (0.021%), neg=0, invalid=96777 0624: dt=1.008000, rms=0.398 (0.039%), neg=0, invalid=96777 0625: dt=0.063000, rms=0.398 (0.000%), neg=0, invalid=96777 0626: dt=0.063000, rms=0.398 (0.003%), neg=0, invalid=96777 0627: dt=0.063000, rms=0.398 (0.005%), neg=0, invalid=96777 0628: dt=0.063000, rms=0.398 (0.007%), neg=0, invalid=96777 0629: dt=0.063000, rms=0.398 (0.009%), neg=0, invalid=96777 0630: dt=0.063000, rms=0.398 (0.010%), neg=0, invalid=96777 0631: dt=0.063000, rms=0.398 (0.010%), neg=0, invalid=96777 0632: dt=0.063000, rms=0.398 (0.011%), neg=0, invalid=96777 0633: dt=0.063000, rms=0.398 (0.011%), neg=0, invalid=96777 0634: dt=0.063000, rms=0.398 (0.011%), neg=0, invalid=96777 0635: dt=0.063000, rms=0.398 (0.011%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.398, neg=0, invalid=96777 iter 0, gcam->neg = 95 after 200 iterations, nbhd size=3, neg = 2 starting rms=0.004, neg=2, removing folds in lattice.... iter 1, dt=0.000125: new neg 0, old_neg 2, delta 2, rms=0.003 (39.230%) 0636: dt=9.316129, rms=0.397 (0.319%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0637: dt=0.108000, rms=0.397 (0.002%), neg=0, invalid=96777 0638: dt=0.108000, rms=0.397 (0.003%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0639: dt=0.108000, rms=0.397 (0.007%), neg=0, invalid=96777 0640: dt=0.108000, rms=0.397 (0.011%), neg=0, invalid=96777 0641: dt=0.108000, rms=0.397 (0.013%), neg=0, invalid=96777 0642: dt=0.108000, rms=0.397 (0.016%), neg=0, invalid=96777 0643: dt=0.108000, rms=0.397 (0.019%), neg=0, invalid=96777 0644: dt=0.108000, rms=0.396 (0.021%), neg=0, invalid=96777 0645: dt=0.108000, rms=0.396 (0.022%), neg=0, invalid=96777 0646: dt=0.108000, rms=0.396 (0.024%), neg=0, invalid=96777 0647: dt=0.108000, rms=0.396 (0.020%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0648: dt=0.108000, rms=0.396 (0.021%), neg=0, invalid=96777 0649: dt=0.108000, rms=0.396 (0.021%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0650: dt=0.108000, rms=0.396 (0.022%), neg=0, invalid=96777 0651: dt=0.108000, rms=0.396 (0.021%), neg=0, invalid=96777 iter 0, gcam->neg = 27 after 200 iterations, nbhd size=2, neg = 1 starting rms=0.003, neg=1, removing folds in lattice.... iter 1, dt=0.000100: new neg 0, old_neg 1, delta 1, rms=0.002 (37.849%) 0652: dt=4.032000, rms=0.396 (0.052%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0653: dt=0.252000, rms=0.396 (0.003%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.401, neg=0, invalid=96777 0654: dt=0.000000, rms=0.401 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.401, neg=0, invalid=96777 0655: dt=0.000060, rms=0.401 (0.000%), neg=0, invalid=96777 0656: dt=0.000000, rms=0.401 (0.000%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.392, neg=0, invalid=96777 iter 0, gcam->neg = 514 after 42 iterations, nbhd size=4, neg = 0 0657: dt=0.726852, rms=0.381 (2.834%), neg=0, invalid=96777 0658: dt=0.000016, rms=0.381 (0.002%), neg=0, invalid=96777 0659: dt=0.000016, rms=0.381 (0.001%), neg=0, invalid=96777 0660: dt=0.000016, rms=0.381 (0.001%), neg=0, invalid=96777 0661: dt=0.000016, rms=0.381 (0.001%), neg=0, invalid=96777 0662: dt=0.000016, rms=0.381 (0.000%), neg=0, invalid=96777 0663: dt=0.000109, rms=0.381 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.381, neg=0, invalid=96777 0664: dt=0.000750, rms=0.381 (0.001%), neg=0, invalid=96777 0665: dt=0.007000, rms=0.381 (0.002%), neg=0, invalid=96777 0666: dt=0.001000, rms=0.381 (0.001%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0667: dt=0.001000, rms=0.381 (0.001%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0668: dt=0.001000, rms=0.381 (0.001%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0669: dt=0.001000, rms=0.381 (0.001%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0670: dt=0.001000, rms=0.381 (0.002%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0671: dt=0.001000, rms=0.381 (0.002%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 25 iterations, nbhd size=4, neg = 0 0672: dt=0.001000, rms=0.381 (0.002%), neg=0, invalid=96777 iter 0, gcam->neg = 18 after 1 iterations, nbhd size=0, neg = 0 0673: dt=0.001000, rms=0.381 (0.002%), neg=0, invalid=96777 iter 0, gcam->neg = 23 after 7 iterations, nbhd size=1, neg = 0 0674: dt=0.001000, rms=0.381 (0.003%), neg=0, invalid=96777 iter 0, gcam->neg = 20 after 1 iterations, nbhd size=0, neg = 0 0675: dt=0.001000, rms=0.381 (0.003%), neg=0, invalid=96777 iter 0, gcam->neg = 21 after 1 iterations, nbhd size=0, neg = 0 0676: dt=0.001000, rms=0.381 (0.003%), neg=0, invalid=96777 iter 0, gcam->neg = 19 after 1 iterations, nbhd size=0, neg = 0 0677: dt=0.001000, rms=0.381 (0.003%), neg=0, invalid=96777 writing output transformation to transforms/talairach.m3z... GCAMwrite registration took 2 hours, 26 minutes and 58 seconds. #-------------------------------------- #@# CA Reg Inv Mon Nov 17 15:54:18 EST 2025 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z Inverting GCAM Saving inverse #-------------------------------------- #@# Remove Neck Mon Nov 17 15:55:14 EST 2025 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /usr/local/freesurfer/stable5_3_0/average/RB_all_2008-03-26.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/usr/local/freesurfer/stable5_3_0/average/RB_all_2008-03-26.gca'... reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... removing structures at least 25 mm from brain... 11829327 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 0 minutes and 52 seconds. #-------------------------------------- #@# SkullLTA Mon Nov 17 15:56:06 EST 2025 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /usr/local/freesurfer/stable5_3_0/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull_2.lta ======= NUMBER OF OPENMP THREADS = 1 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 5 using previously computed transform transforms/talairach.lta reading 1 input volumes... logging results to talairach_with_skull_2.log reading '/usr/local/freesurfer/stable5_3_0/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu_noneck.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=14.0 skull bounding box = (32, 24, 0) --> (206, 219, 179) using (90, 89, 90) as brain centroid... mean wm in atlas = 126, using box (69,65,68) --> (111, 113,112) to find MRI wm before smoothing, mri peak at 105 after smoothing, mri peak at 105, scaling input intensities by 1.200 scaling channel 0 by 1.2 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.2, old_max_log_p =-6898.7 (thresh=-6891.8) 1.087 0.023 -0.089 -4.731; 0.047 1.027 0.589 -42.004; 0.104 -0.616 1.059 71.491; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.2, old_max_log_p =-4.2 (thresh=-4.2) 1.087 0.023 -0.089 -4.731; 0.050 1.104 0.633 -54.237; 0.096 -0.570 0.979 74.082; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.2, old_max_log_p =-4.2 (thresh=-4.2) 1.087 0.023 -0.089 -4.731; 0.050 1.104 0.633 -54.237; 0.096 -0.570 0.979 74.082; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.2, old_max_log_p =-4.2 (thresh=-4.2) 1.107 0.023 -0.091 -7.086; 0.050 1.104 0.633 -52.362; 0.098 -0.581 0.998 75.358; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.2, old_max_log_p =-4.2 (thresh=-4.2) 1.086 0.023 -0.089 -4.595; 0.050 1.104 0.633 -52.362; 0.098 -0.581 0.998 75.358; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.1, old_max_log_p =-4.2 (thresh=-4.2) 1.090 0.009 -0.086 -3.903; 0.058 1.115 0.617 -53.575; 0.090 -0.563 1.009 73.594; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 1.095 0.000 -0.069 -4.921; 0.056 1.125 0.601 -53.225; 0.073 -0.543 1.017 72.944; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3481 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.09546 0.00029 -0.06948 -4.92105; 0.05634 1.12529 0.60086 -53.22477; 0.07286 -0.54301 1.01743 72.94405; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.09546 0.00029 -0.06948 -4.92105; 0.05634 1.12529 0.60086 -53.22477; 0.07286 -0.54301 1.01743 72.94405; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 4 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.095 0.000 -0.069 -4.921; 0.056 1.125 0.601 -53.225; 0.073 -0.543 1.017 72.944; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -4.1 (old=-6898.7) transform before final EM align: 1.095 0.000 -0.069 -4.921; 0.056 1.125 0.601 -53.225; 0.073 -0.543 1.017 72.944; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 382743 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.09546 0.00029 -0.06948 -4.92105; 0.05634 1.12529 0.60086 -53.22477; 0.07286 -0.54301 1.01743 72.94405; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.09546 0.00029 -0.06948 -4.92105; 0.05634 1.12529 0.60086 -53.22477; 0.07286 -0.54301 1.01743 72.94405; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = 4.5 tol 0.000000 final transform: 1.095 0.000 -0.069 -4.921; 0.056 1.125 0.601 -53.225; 0.073 -0.543 1.017 72.944; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull_2.lta... registration took 21 minutes and 28 seconds. #-------------------------------------- #@# SubCort Seg Mon Nov 17 16:17:35 EST 2025 mri_ca_label -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/stable5_3_0/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz sysname Linux hostname r440-30.nmr.mgh.harvard.edu machine x86_64 setenv SUBJECTS_DIR /autofs/space/hope_002/users/PBR28_HOPE/data/fs cd /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri mri_ca_label -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/stable5_3_0/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes... reading classifier array from /usr/local/freesurfer/stable5_3_0/average/RB_all_2008-03-26.gca... reading input volume from norm.mgz... average std[0] = 6.9 reading transform from transforms/talairach.m3z... Atlas used for the 3D morph was /usr/local/freesurfer/stable5_3_0/average/RB_all_2008-03-26.gca average std = 6.9 using min determinant for regularization = 4.7 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15151 (27) mri peak = 0.10923 (13) Left_Lateral_Ventricle (4): linear fit = 0.41 x + 0.0 (4341 voxels, overlap=0.007) Left_Lateral_Ventricle (4): linear fit = 0.41 x + 0.0 (4341 voxels, peak = 11), gca=11.2 gca peak = 0.14982 (20) mri peak = 0.11971 (14) Right_Lateral_Ventricle (43): linear fit = 0.56 x + 0.0 (3705 voxels, overlap=0.008) Right_Lateral_Ventricle (43): linear fit = 0.56 x + 0.0 (3705 voxels, peak = 11), gca=11.1 gca peak = 0.28003 (97) mri peak = 0.12435 (109) Right_Pallidum (52): linear fit = 1.10 x + 0.0 (255 voxels, overlap=0.077) Right_Pallidum (52): linear fit = 1.10 x + 0.0 (255 voxels, peak = 106), gca=106.2 gca peak = 0.18160 (96) mri peak = 0.04812 (95) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (54 voxels, overlap=0.919) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (54 voxels, peak = 101), gca=101.3 gca peak = 0.27536 (62) mri peak = 0.09034 (74) Right_Hippocampus (53): linear fit = 1.18 x + 0.0 (635 voxels, overlap=0.020) Right_Hippocampus (53): linear fit = 1.18 x + 0.0 (635 voxels, peak = 73), gca=73.5 gca peak = 0.32745 (63) mri peak = 0.09241 (80) Left_Hippocampus (17): linear fit = 1.22 x + 0.0 (449 voxels, overlap=0.023) Left_Hippocampus (17): linear fit = 1.22 x + 0.0 (449 voxels, peak = 77), gca=76.5 gca peak = 0.08597 (105) mri peak = 0.07935 (109) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (29458 voxels, overlap=0.653) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (29458 voxels, peak = 110), gca=109.7 gca peak = 0.09209 (106) mri peak = 0.06033 (109) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (28878 voxels, overlap=0.785) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (28878 voxels, peak = 110), gca=109.7 gca peak = 0.07826 (63) mri peak = 0.03333 (74) Left_Cerebral_Cortex (3): linear fit = 1.14 x + 0.0 (17845 voxels, overlap=0.477) Left_Cerebral_Cortex (3): linear fit = 1.14 x + 0.0 (17845 voxels, peak = 72), gca=72.1 gca peak = 0.08598 (64) mri peak = 0.03645 (73) Right_Cerebral_Cortex (42): linear fit = 1.16 x + 0.0 (16086 voxels, overlap=0.405) Right_Cerebral_Cortex (42): linear fit = 1.16 x + 0.0 (16086 voxels, peak = 75), gca=74.6 gca peak = 0.24164 (71) mri peak = 0.09149 (84) Right_Caudate (50): linear fit = 1.15 x + 0.0 (618 voxels, overlap=0.017) Right_Caudate (50): linear fit = 1.15 x + 0.0 (618 voxels, peak = 82), gca=82.0 gca peak = 0.18227 (75) mri peak = 0.12712 (88) Left_Caudate (11): linear fit = 1.12 x + 0.0 (473 voxels, overlap=0.243) Left_Caudate (11): linear fit = 1.12 x + 0.0 (473 voxels, peak = 84), gca=83.6 gca peak = 0.10629 (62) mri peak = 0.05187 (85) Left_Cerebellum_Cortex (8): linear fit = 1.38 x + 0.0 (18048 voxels, overlap=0.002) Left_Cerebellum_Cortex (8): linear fit = 1.38 x + 0.0 (18048 voxels, peak = 86), gca=85.9 gca peak = 0.11668 (59) mri peak = 0.04259 (83) Right_Cerebellum_Cortex (47): linear fit = 1.35 x + 0.0 (23108 voxels, overlap=0.001) Right_Cerebellum_Cortex (47): linear fit = 1.35 x + 0.0 (23108 voxels, peak = 79), gca=79.4 gca peak = 0.17849 (88) mri peak = 0.07177 (97) Left_Cerebellum_White_Matter (7): linear fit = 1.10 x + 0.0 (3957 voxels, overlap=0.432) Left_Cerebellum_White_Matter (7): linear fit = 1.10 x + 0.0 (3957 voxels, peak = 96), gca=96.4 gca peak = 0.16819 (86) mri peak = 0.09520 (90) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (2243 voxels, overlap=0.896) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (2243 voxels, peak = 89), gca=89.0 gca peak = 0.41688 (64) mri peak = 0.10435 (82) Left_Amygdala (18): linear fit = 1.27 x + 0.0 (230 voxels, overlap=0.073) Left_Amygdala (18): linear fit = 1.27 x + 0.0 (230 voxels, peak = 82), gca=81.6 gca peak = 0.42394 (62) mri peak = 0.15385 (75) Right_Amygdala (54): linear fit = 1.22 x + 0.0 (273 voxels, overlap=0.059) Right_Amygdala (54): linear fit = 1.22 x + 0.0 (273 voxels, peak = 75), gca=75.3 gca peak = 0.10041 (96) mri peak = 0.06663 (100) Left_Thalamus_Proper (10): linear fit = 1.10 x + 0.0 (3693 voxels, overlap=0.453) Left_Thalamus_Proper (10): linear fit = 1.10 x + 0.0 (3693 voxels, peak = 105), gca=105.1 gca peak = 0.13978 (88) mri peak = 0.06849 (99) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (3596 voxels, overlap=0.328) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (3596 voxels, peak = 99), gca=99.0 gca peak = 0.08514 (81) mri peak = 0.07264 (90) Left_Putamen (12): linear fit = 1.09 x + 0.0 (1059 voxels, overlap=0.633) Left_Putamen (12): linear fit = 1.09 x + 0.0 (1059 voxels, peak = 88), gca=87.9 gca peak = 0.09624 (82) mri peak = 0.06828 (91) Right_Putamen (51): linear fit = 1.12 x + 0.0 (1112 voxels, overlap=0.493) Right_Putamen (51): linear fit = 1.12 x + 0.0 (1112 voxels, peak = 92), gca=92.2 gca peak = 0.07543 (88) mri peak = 0.07138 (90) Brain_Stem (16): linear fit = 1.05 x + 0.0 (11472 voxels, overlap=0.658) Brain_Stem (16): linear fit = 1.05 x + 0.0 (11472 voxels, peak = 93), gca=92.8 gca peak = 0.12757 (95) mri peak = 0.07278 (98) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (729 voxels, overlap=0.560) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (729 voxels, peak = 104), gca=104.0 gca peak = 0.17004 (92) mri peak = 0.10072 (101) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (838 voxels, overlap=0.467) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (838 voxels, peak = 100), gca=99.8 gca peak = 0.21361 (36) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.26069 (23) mri peak = 0.10196 (14) Fourth_Ventricle (15): linear fit = 0.56 x + 0.0 (140 voxels, overlap=0.074) Fourth_Ventricle (15): linear fit = 0.56 x + 0.0 (140 voxels, peak = 13), gca=12.8 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.31795 (35) gca peak Third_Ventricle = 0.21361 (36) gca peak Fourth_Ventricle = 0.26069 (23) gca peak CSF = 0.14367 (38) gca peak Left_Accumbens_area = 0.57033 (70) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65201 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.31129 (32) gca peak Right_Accumbens_area = 0.30219 (72) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.72939 (42) gca peak WM_hypointensities = 0.14821 (82) gca peak non_WM_hypointensities = 0.10354 (53) gca peak Optic_Chiasm = 0.34849 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.20 x + 0.0 estimating mean wm scale to be 1.04 x + 0.0 estimating mean csf scale to be 0.49 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.30618 (11) mri peak = 0.10923 (13) Left_Lateral_Ventricle (4): linear fit = 1.04 x + 0.0 (4341 voxels, overlap=0.992) Left_Lateral_Ventricle (4): linear fit = 1.04 x + 0.0 (4341 voxels, peak = 11), gca=11.5 gca peak = 0.21905 (12) mri peak = 0.11971 (14) Right_Lateral_Ventricle (43): linear fit = 1.04 x + 0.0 (3705 voxels, overlap=0.985) Right_Lateral_Ventricle (43): linear fit = 1.04 x + 0.0 (3705 voxels, peak = 13), gca=12.5 gca peak = 0.22198 (107) mri peak = 0.12435 (109) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (255 voxels, overlap=1.006) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (255 voxels, peak = 107), gca=107.0 gca peak = 0.18323 (101) mri peak = 0.04812 (95) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (54 voxels, overlap=0.891) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (54 voxels, peak = 102), gca=101.5 gca peak = 0.22476 (74) mri peak = 0.09034 (74) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (635 voxels, overlap=0.917) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (635 voxels, peak = 73), gca=72.9 gca peak = 0.24098 (81) mri peak = 0.09241 (80) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (449 voxels, overlap=1.000) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (449 voxels, peak = 80), gca=79.8 gca peak = 0.08176 (110) mri peak = 0.07935 (109) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (29458 voxels, overlap=0.806) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (29458 voxels, peak = 110), gca=110.0 gca peak = 0.08542 (110) mri peak = 0.06033 (109) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (28878 voxels, overlap=0.853) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (28878 voxels, peak = 109), gca=109.4 gca peak = 0.06820 (72) mri peak = 0.03333 (74) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (17845 voxels, overlap=0.850) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (17845 voxels, peak = 72), gca=72.0 gca peak = 0.07510 (74) mri peak = 0.03645 (73) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (16086 voxels, overlap=0.897) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (16086 voxels, peak = 74), gca=74.0 gca peak = 0.28827 (85) mri peak = 0.09149 (84) Right_Caudate (50): linear fit = 0.99 x + 0.0 (618 voxels, overlap=1.000) Right_Caudate (50): linear fit = 0.99 x + 0.0 (618 voxels, peak = 84), gca=83.7 gca peak = 0.16044 (83) mri peak = 0.12712 (88) Left_Caudate (11): linear fit = 1.00 x + 0.0 (473 voxels, overlap=0.998) Left_Caudate (11): linear fit = 1.00 x + 0.0 (473 voxels, peak = 83), gca=83.0 gca peak = 0.08043 (86) mri peak = 0.05187 (85) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (18048 voxels, overlap=0.960) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (18048 voxels, peak = 86), gca=85.6 gca peak = 0.09874 (80) mri peak = 0.04259 (83) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (23108 voxels, overlap=0.977) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (23108 voxels, peak = 80), gca=79.6 gca peak = 0.16129 (96) mri peak = 0.07177 (97) Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (3957 voxels, overlap=0.988) Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (3957 voxels, peak = 97), gca=97.4 gca peak = 0.16498 (89) mri peak = 0.09520 (90) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (2243 voxels, overlap=0.989) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (2243 voxels, peak = 89), gca=88.6 gca peak = 0.30068 (81) mri peak = 0.10435 (82) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (230 voxels, overlap=1.014) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (230 voxels, peak = 81), gca=81.0 gca peak = 0.36275 (76) mri peak = 0.15385 (75) Right_Amygdala (54): linear fit = 0.99 x + 0.0 (273 voxels, overlap=1.026) Right_Amygdala (54): linear fit = 0.99 x + 0.0 (273 voxels, peak = 75), gca=74.9 gca peak = 0.09437 (105) mri peak = 0.06663 (100) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3693 voxels, overlap=0.913) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3693 voxels, peak = 104), gca=104.5 gca peak = 0.12742 (99) mri peak = 0.06849 (99) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3596 voxels, overlap=0.951) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3596 voxels, peak = 99), gca=99.0 gca peak = 0.07808 (88) mri peak = 0.07264 (90) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1059 voxels, overlap=0.940) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1059 voxels, peak = 88), gca=87.6 gca peak = 0.08286 (85) mri peak = 0.06828 (91) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1112 voxels, overlap=0.859) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1112 voxels, peak = 85), gca=85.4 gca peak = 0.07145 (93) mri peak = 0.07138 (90) Brain_Stem (16): linear fit = 1.00 x + 0.0 (11472 voxels, overlap=0.799) Brain_Stem (16): linear fit = 1.00 x + 0.0 (11472 voxels, peak = 93), gca=92.5 gca peak = 0.11587 (100) mri peak = 0.07278 (98) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (729 voxels, overlap=0.811) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (729 voxels, peak = 100), gca=100.0 gca peak = 0.16039 (100) mri peak = 0.10072 (101) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (838 voxels, overlap=0.839) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (838 voxels, peak = 100), gca=100.5 gca peak = 0.29663 (18) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.31312 (11) mri peak = 0.10196 (14) Fourth_Ventricle (15): linear fit = 1.21 x + 0.0 (140 voxels, overlap=0.979) Fourth_Ventricle (15): linear fit = 1.21 x + 0.0 (140 voxels, peak = 13), gca=13.3 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.22716 (43) gca peak Third_Ventricle = 0.29663 (18) gca peak CSF = 0.26493 (20) gca peak Left_Accumbens_area = 0.56977 (78) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.63638 (62) gca peak Left_choroid_plexus = 0.09086 (48) gca peak Right_Inf_Lat_Vent = 0.23884 (38) gca peak Right_Accumbens_area = 0.31096 (83) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.45852 (22) gca peak WM_hypointensities = 0.17672 (85) gca peak non_WM_hypointensities = 0.12111 (55) gca peak Optic_Chiasm = 0.34847 (76) not using caudate to estimate GM means estimating mean gm scale to be 0.99 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.10 x + 0.0 Right_Pallidum too bright - rescaling by 0.995 (from 1.000) to 106.4 (was 107.0) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 26506 gm and wm labels changed (%15 to gray, %85 to white out of all changed labels) 387 hippocampal voxels changed. 4 amygdala voxels changed. pass 1: 71123 changed. image ll: -2.164, PF=1.000 pass 2: 10633 changed. image ll: -2.161, PF=1.000 pass 3: 3392 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 12 minutes and 2 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/transforms/cc_up.lta PBRHOPE_HOPE086_PETMR will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/transforms/cc_up.lta reading aseg from /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/aseg.auto_noCCseg.mgz reading norm from /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/norm.mgz 42186 voxels in left wm, 57302 in right wm, xrange [115, 130] searching rotation angles z=[-7 7], y=[-13 1] 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 searching scale 1 Z rot 5.0 searching scale 1 Z rot 5.3 searching scale 1 Z rot 5.5 searching scale 1 Z rot 5.8 searching scale 1 Z rot 6.0 searching scale 1 Z rot 6.3 searching scale 1 Z rot 6.5 searching scale 1 Z rot 6.8 global minimum found at slice 123.1, rotations (-5.69, 0.03) final transformation (x=123.1, yr=-5.693, zr=0.026): 0.995 -0.000 -0.099 12.721; 0.000 1.000 -0.000 22.947; 0.099 0.000 0.995 44.146; 0.000 0.000 0.000 1.000; updating x range to be [126, 130] in xformed coordinates best xformed slice 128 cc center is found at 128 144 107 eigenvectors: 0.000 0.001 1.000; -0.378 -0.926 0.001; 0.926 -0.378 0.000; error in mid anterior detected - correcting... writing aseg with callosum to /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/aseg.auto.mgz... corpus callosum matter segmentation took 1.0 minutes #-------------------------------------- #@# Merge ASeg Mon Nov 17 16:30:35 EST 2025 cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# Intensity Normalization2 Mon Nov 17 16:30:35 EST 2025 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 2309 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 109 gm peak at 83 (83), valley at 34 (34) csf peak at 12, setting threshold to 59 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 109 gm peak at 82 (82), valley at 57 (57) csf peak at 12, setting threshold to 58 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 2 minutes and 43 seconds. #-------------------------------------------- #@# Mask BFS Mon Nov 17 16:33:19 EST 2025 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1466395 voxels in mask (pct= 8.74) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Mon Nov 17 16:33:21 EST 2025 mri_segment brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (103.0): 103.8 +- 6.0 [80.0 --> 125.0] GM (73.0) : 71.2 +- 10.8 [30.0 --> 96.0] setting bottom of white matter range to 81.9 setting top of gray matter range to 92.7 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... 5383 sparsely connected voxels removed... thickening thin strands.... 20 segments, 2726 filled 1597 bright non-wm voxels segmented. 4096 diagonally connected voxels added... white matter segmentation took 1.3 minutes writing output to wm.seg.mgz... mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.42 minutes reading wm segmentation from wm.seg.mgz... 526 voxels added to wm to prevent paths from MTL structures to cortex 3056 additional wm voxels added 0 additional wm voxels added SEG EDIT: 65869 voxels turned on, 47767 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 0 new 0 115,126,128 old 0 new 0 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 38 found - 38 modified | TOTAL: 38 pass 2 (xy+): 0 found - 38 modified | TOTAL: 38 pass 1 (xy-): 29 found - 29 modified | TOTAL: 67 pass 2 (xy-): 0 found - 29 modified | TOTAL: 67 pass 1 (yz+): 46 found - 46 modified | TOTAL: 113 pass 2 (yz+): 0 found - 46 modified | TOTAL: 113 pass 1 (yz-): 26 found - 26 modified | TOTAL: 139 pass 2 (yz-): 0 found - 26 modified | TOTAL: 139 pass 1 (xz+): 30 found - 30 modified | TOTAL: 169 pass 2 (xz+): 0 found - 30 modified | TOTAL: 169 pass 1 (xz-): 33 found - 33 modified | TOTAL: 202 pass 2 (xz-): 0 found - 33 modified | TOTAL: 202 Iteration Number : 1 pass 1 (+++): 39 found - 39 modified | TOTAL: 39 pass 2 (+++): 0 found - 39 modified | TOTAL: 39 pass 1 (+++): 23 found - 23 modified | TOTAL: 62 pass 2 (+++): 0 found - 23 modified | TOTAL: 62 pass 1 (+++): 30 found - 30 modified | TOTAL: 92 pass 2 (+++): 0 found - 30 modified | TOTAL: 92 pass 1 (+++): 40 found - 40 modified | TOTAL: 132 pass 2 (+++): 0 found - 40 modified | TOTAL: 132 Iteration Number : 1 pass 1 (++): 97 found - 97 modified | TOTAL: 97 pass 2 (++): 0 found - 97 modified | TOTAL: 97 pass 1 (+-): 89 found - 89 modified | TOTAL: 186 pass 2 (+-): 0 found - 89 modified | TOTAL: 186 pass 1 (--): 121 found - 121 modified | TOTAL: 307 pass 2 (--): 0 found - 121 modified | TOTAL: 307 pass 1 (-+): 55 found - 55 modified | TOTAL: 362 pass 2 (-+): 0 found - 55 modified | TOTAL: 362 Iteration Number : 2 pass 1 (xy+): 11 found - 11 modified | TOTAL: 11 pass 2 (xy+): 0 found - 11 modified | TOTAL: 11 pass 1 (xy-): 11 found - 11 modified | TOTAL: 22 pass 2 (xy-): 0 found - 11 modified | TOTAL: 22 pass 1 (yz+): 8 found - 8 modified | TOTAL: 30 pass 2 (yz+): 0 found - 8 modified | TOTAL: 30 pass 1 (yz-): 9 found - 9 modified | TOTAL: 39 pass 2 (yz-): 0 found - 9 modified | TOTAL: 39 pass 1 (xz+): 11 found - 11 modified | TOTAL: 50 pass 2 (xz+): 0 found - 11 modified | TOTAL: 50 pass 1 (xz-): 6 found - 6 modified | TOTAL: 56 pass 2 (xz-): 0 found - 6 modified | TOTAL: 56 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 6 found - 6 modified | TOTAL: 6 pass 2 (+++): 0 found - 6 modified | TOTAL: 6 pass 1 (+++): 6 found - 6 modified | TOTAL: 12 pass 2 (+++): 0 found - 6 modified | TOTAL: 12 pass 1 (+++): 0 found - 0 modified | TOTAL: 12 Iteration Number : 2 pass 1 (++): 5 found - 5 modified | TOTAL: 5 pass 2 (++): 0 found - 5 modified | TOTAL: 5 pass 1 (+-): 3 found - 3 modified | TOTAL: 8 pass 2 (+-): 0 found - 3 modified | TOTAL: 8 pass 1 (--): 3 found - 3 modified | TOTAL: 11 pass 2 (--): 0 found - 3 modified | TOTAL: 11 pass 1 (-+): 4 found - 4 modified | TOTAL: 15 pass 2 (-+): 0 found - 4 modified | TOTAL: 15 Iteration Number : 3 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 1 found - 1 modified | TOTAL: 2 pass 2 (xy-): 0 found - 1 modified | TOTAL: 2 pass 1 (yz+): 2 found - 2 modified | TOTAL: 4 pass 2 (yz+): 0 found - 2 modified | TOTAL: 4 pass 1 (yz-): 2 found - 2 modified | TOTAL: 6 pass 2 (yz-): 0 found - 2 modified | TOTAL: 6 pass 1 (xz+): 0 found - 0 modified | TOTAL: 6 pass 1 (xz-): 0 found - 0 modified | TOTAL: 6 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 (--): 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 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 = 787 (out of 531120: 0.148177) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Mon Nov 17 16:35:10 EST 2025 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 1.087 0.023 -0.089 -4.731; 0.057 0.867 0.681 -39.773; 0.085 -0.640 0.851 100.734; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.087 0.023 -0.089 -4.731; 0.057 0.867 0.681 -39.773; 0.085 -0.640 0.851 100.734; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1850 (min = 350, max = 1400), aspect = 0.45 (min = 0.10, max = 0.75) need search nearby using seed (126, 97, 88), TAL = (2.0, -40.0, 31.0) talairach voxel to voxel transform 0.913 0.029 0.072 -1.786; 0.007 0.725 -0.580 87.332; -0.085 0.542 0.732 -52.590; 0.000 0.000 0.000 1.000; segmentation indicates cc at (126, 97, 88) --> (2.0, -40.0, 31.0) done. writing output to filled.mgz... filling took 0.6 minutes talairach cc position changed to (2.00, -40.00, 31.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, -40.00, 31.00) SRC: (105.94, 107.42, 55.24) search lh wm seed point around talairach space (-16.00, -40.00, 31.00), SRC: (138.80, 107.68, 52.16) 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 Mon Nov 17 16:35:44 EST 2025 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 1 found - 1 modified | TOTAL: 3 pass 2 (xy-): 0 found - 1 modified | TOTAL: 3 pass 1 (yz+): 0 found - 0 modified | TOTAL: 3 pass 1 (yz-): 4 found - 4 modified | TOTAL: 7 pass 2 (yz-): 0 found - 4 modified | TOTAL: 7 pass 1 (xz+): 1 found - 1 modified | TOTAL: 8 pass 2 (xz+): 0 found - 1 modified | TOTAL: 8 pass 1 (xz-): 3 found - 3 modified | TOTAL: 11 pass 2 (xz-): 0 found - 3 modified | TOTAL: 11 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 1 found - 1 modified | TOTAL: 2 pass 2 (-+): 0 found - 1 modified | TOTAL: 2 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 13 (out of 256529: 0.005068) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 10: 1519 vertices, 1670 faces slice 20: 10071 vertices, 10429 faces slice 30: 22783 vertices, 23227 faces slice 40: 35297 vertices, 35698 faces slice 50: 47304 vertices, 47676 faces slice 60: 58212 vertices, 58596 faces slice 70: 69059 vertices, 69460 faces slice 80: 79800 vertices, 80199 faces slice 90: 89756 vertices, 90158 faces slice 100: 99454 vertices, 99862 faces slice 110: 107690 vertices, 108032 faces slice 120: 115299 vertices, 115624 faces slice 130: 121368 vertices, 121650 faces slice 140: 126310 vertices, 126525 faces slice 150: 129042 vertices, 129173 faces slice 160: 129318 vertices, 129404 faces slice 170: 129318 vertices, 129404 faces slice 180: 129318 vertices, 129404 faces slice 190: 129318 vertices, 129404 faces slice 200: 129318 vertices, 129404 faces slice 210: 129318 vertices, 129404 faces slice 220: 129318 vertices, 129404 faces slice 230: 129318 vertices, 129404 faces slice 240: 129318 vertices, 129404 faces slice 250: 129318 vertices, 129404 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 129318 voxel in cpt #1: X=-86 [v=129318,e=388212,f=258808] located at (-21.103296, -60.028488, 24.934959) For the whole surface: X=-86 [v=129318,e=388212,f=258808] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Mon Nov 17 16:35:49 EST 2025 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Mon Nov 17 16:35:52 EST 2025 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/scripts avg radius = 46.8 mm, total surface area = 67592 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.4 minutes Not saving sulc step 000: RMS=0.104 (target=0.015) step 005: RMS=0.078 (target=0.015) step 010: RMS=0.059 (target=0.015) step 015: RMS=0.051 (target=0.015) step 020: RMS=0.044 (target=0.015) step 025: RMS=0.039 (target=0.015) step 030: RMS=0.036 (target=0.015) step 035: RMS=0.034 (target=0.015) step 040: RMS=0.033 (target=0.015) step 045: RMS=0.032 (target=0.015) step 050: RMS=0.031 (target=0.015) step 055: RMS=0.031 (target=0.015) step 060: RMS=0.031 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Mon Nov 17 16:36:15 EST 2025 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.00 +- 0.60 (0.00-->6.70) (max @ vno 100008 --> 100009) face area 0.03 +- 0.04 (-0.16-->0.96) scaling brain by 0.350... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=174.277, avgs=0 005/300: dt: 0.9000, rms radial error=174.022, avgs=0 010/300: dt: 0.9000, rms radial error=173.475, avgs=0 015/300: dt: 0.9000, rms radial error=172.756, avgs=0 020/300: dt: 0.9000, rms radial error=171.939, avgs=0 025/300: dt: 0.9000, rms radial error=171.066, avgs=0 030/300: dt: 0.9000, rms radial error=170.161, avgs=0 035/300: dt: 0.9000, rms radial error=169.238, avgs=0 040/300: dt: 0.9000, rms radial error=168.306, avgs=0 045/300: dt: 0.9000, rms radial error=167.371, avgs=0 050/300: dt: 0.9000, rms radial error=166.436, avgs=0 055/300: dt: 0.9000, rms radial error=165.502, avgs=0 060/300: dt: 0.9000, rms radial error=164.572, avgs=0 065/300: dt: 0.9000, rms radial error=163.646, avgs=0 070/300: dt: 0.9000, rms radial error=162.723, avgs=0 075/300: dt: 0.9000, rms radial error=161.805, avgs=0 080/300: dt: 0.9000, rms radial error=160.891, avgs=0 085/300: dt: 0.9000, rms radial error=159.982, avgs=0 090/300: dt: 0.9000, rms radial error=159.078, avgs=0 095/300: dt: 0.9000, rms radial error=158.178, avgs=0 100/300: dt: 0.9000, rms radial error=157.282, avgs=0 105/300: dt: 0.9000, rms radial error=156.392, avgs=0 110/300: dt: 0.9000, rms radial error=155.505, avgs=0 115/300: dt: 0.9000, rms radial error=154.624, avgs=0 120/300: dt: 0.9000, rms radial error=153.747, avgs=0 125/300: dt: 0.9000, rms radial error=152.875, avgs=0 130/300: dt: 0.9000, rms radial error=152.012, avgs=0 135/300: dt: 0.9000, rms radial error=151.155, avgs=0 140/300: dt: 0.9000, rms radial error=150.307, avgs=0 145/300: dt: 0.9000, rms radial error=149.464, avgs=0 150/300: dt: 0.9000, rms radial error=148.627, avgs=0 155/300: dt: 0.9000, rms radial error=147.794, avgs=0 160/300: dt: 0.9000, rms radial error=146.966, avgs=0 165/300: dt: 0.9000, rms radial error=146.142, avgs=0 170/300: dt: 0.9000, rms radial error=145.323, avgs=0 175/300: dt: 0.9000, rms radial error=144.508, avgs=0 180/300: dt: 0.9000, rms radial error=143.698, avgs=0 185/300: dt: 0.9000, rms radial error=142.892, avgs=0 190/300: dt: 0.9000, rms radial error=142.090, avgs=0 195/300: dt: 0.9000, rms radial error=141.293, avgs=0 200/300: dt: 0.9000, rms radial error=140.500, avgs=0 205/300: dt: 0.9000, rms radial error=139.711, avgs=0 210/300: dt: 0.9000, rms radial error=138.926, avgs=0 215/300: dt: 0.9000, rms radial error=138.146, avgs=0 220/300: dt: 0.9000, rms radial error=137.370, avgs=0 225/300: dt: 0.9000, rms radial error=136.599, avgs=0 230/300: dt: 0.9000, rms radial error=135.831, avgs=0 235/300: dt: 0.9000, rms radial error=135.068, avgs=0 240/300: dt: 0.9000, rms radial error=134.309, avgs=0 245/300: dt: 0.9000, rms radial error=133.554, avgs=0 250/300: dt: 0.9000, rms radial error=132.803, avgs=0 255/300: dt: 0.9000, rms radial error=132.057, avgs=0 260/300: dt: 0.9000, rms radial error=131.314, avgs=0 265/300: dt: 0.9000, rms radial error=130.576, avgs=0 270/300: dt: 0.9000, rms radial error=129.842, avgs=0 275/300: dt: 0.9000, rms radial error=129.112, avgs=0 280/300: dt: 0.9000, rms radial error=128.386, avgs=0 285/300: dt: 0.9000, rms radial error=127.663, avgs=0 290/300: dt: 0.9000, rms radial error=126.945, avgs=0 295/300: dt: 0.9000, rms radial error=126.231, avgs=0 300/300: dt: 0.9000, rms radial error=125.521, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 14579.10 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 = 2316.71 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00018 epoch 3 (K=160.0), pass 1, starting sse = 223.74 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/10 = 0.00629 epoch 4 (K=640.0), pass 1, starting sse = 16.72 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.13/14 = 0.00893 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.05 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Mon Nov 17 16:39:01 EST 2025 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 PBRHOPE_HOPE086_PETMR lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ before topology correction, eno=-86 (nv=129318, nf=258808, ne=388212, g=44) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations marking ambiguous vertices... 5903 ambiguous faces found in tessellation segmenting defects... 41 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 5 into 2 -merging segment 14 into 13 39 defects to be corrected 0 vertices coincident reading input surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.3977 (-4.6989) -vertex loglikelihood: -6.2293 (-3.1147) -normal dot loglikelihood: -3.6066 (-3.6066) -quad curv loglikelihood: -6.3206 (-3.1603) Total Loglikelihood : -25.5542 CORRECTING DEFECT 0 (vertices=255, convex hull=107) After retessellation of defect 0, euler #=-37 (125824,376171,250310) : difference with theory (-36) = 1 CORRECTING DEFECT 1 (vertices=39, convex hull=26) After retessellation of defect 1, euler #=-36 (125827,376187,250324) : difference with theory (-35) = 1 CORRECTING DEFECT 2 (vertices=67, convex hull=100) After retessellation of defect 2, euler #=-34 (125843,376286,250409) : difference with theory (-34) = 0 CORRECTING DEFECT 3 (vertices=26, convex hull=58) After retessellation of defect 3, euler #=-33 (125851,376334,250450) : difference with theory (-33) = 0 CORRECTING DEFECT 4 (vertices=74, convex hull=58) After retessellation of defect 4, euler #=-32 (125865,376398,250501) : difference with theory (-32) = 0 CORRECTING DEFECT 5 (vertices=18, convex hull=54) After retessellation of defect 5, euler #=-31 (125874,376446,250541) : difference with theory (-31) = 0 CORRECTING DEFECT 6 (vertices=20, convex hull=50) After retessellation of defect 6, euler #=-30 (125885,376500,250585) : difference with theory (-30) = 0 CORRECTING DEFECT 7 (vertices=42, convex hull=73) After retessellation of defect 7, euler #=-29 (125910,376608,250669) : difference with theory (-29) = 0 CORRECTING DEFECT 8 (vertices=12, convex hull=38) After retessellation of defect 8, euler #=-28 (125913,376633,250692) : difference with theory (-28) = 0 CORRECTING DEFECT 9 (vertices=18, convex hull=51) After retessellation of defect 9, euler #=-27 (125922,376676,250727) : difference with theory (-27) = 0 CORRECTING DEFECT 10 (vertices=28, convex hull=55) After retessellation of defect 10, euler #=-26 (125933,376732,250773) : difference with theory (-26) = 0 CORRECTING DEFECT 11 (vertices=18, convex hull=27) After retessellation of defect 11, euler #=-25 (125937,376752,250790) : difference with theory (-25) = 0 CORRECTING DEFECT 12 (vertices=201, convex hull=139) After retessellation of defect 12, euler #=-23 (126004,377013,250986) : difference with theory (-24) = -1 CORRECTING DEFECT 13 (vertices=961, convex hull=551) After retessellation of defect 13, euler #=-23 (126391,378467,252053) : difference with theory (-23) = 0 CORRECTING DEFECT 14 (vertices=11, convex hull=25) After retessellation of defect 14, euler #=-22 (126395,378486,252069) : difference with theory (-22) = 0 CORRECTING DEFECT 15 (vertices=45, convex hull=81) After retessellation of defect 15, euler #=-21 (126419,378590,252150) : difference with theory (-21) = 0 CORRECTING DEFECT 16 (vertices=20, convex hull=52) After retessellation of defect 16, euler #=-20 (126428,378639,252191) : difference with theory (-20) = 0 CORRECTING DEFECT 17 (vertices=33, convex hull=49) After retessellation of defect 17, euler #=-19 (126446,378711,252246) : difference with theory (-19) = 0 CORRECTING DEFECT 18 (vertices=26, convex hull=51) After retessellation of defect 18, euler #=-18 (126454,378755,252283) : difference with theory (-18) = 0 CORRECTING DEFECT 19 (vertices=171, convex hull=117) After retessellation of defect 19, euler #=-17 (126515,378991,252459) : difference with theory (-17) = 0 CORRECTING DEFECT 20 (vertices=34, convex hull=29) After retessellation of defect 20, euler #=-16 (126523,379023,252484) : difference with theory (-16) = 0 CORRECTING DEFECT 21 (vertices=78, convex hull=107) After retessellation of defect 21, euler #=-15 (126561,379181,252605) : difference with theory (-15) = 0 CORRECTING DEFECT 22 (vertices=41, convex hull=26) After retessellation of defect 22, euler #=-14 (126568,379213,252631) : difference with theory (-14) = 0 CORRECTING DEFECT 23 (vertices=453, convex hull=87) After retessellation of defect 23, euler #=-13 (126590,379323,252720) : difference with theory (-13) = 0 CORRECTING DEFECT 24 (vertices=54, convex hull=85) After retessellation of defect 24, euler #=-12 (126619,379445,252814) : difference with theory (-12) = 0 CORRECTING DEFECT 25 (vertices=66, convex hull=35) After retessellation of defect 25, euler #=-11 (126629,379486,252846) : difference with theory (-11) = 0 CORRECTING DEFECT 26 (vertices=27, convex hull=51) After retessellation of defect 26, euler #=-10 (126639,379535,252886) : difference with theory (-10) = 0 CORRECTING DEFECT 27 (vertices=61, convex hull=87) After retessellation of defect 27, euler #=-9 (126675,379680,252996) : difference with theory (-9) = 0 CORRECTING DEFECT 28 (vertices=100, convex hull=92) After retessellation of defect 28, euler #=-8 (126710,379824,253106) : difference with theory (-8) = 0 CORRECTING DEFECT 29 (vertices=135, convex hull=74) After retessellation of defect 29, euler #=-7 (126732,379923,253184) : difference with theory (-7) = 0 CORRECTING DEFECT 30 (vertices=41, convex hull=32) After retessellation of defect 30, euler #=-6 (126742,379964,253216) : difference with theory (-6) = 0 CORRECTING DEFECT 31 (vertices=33, convex hull=71) After retessellation of defect 31, euler #=-5 (126757,380035,253273) : difference with theory (-5) = 0 CORRECTING DEFECT 32 (vertices=36, convex hull=57) After retessellation of defect 32, euler #=-4 (126775,380113,253334) : difference with theory (-4) = 0 CORRECTING DEFECT 33 (vertices=51, convex hull=77) After retessellation of defect 33, euler #=-3 (126796,380206,253407) : difference with theory (-3) = 0 CORRECTING DEFECT 34 (vertices=24, convex hull=64) After retessellation of defect 34, euler #=-2 (126810,380275,253463) : difference with theory (-2) = 0 CORRECTING DEFECT 35 (vertices=86, convex hull=146) After retessellation of defect 35, euler #=-1 (126850,380461,253610) : difference with theory (-1) = 0 CORRECTING DEFECT 36 (vertices=52, convex hull=81) After retessellation of defect 36, euler #=0 (126868,380554,253686) : difference with theory (0) = 0 CORRECTING DEFECT 37 (vertices=21, convex hull=56) After retessellation of defect 37, euler #=1 (126877,380601,253725) : difference with theory (1) = 0 CORRECTING DEFECT 38 (vertices=48, convex hull=64) After retessellation of defect 38, euler #=2 (126893,380673,253782) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.23 (0.01-->10.21) (max @ vno 61522 --> 69091) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.23 (0.01-->10.21) (max @ vno 61522 --> 69091) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 104 mutations (32.7%), 214 crossovers (67.3%), 122 vertices were eliminated building final representation... 2425 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=126893, nf=253782, ne=380673, g=0) writing corrected surface to /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 15.0 minutes 0 defective edges removing intersecting faces 000: 370 intersecting 001: 18 intersecting 002: 7 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 126893 - 380673 + 253782 = 2 --> 0 holes F =2V-4: 253782 = 253786-4 (0) 2E=3F: 761346 = 761346 (0) total defect index = 0 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 118 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Mon Nov 17 16:54:04 EST 2025 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs PBRHOPE_HOPE086_PETMR lh only generating white matter surface not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/filled.mgz... reading volume /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/brain.finalsurfs.mgz... reading volume /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/wm.mgz... 11566 bright wm thresholded. 1758 bright non-wm voxels segmented. reading original surface position from /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.orig... computing class statistics... border white: 244849 voxels (1.46%) border gray 269780 voxels (1.61%) WM (93.0): 94.3 +- 7.3 [70.0 --> 110.0] GM (82.0) : 80.2 +- 11.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 60.4 (was 70) setting MAX_BORDER_WHITE to 108.3 (was 105) setting MIN_BORDER_WHITE to 72.0 (was 85) setting MAX_CSF to 48.7 (was 40) setting MAX_GRAY to 93.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 66.2 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 37.1 (was 40) repositioning cortical surface to gray/white boundary reading volume /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.02-->4.99) (max @ vno 126284 --> 126353) face area 0.28 +- 0.12 (0.00-->4.03) mean absolute distance = 0.83 +- 1.10 3891 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=101, GM=72 mean inside = 93.3, mean outside = 77.1 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group mean border=82.2, 287 (287) missing vertices, mean dist 0.2 [0.9 (%36.7)->0.8 (%63.3))] %46 local maxima, %49 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=r440-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.26 (0.06-->5.60) (max @ vno 126031 --> 74306) face area 0.28 +- 0.13 (0.00-->3.15) mean absolute distance = 0.44 +- 0.82 4074 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4445290.5, rms=9.38 001: dt: 0.5000, sse=5163632.0, rms=6.617 (0.000%) 002: dt: 0.5000, sse=5548852.0, rms=4.997 (0.000%) 003: dt: 0.5000, sse=5870404.0, rms=4.054 (0.000%) 004: dt: 0.5000, sse=6101612.0, rms=3.497 (0.000%) 005: dt: 0.5000, sse=6250275.0, rms=3.224 (0.000%) 006: dt: 0.5000, sse=6379356.0, rms=3.076 (0.000%) 007: dt: 0.5000, sse=6418664.0, rms=3.017 (0.000%) 008: dt: 0.5000, sse=6455065.0, rms=2.956 (0.000%) rms = 2.94, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=6468564.5, rms=2.942 (0.000%) 010: dt: 0.2500, sse=4015825.0, rms=2.060 (0.000%) 011: dt: 0.2500, sse=3712366.8, rms=1.870 (0.000%) rms = 1.83, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=3597953.0, rms=1.830 (0.000%) rms = 1.79, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=3533842.0, rms=1.793 (0.000%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 1 vertex label from ripped group mean border=84.2, 155 (84) missing vertices, mean dist -0.2 [0.5 (%62.4)->0.3 (%37.6))] %56 local maxima, %39 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=r440-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.09-->5.47) (max @ vno 126284 --> 126353) face area 0.35 +- 0.16 (0.00-->3.95) mean absolute distance = 0.36 +- 0.54 4134 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3899898.5, rms=3.75 014: dt: 0.5000, sse=4355903.0, rms=2.509 (0.000%) 015: dt: 0.5000, sse=4848252.0, rms=2.420 (0.000%) rms = 2.38, time step reduction 1 of 3 to 0.250... 016: dt: 0.5000, sse=5152660.0, rms=2.379 (0.000%) 017: dt: 0.2500, sse=4097105.8, rms=1.674 (0.000%) 018: dt: 0.2500, sse=3887101.2, rms=1.519 (0.000%) rms = 1.50, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=3803263.5, rms=1.496 (0.000%) rms = 1.46, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=3753966.8, rms=1.463 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 4 vertex label from ripped group mean border=86.6, 141 (46) missing vertices, mean dist -0.2 [0.4 (%66.8)->0.2 (%33.2))] %72 local maxima, %23 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=r440-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.05-->5.39) (max @ vno 126284 --> 126353) face area 0.34 +- 0.16 (0.00-->4.18) mean absolute distance = 0.30 +- 0.43 3285 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3962810.2, rms=3.41 021: dt: 0.5000, sse=4260381.5, rms=2.196 (0.000%) rms = 2.24, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=4030963.2, rms=1.728 (0.000%) 023: dt: 0.2500, sse=3967544.0, rms=1.415 (0.000%) 024: dt: 0.2500, sse=3909164.8, rms=1.344 (0.000%) rms = 1.34, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=3875519.0, rms=1.336 (0.000%) rms = 1.32, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=3846271.5, rms=1.316 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group mean border=87.7, 128 (22) missing vertices, mean dist -0.1 [0.3 (%58.0)->0.2 (%42.0))] %79 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=r440-, 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=3872377.5, rms=1.89 027: dt: 0.5000, sse=4836522.5, rms=1.532 (0.000%) rms = 1.93, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=4394154.0, rms=1.165 (0.000%) 029: dt: 0.2500, sse=4201144.0, rms=1.088 (0.000%) rms = 1.05, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=4259229.5, rms=1.052 (0.000%) rms = 1.05, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=4244308.0, rms=1.046 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group generating cortex label... 13 non-cortical segments detected only using segment with 1824 vertices erasing segment 1 (vno[0] = 59406) erasing segment 2 (vno[0] = 64755) erasing segment 3 (vno[0] = 72379) erasing segment 4 (vno[0] = 72397) erasing segment 5 (vno[0] = 82547) erasing segment 6 (vno[0] = 83292) erasing segment 7 (vno[0] = 97880) erasing segment 8 (vno[0] = 101079) erasing segment 9 (vno[0] = 101128) erasing segment 10 (vno[0] = 101858) erasing segment 11 (vno[0] = 104262) erasing segment 12 (vno[0] = 105769) writing cortex label to /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/label/lh.cortex.label... writing curvature file /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.curv writing smoothed area to lh.area writing curvature file /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.area vertex spacing 0.88 +- 0.25 (0.04-->5.52) (max @ vno 126031 --> 74306) face area 0.33 +- 0.16 (0.00-->4.02) refinement took 3.4 minutes #-------------------------------------------- #@# Smooth2 lh Mon Nov 17 16:57:31 EST 2025 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 lh Mon Nov 17 16:57:34 EST 2025 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 47.0 mm, total surface area = 75625 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.115 (target=0.015) step 005: RMS=0.081 (target=0.015) step 010: RMS=0.059 (target=0.015) step 015: RMS=0.047 (target=0.015) step 020: RMS=0.039 (target=0.015) step 025: RMS=0.032 (target=0.015) step 030: RMS=0.027 (target=0.015) step 035: RMS=0.024 (target=0.015) step 040: RMS=0.021 (target=0.015) step 045: RMS=0.018 (target=0.015) step 050: RMS=0.016 (target=0.015) step 055: RMS=0.016 (target=0.015) inflation complete. inflation took 0.4 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 159 vertices thresholded to be in k1 ~ [-0.18 1.57], k2 ~ [-0.10 0.06] total integrated curvature = 0.621*4pi (7.803) --> 0 handles ICI = 1.4, FI = 7.7, variation=134.960 114 vertices thresholded to be in [-0.08 0.01] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 104 vertices thresholded to be in [-0.12 0.43] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.017, std = 0.021 done. #----------------------------------------- #@# Curvature Stats lh Mon Nov 17 16:58:50 EST 2025 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm PBRHOPE_HOPE086_PETMR 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 [ PBRHOPE_HOPE086_PETMR/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 [ 227 ] Gb_filter = 0 WARN: S lookup min: -0.900379 WARN: S explicit min: 0.000000 vertex = 1389 #-------------------------------------------- #@# Sphere lh Mon Nov 17 16:58:54 EST 2025 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... scaling brain by 0.329... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=r440-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.35 pass 1: epoch 2 of 3 starting distance error %19.32 unfolding complete - removing small folds... starting distance error %19.26 removing remaining folds... final distance error %19.27 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/lh.sphere spherical transformation took 0.49 hours expanding nbhd size to 1 #-------------------------------------------- #@# Surf Reg lh Mon Nov 17 17:28:29 EST 2025 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/scripts mris_register -curv ../surf/lh.sphere /usr/local/freesurfer/stable5_3_0/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /usr/local/freesurfer/stable5_3_0/average/lh.average.curvature.filled.buckner40.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=r440-, 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=r440-, 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 = 0.570 curvature mean = 0.053, std = 0.934 curvature mean = 0.026, std = 0.858 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 0.00, -16.00) sse = 306718.1, tmin=0.6205 d=32.00 min @ (-8.00, -8.00, 0.00) sse = 210847.7, tmin=1.2433 d=16.00 min @ (4.00, 0.00, 0.00) sse = 205585.0, tmin=1.8651 d=8.00 min @ (-2.00, -2.00, 0.00) sse = 197596.3, tmin=2.4893 d=4.00 min @ (0.00, 1.00, 0.00) sse = 197245.4, tmin=3.1169 d=2.00 min @ (0.00, -0.50, 0.00) sse = 196895.7, tmin=3.7379 d=1.00 min @ (-0.25, 0.00, 0.00) sse = 196797.9, tmin=4.3582 tol=1.0e+00, sigma=0.5, host=r440-, 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 4.99 min curvature mean = 0.018, std = 0.962 curvature mean = 0.010, std = 0.942 curvature mean = 0.017, std = 0.974 curvature mean = 0.004, std = 0.975 curvature mean = 0.014, std = 0.976 curvature mean = 0.001, std = 0.989 2 Reading smoothwm curvature mean = -0.030, std = 0.309 curvature mean = 0.003, std = 0.067 curvature mean = 0.059, std = 0.340 curvature mean = 0.003, std = 0.080 curvature mean = 0.026, std = 0.526 curvature mean = 0.002, std = 0.086 curvature mean = 0.013, std = 0.656 curvature mean = 0.002, std = 0.089 curvature mean = 0.004, std = 0.756 MRISregister() return, current seed 0 writing registered surface to ../surf/lh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white lh Mon Nov 17 17:43:54 EST 2025 mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white... writing curvature file ../surf/lh.jacobian_white #-------------------------------------------- #@# AvgCurv lh Mon Nov 17 17:43:56 EST 2025 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/scripts mrisp_paint -a 5 /usr/local/freesurfer/stable5_3_0/average/lh.average.curvature.filled.buckner40.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 /usr/local/freesurfer/stable5_3_0/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Mon Nov 17 17:43:57 EST 2025 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 PBRHOPE_HOPE086_PETMR lh ../surf/lh.sphere.reg /usr/local/freesurfer/stable5_3_0/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/stable5_3_0/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 1.0 using min determinant for regularization = 0.011 0 singular and 384 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1341 labels changed using aseg relabeling using gibbs priors... 000: 2895 changed, 126893 examined... 001: 690 changed, 12285 examined... 002: 177 changed, 3766 examined... 003: 72 changed, 1076 examined... 004: 29 changed, 408 examined... 005: 13 changed, 159 examined... 006: 8 changed, 75 examined... 007: 6 changed, 48 examined... 008: 4 changed, 30 examined... 009: 1 changed, 16 examined... 010: 0 changed, 7 examined... 226 labels changed using aseg 000: 120 total segments, 78 labels (398 vertices) changed 001: 47 total segments, 8 labels (27 vertices) changed 002: 39 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 49 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1593 vertices marked for relabeling... 1593 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 40 seconds. #-------------------------------------------- #@# Make Pial Surf lh Mon Nov 17 17:44:38 EST 2025 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs PBRHOPE_HOPE086_PETMR lh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/filled.mgz... reading volume /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/brain.finalsurfs.mgz... reading volume /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/wm.mgz... 11566 bright wm thresholded. 1758 bright non-wm voxels segmented. reading original surface position from /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.orig... computing class statistics... border white: 244849 voxels (1.46%) border gray 269780 voxels (1.61%) WM (93.0): 94.3 +- 7.3 [70.0 --> 110.0] GM (82.0) : 80.2 +- 11.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 60.4 (was 70) setting MAX_BORDER_WHITE to 108.3 (was 105) setting MIN_BORDER_WHITE to 72.0 (was 85) setting MAX_CSF to 48.7 (was 40) setting MAX_GRAY to 93.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 66.2 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 37.1 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=101, GM=72 mean inside = 93.3, mean outside = 77.1 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.02-->4.99) (max @ vno 126284 --> 126353) face area 0.28 +- 0.12 (0.00-->4.03) mean absolute distance = 0.84 +- 1.11 3772 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 1 with 365 points - only 0.00% unknown deleting segment 3 with 26 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 3 points - only 0.00% unknown mean border=82.2, 287 (287) missing vertices, mean dist 0.2 [0.9 (%36.7)->0.8 (%63.3))] %46 local maxima, %49 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=r440-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.26 (0.06-->5.60) (max @ vno 126031 --> 74306) face area 0.28 +- 0.13 (0.00-->3.15) mean absolute distance = 0.44 +- 0.82 4103 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4453267.0, rms=9.37 001: dt: 0.5000, sse=5177005.5, rms=6.611 (0.000%) 002: dt: 0.5000, sse=5564290.0, rms=4.992 (0.000%) 003: dt: 0.5000, sse=5890923.0, rms=4.050 (0.000%) 004: dt: 0.5000, sse=6120898.5, rms=3.494 (0.000%) 005: dt: 0.5000, sse=6271450.0, rms=3.221 (0.000%) 006: dt: 0.5000, sse=6400363.5, rms=3.074 (0.000%) 007: dt: 0.5000, sse=6444264.5, rms=3.015 (0.000%) 008: dt: 0.5000, sse=6477744.0, rms=2.954 (0.000%) rms = 2.94, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=6494689.5, rms=2.940 (0.000%) 010: dt: 0.2500, sse=4032629.8, rms=2.059 (0.000%) 011: dt: 0.2500, sse=3728536.0, rms=1.870 (0.000%) rms = 1.83, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=3613735.5, rms=1.830 (0.000%) rms = 1.79, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=3550304.8, rms=1.793 (0.000%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 1 vertex label from ripped group deleting segment 4 with 1 points - only 0.00% unknown deleting segment 5 with 254 points - only 0.00% unknown deleting segment 7 with 29 points - only 0.00% unknown deleting segment 9 with 6 points - only 0.00% unknown mean border=84.2, 155 (84) missing vertices, mean dist -0.2 [0.5 (%62.4)->0.3 (%37.6))] %56 local maxima, %39 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=r440-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.09-->5.47) (max @ vno 126284 --> 126353) face area 0.35 +- 0.16 (0.00-->3.95) mean absolute distance = 0.36 +- 0.54 4165 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3917246.2, rms=3.74 014: dt: 0.5000, sse=4376915.0, rms=2.507 (0.000%) 015: dt: 0.5000, sse=4870160.5, rms=2.418 (0.000%) rms = 2.38, time step reduction 1 of 3 to 0.250... 016: dt: 0.5000, sse=5173472.0, rms=2.378 (0.000%) 017: dt: 0.2500, sse=4116861.2, rms=1.673 (0.000%) 018: dt: 0.2500, sse=3906137.0, rms=1.519 (0.000%) rms = 1.50, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=3822085.5, rms=1.495 (0.000%) rms = 1.46, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=3772539.2, rms=1.463 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 1 with 1 points - only 0.00% unknown deleting segment 2 with 285 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 3 points - only 0.00% unknown deleting segment 4 with 19 points - only 0.00% unknown deleting segment 5 with 6 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 8 with 7 points - only 42.86% unknown mean border=86.6, 142 (46) missing vertices, mean dist -0.2 [0.4 (%66.7)->0.2 (%33.3))] %72 local maxima, %23 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=r440-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.05-->5.39) (max @ vno 126284 --> 126353) face area 0.34 +- 0.16 (0.00-->4.18) mean absolute distance = 0.30 +- 0.43 3297 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3982371.8, rms=3.41 021: dt: 0.5000, sse=4280970.0, rms=2.194 (0.000%) rms = 2.23, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=4051164.5, rms=1.727 (0.000%) 023: dt: 0.2500, sse=3987983.5, rms=1.415 (0.000%) 024: dt: 0.2500, sse=3928357.8, rms=1.344 (0.000%) rms = 1.34, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=3895001.2, rms=1.336 (0.000%) rms = 1.32, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=3865671.2, rms=1.317 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 1 with 296 points - only 0.00% unknown deleting segment 2 with 11 points - only 0.00% unknown deleting segment 3 with 35 points - only 0.00% unknown removing 4 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 5 with 4 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 7 with 1 points - only 0.00% unknown mean border=87.7, 129 (22) missing vertices, mean dist -0.1 [0.3 (%57.9)->0.2 (%42.1))] %79 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=r440-, 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 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=3891996.8, rms=1.89 027: dt: 0.5000, sse=4863459.0, rms=1.531 (0.000%) rms = 1.93, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=4419926.0, rms=1.166 (0.000%) 029: dt: 0.2500, sse=4226181.5, rms=1.089 (0.000%) rms = 1.05, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=4284310.0, rms=1.053 (0.000%) rms = 1.05, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=4269626.0, rms=1.047 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group smoothing surface for 5 iterations... mean border=60.8, 171 (171) missing vertices, mean dist 1.7 [0.1 (%0.0)->2.2 (%100.0))] %31 local maxima, %43 large gradients and %20 min vals, 1018 gradients ignored tol=1.0e-04, sigma=2.0, host=r440-, 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=20586552.0, rms=27.44 001: dt: 0.5000, sse=16345519.0, rms=24.014 (0.000%) 002: dt: 0.5000, sse=13078539.0, rms=21.016 (0.000%) 003: dt: 0.5000, sse=10791890.0, rms=18.454 (0.000%) 004: dt: 0.5000, sse=9320913.0, rms=16.222 (0.000%) 005: dt: 0.5000, sse=8256407.0, rms=14.264 (0.000%) 006: dt: 0.5000, sse=7461048.0, rms=12.554 (0.000%) 007: dt: 0.5000, sse=6881988.5, rms=11.015 (0.000%) 008: dt: 0.5000, sse=6551747.5, rms=9.611 (0.000%) 009: dt: 0.5000, sse=6282677.0, rms=8.302 (0.000%) 010: dt: 0.5000, sse=6146468.5, rms=7.147 (0.000%) 011: dt: 0.5000, sse=6115288.5, rms=6.211 (0.000%) 012: dt: 0.5000, sse=6185715.0, rms=5.524 (0.000%) 013: dt: 0.5000, sse=6194826.5, rms=5.069 (0.000%) 014: dt: 0.5000, sse=6271710.5, rms=4.786 (0.000%) 015: dt: 0.5000, sse=6280744.0, rms=4.605 (0.000%) 016: dt: 0.5000, sse=6323038.5, rms=4.477 (0.000%) 017: dt: 0.5000, sse=6322941.5, rms=4.394 (0.000%) 018: dt: 0.5000, sse=6372113.0, rms=4.329 (0.000%) rms = 4.29, time step reduction 1 of 3 to 0.250... 019: dt: 0.5000, sse=6354897.5, rms=4.294 (0.000%) 020: dt: 0.2500, sse=4272575.0, rms=3.350 (0.000%) 021: dt: 0.2500, sse=4049591.5, rms=3.080 (0.000%) rms = 3.04, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=3921079.5, rms=3.043 (0.000%) 023: dt: 0.1250, sse=3673075.0, rms=2.807 (0.000%) rms = 2.78, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=3644352.5, rms=2.775 (0.000%) positioning took 1.6 minutes mean border=57.6, 786 (45) missing vertices, mean dist 0.2 [0.2 (%39.2)->0.5 (%60.8))] %46 local maxima, %34 large gradients and %15 min vals, 408 gradients ignored tol=1.0e-04, sigma=1.0, host=r440-, 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=4447808.5, rms=5.72 025: dt: 0.5000, sse=4536351.5, rms=4.473 (0.000%) 026: dt: 0.5000, sse=5801690.0, rms=4.389 (0.000%) rms = 4.36, time step reduction 1 of 3 to 0.250... 027: dt: 0.5000, sse=5630241.5, rms=4.357 (0.000%) 028: dt: 0.2500, sse=4461076.0, rms=3.197 (0.000%) 029: dt: 0.2500, sse=4357673.0, rms=2.884 (0.000%) rms = 2.88, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=4253713.5, rms=2.878 (0.000%) 031: dt: 0.1250, sse=4032736.8, rms=2.584 (0.000%) rms = 2.54, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=3999437.8, rms=2.541 (0.000%) positioning took 0.5 minutes mean border=55.6, 988 (31) missing vertices, mean dist 0.1 [0.2 (%37.8)->0.4 (%62.2))] %55 local maxima, %25 large gradients and %15 min vals, 381 gradients ignored tol=1.0e-04, sigma=0.5, host=r440-, 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=4201597.0, rms=3.76 rms = 4.06, time step reduction 1 of 3 to 0.250... 033: dt: 0.2500, sse=4029882.2, rms=3.140 (0.000%) 034: dt: 0.2500, sse=4006512.8, rms=2.731 (0.000%) 035: dt: 0.2500, sse=4129016.2, rms=2.621 (0.000%) rms = 2.62, time step reduction 2 of 3 to 0.125... 036: dt: 0.2500, sse=4192613.8, rms=2.617 (0.000%) 037: dt: 0.1250, sse=4034442.0, rms=2.448 (0.000%) rms = 2.41, time step reduction 3 of 3 to 0.062... 038: dt: 0.1250, sse=4032799.5, rms=2.415 (0.000%) positioning took 0.4 minutes mean border=54.7, 1903 (29) missing vertices, mean dist 0.1 [0.2 (%43.5)->0.3 (%56.5))] %59 local maxima, %20 large gradients and %14 min vals, 340 gradients ignored tol=1.0e-04, sigma=0.2, host=r440-, 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=4073710.5, rms=2.77 rms = 3.41, time step reduction 1 of 3 to 0.250... 039: dt: 0.2500, sse=3984913.5, rms=2.486 (0.000%) 040: dt: 0.2500, sse=4086851.2, rms=2.382 (0.000%) rms = 2.37, time step reduction 2 of 3 to 0.125... 041: dt: 0.2500, sse=4145841.8, rms=2.365 (0.000%) 042: dt: 0.1250, sse=4069846.8, rms=2.268 (0.000%) rms = 2.25, time step reduction 3 of 3 to 0.062... 043: dt: 0.1250, sse=4070157.2, rms=2.252 (0.000%) positioning took 0.4 minutes writing curvature file /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.area.pial vertex spacing 0.99 +- 0.40 (0.05-->9.03) (max @ vno 126387 --> 126385) face area 0.39 +- 0.28 (0.00-->11.16) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 126893 vertices processed 25000 of 126893 vertices processed 50000 of 126893 vertices processed 75000 of 126893 vertices processed 100000 of 126893 vertices processed 125000 of 126893 vertices processed 0 of 126893 vertices processed 25000 of 126893 vertices processed 50000 of 126893 vertices processed 75000 of 126893 vertices processed 100000 of 126893 vertices processed 125000 of 126893 vertices processed thickness calculation complete, 235:547 truncations. 35127 vertices at 0 distance 89831 vertices at 1 distance 74098 vertices at 2 distance 29142 vertices at 3 distance 8835 vertices at 4 distance 2743 vertices at 5 distance 914 vertices at 6 distance 320 vertices at 7 distance 154 vertices at 8 distance 90 vertices at 9 distance 48 vertices at 10 distance 32 vertices at 11 distance 19 vertices at 12 distance 8 vertices at 13 distance 5 vertices at 14 distance 10 vertices at 15 distance 13 vertices at 16 distance 11 vertices at 17 distance 15 vertices at 18 distance 11 vertices at 19 distance 16 vertices at 20 distance writing curvature file /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.thickness positioning took 6.8 minutes #-------------------------------------------- #@# Surf Volume lh Mon Nov 17 17:51:26 EST 2025 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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_calc -o lh.volume lh.area.mid mul lh.thickness Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# WM/GM Contrast lh Mon Nov 17 17:51:27 EST 2025 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/scripts pctsurfcon --s PBRHOPE_HOPE086_PETMR --lh-only Log file is /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/scripts/pctsurfcon.log Mon Nov 17 17:51:27 EST 2025 setenv SUBJECTS_DIR /autofs/space/hope_002/users/PBR28_HOPE/data/fs cd /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/scripts /usr/local/freesurfer/stable5_3_0/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux r440-30.nmr.mgh.harvard.edu 4.18.0-553.79.1.el8_10.x86_64 #1 SMP Wed Oct 15 12:48:32 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 mri_vol2surf --mov /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/tmp.pctsurfcon.2466359/lh.wm.mgh --regheader PBRHOPE_HOPE086_PETMR --cortex srcvol = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 INFO: changing type to float Done loading volume Computing registration from header. Using /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/orig.mgz as target reference. Loading label /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/label/lh.cortex.label Reading surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 = 68204 Masking with /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/label/lh.cortex.label Writing to /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/tmp.pctsurfcon.2466359/lh.wm.mgh Dim: 126893 1 1 mri_vol2surf --mov /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/tmp.pctsurfcon.2466359/lh.gm.mgh --projfrac 0.3 --regheader PBRHOPE_HOPE086_PETMR --cortex srcvol = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 INFO: changing type to float Done loading volume Computing registration from header. Using /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/orig.mgz as target reference. Loading label /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/label/lh.cortex.label Reading surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.white Done reading source surface Reading thickness /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 = 82079 Masking with /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/label/lh.cortex.label Writing to /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/tmp.pctsurfcon.2466359/lh.gm.mgh Dim: 126893 1 1 mri_concat /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/tmp.pctsurfcon.2466359/lh.wm.mgh /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/tmp.pctsurfcon.2466359/lh.gm.mgh --paired-diff-norm --mul 100 --o /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.w-g.pct.mgh mri_segstats --in /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.w-g.pct.mgh --annot PBRHOPE_HOPE086_PETMR lh aparc --sum /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/stats/lh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --in /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.w-g.pct.mgh --annot PBRHOPE_HOPE086_PETMR lh aparc --sum /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/stats/lh.w-g.pct.stats --snr sysname Linux hostname r440-30.nmr.mgh.harvard.edu machine x86_64 user ek657 UseRobust 0 Constructing seg from annotation Reading annotation reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Seg base 1000 Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.w-g.pct.mgh Vertex Area is 0.652206 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 1000 unknown 0 0.000 1 1001 bankssts 1383 955.973 2 1002 caudalanteriorcingulate 1012 682.050 3 1003 caudalmiddlefrontal 3499 2333.429 4 1004 corpuscallosum 0 0.000 5 1005 cuneus 2160 1176.370 6 1006 entorhinal 375 245.025 7 1007 fusiform 5027 3378.061 8 1008 inferiorparietal 6315 4170.676 9 1009 inferiortemporal 4036 2707.778 10 1010 isthmuscingulate 1626 1009.366 11 1011 lateraloccipital 6893 4349.547 12 1012 lateralorbitofrontal 3597 2367.792 13 1013 lingual 4020 2511.073 14 1014 medialorbitofrontal 2576 1673.433 15 1015 middletemporal 3853 2598.232 16 1016 parahippocampal 1205 788.017 17 1017 paracentral 1989 1246.887 18 1018 parsopercularis 1884 1254.318 19 1019 parsorbitalis 716 484.448 20 1020 parstriangularis 1416 987.086 21 1021 pericalcarine 1566 1046.956 22 1022 postcentral 6567 4072.481 23 1023 posteriorcingulate 2041 1327.055 24 1024 precentral 8065 4867.042 25 1025 precuneus 5527 3704.357 26 1026 rostralanteriorcingulate 1098 744.270 27 1027 rostralmiddlefrontal 8086 5456.408 28 1028 superiorfrontal 9016 6181.396 29 1029 superiorparietal 7521 4815.389 30 1030 superiortemporal 4715 3122.580 31 1031 supramarginal 5875 3877.844 32 1032 frontalpole 217 142.473 33 1033 temporalpole 501 368.917 34 1034 transversetemporal 763 426.984 35 1035 insula 3461 2258.036 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats lh Mon Nov 17 17:51:33 EST 2025 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/scripts mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab PBRHOPE_HOPE086_PETMR lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/wm.mgz... reading input surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.white... reading input pial surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.pial... reading input white surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/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 1383 956 2479 2.308 0.612 0.108 0.041 12 1.6 bankssts 1012 682 1932 2.725 0.570 0.193 0.077 34 3.1 caudalanteriorcingulate 3499 2333 5754 2.228 0.548 0.145 0.060 48 8.5 caudalmiddlefrontal 2160 1176 2380 1.845 0.423 0.160 0.089 54 8.3 cuneus 375 245 1350 3.859 0.858 0.112 0.033 2 0.5 entorhinal 5027 3378 9907 2.522 0.617 0.155 0.062 93 12.7 fusiform 6315 4171 10010 2.180 0.527 0.130 0.052 105 10.1 inferiorparietal 4036 2708 8789 2.858 0.669 0.153 0.062 69 10.8 inferiortemporal 1626 1009 2167 2.079 0.671 0.164 0.116 99 5.0 isthmuscingulate 6893 4350 9535 2.001 0.513 0.150 0.055 166 15.7 lateraloccipital 3597 2368 5912 2.375 0.634 0.163 0.075 62 11.3 lateralorbitofrontal 4020 2511 5311 1.976 0.623 0.160 0.072 76 12.5 lingual 2576 1673 4335 2.212 0.758 0.157 0.080 58 8.6 medialorbitofrontal 3853 2598 9408 2.897 0.734 0.155 0.088 123 10.0 middletemporal 1205 788 2019 2.240 0.621 0.109 0.039 10 2.1 parahippocampal 1989 1247 2914 2.147 0.441 0.144 0.126 123 8.7 paracentral 1884 1254 3341 2.361 0.548 0.148 0.056 28 4.6 parsopercularis 716 484 1726 2.719 0.722 0.187 0.077 15 2.4 parsorbitalis 1416 987 2368 2.249 0.594 0.146 0.052 20 3.1 parstriangularis 1566 1047 1348 1.378 0.322 0.157 0.072 25 4.6 pericalcarine 6567 4072 8442 1.851 0.543 0.133 0.063 133 15.8 postcentral 2041 1327 3214 2.192 0.566 0.165 0.064 39 5.3 posteriorcingulate 8065 4867 12718 2.388 0.571 0.134 0.068 145 22.9 precentral 5527 3704 8776 2.165 0.547 0.153 0.062 106 14.2 precuneus 1098 744 2293 2.691 0.741 0.179 0.080 27 4.0 rostralanteriorcingulate 8086 5456 13183 2.093 0.541 0.162 0.087 155 21.8 rostralmiddlefrontal 9016 6181 17100 2.423 0.561 0.162 0.119 540 35.4 superiorfrontal 7521 4815 10563 1.987 0.481 0.132 0.048 104 16.1 superiorparietal 4715 3123 8609 2.540 0.600 0.136 0.050 65 10.1 superiortemporal 5875 3878 10083 2.307 0.617 0.143 0.054 107 11.8 supramarginal 217 142 579 2.752 0.601 0.228 0.108 9 1.0 frontalpole 501 369 2347 3.959 0.678 0.169 0.061 10 1.3 temporalpole 763 427 1063 2.276 0.432 0.129 0.056 9 1.7 transversetemporal 3461 2258 6215 2.683 0.859 0.132 0.086 93 12.8 insula #----------------------------------------- #@# Cortical Parc 2 lh Mon Nov 17 17:51:43 EST 2025 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 PBRHOPE_HOPE086_PETMR lh ../surf/lh.sphere.reg /usr/local/freesurfer/stable5_3_0/average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/stable5_3_0/average/lh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 3.9 0.2 using min determinant for regularization = 0.000 0 singular and 1066 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 105 labels changed using aseg relabeling using gibbs priors... 000: 8871 changed, 126893 examined... 001: 2192 changed, 34003 examined... 002: 689 changed, 11181 examined... 003: 310 changed, 3856 examined... 004: 129 changed, 1719 examined... 005: 64 changed, 739 examined... 006: 29 changed, 372 examined... 007: 17 changed, 181 examined... 008: 5 changed, 101 examined... 009: 4 changed, 31 examined... 010: 1 changed, 22 examined... 011: 0 changed, 7 examined... 25 labels changed using aseg 000: 274 total segments, 192 labels (1837 vertices) changed 001: 97 total segments, 16 labels (150 vertices) changed 002: 81 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 128 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 828 vertices marked for relabeling... 828 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 45 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Mon Nov 17 17:52:29 EST 2025 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/scripts mris_anatomical_stats -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 PBRHOPE_HOPE086_PETMR lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/wm.mgz... reading input surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.white... reading input pial surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.pial... reading input white surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.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 1232 815 1978 2.094 0.646 0.186 0.088 32 4.2 G_and_S_frontomargin 2016 1297 2785 1.987 0.475 0.147 0.056 92 5.3 G_and_S_occipital_inf 1505 864 2336 2.285 0.490 0.147 0.126 44 5.6 G_and_S_paracentral 1317 861 2422 2.333 0.482 0.155 0.076 23 4.5 G_and_S_subcentral 589 395 1406 2.773 0.525 0.196 0.083 17 2.1 G_and_S_transv_frontopol 1853 1300 3546 2.430 0.641 0.150 0.054 28 4.5 G_and_S_cingul-Ant 1162 830 1998 2.266 0.530 0.167 0.067 29 3.1 G_and_S_cingul-Mid-Ant 1275 872 2102 2.251 0.499 0.155 0.059 20 2.9 G_and_S_cingul-Mid-Post 603 389 1097 2.377 0.458 0.202 0.099 18 2.5 G_cingul-Post-dorsal 427 253 571 2.246 0.777 0.179 0.224 71 1.8 G_cingul-Post-ventral 1966 1052 2308 1.825 0.443 0.159 0.097 53 8.4 G_cuneus 1207 787 2464 2.455 0.506 0.162 0.068 23 3.6 G_front_inf-Opercular 246 177 566 2.503 0.779 0.185 0.069 5 0.7 G_front_inf-Orbital 850 593 1783 2.339 0.532 0.171 0.070 17 2.7 G_front_inf-Triangul 4462 2981 8759 2.312 0.513 0.173 0.116 101 14.5 G_front_middle 6239 4189 13068 2.511 0.556 0.187 0.183 633 36.9 G_front_sup 586 357 1194 2.882 0.863 0.176 0.255 62 6.4 G_Ins_lg_and_S_cent_ins 710 441 1916 3.235 0.830 0.159 0.086 15 2.5 G_insular_short 2076 1323 3873 2.326 0.463 0.164 0.058 42 4.9 G_occipital_middle 1540 873 1962 1.981 0.499 0.145 0.063 27 4.5 G_occipital_sup 2277 1477 4754 2.604 0.526 0.167 0.068 50 6.1 G_oc-temp_lat-fusifor 2677 1600 3729 1.949 0.674 0.171 0.090 63 10.2 G_oc-temp_med-Lingual 1154 710 2582 2.760 0.910 0.111 0.038 10 1.9 G_oc-temp_med-Parahip 2368 1537 4932 2.507 0.686 0.182 0.099 56 9.8 G_orbital 2226 1418 3984 2.268 0.614 0.145 0.058 81 4.4 G_pariet_inf-Angular 3183 2113 6331 2.449 0.616 0.156 0.065 59 7.6 G_pariet_inf-Supramar 2920 1797 4773 2.137 0.488 0.138 0.059 56 7.7 G_parietal_sup 2760 1546 3580 1.882 0.505 0.141 0.086 95 8.6 G_postcentral 3123 1641 5611 2.642 0.586 0.139 0.076 66 10.8 G_precentral 3428 2246 6059 2.203 0.552 0.168 0.080 86 11.1 G_precuneus 951 608 1942 2.328 0.683 0.176 0.121 35 5.0 G_rectus 386 235 585 2.460 0.743 0.164 0.086 7 1.3 G_subcallosal 583 305 831 2.177 0.437 0.128 0.063 7 1.6 G_temp_sup-G_T_transv 1870 1206 4135 2.604 0.608 0.158 0.072 41 6.0 G_temp_sup-Lateral 354 239 866 3.185 0.638 0.117 0.045 2 0.7 G_temp_sup-Plan_polar 976 650 1742 2.506 0.526 0.122 0.039 10 1.3 G_temp_sup-Plan_tempo 2329 1548 6093 2.912 0.682 0.168 0.078 53 8.0 G_temporal_inf 2553 1664 6708 3.050 0.703 0.162 0.115 107 8.1 G_temporal_middle 209 140 262 1.880 0.513 0.119 0.038 2 0.3 Lat_Fis-ant-Horizont 173 126 240 1.886 0.485 0.114 0.025 1 0.2 Lat_Fis-ant-Vertical 1504 1012 1886 2.116 0.511 0.128 0.039 12 2.6 Lat_Fis-post 2129 1290 2604 1.874 0.535 0.157 0.063 34 5.7 Pole_occipital 1457 1052 5445 3.545 0.775 0.165 0.071 32 4.1 Pole_temporal 2004 1365 2154 1.716 0.613 0.148 0.057 29 4.5 S_calcarine 2929 1961 3217 1.849 0.639 0.125 0.038 22 4.9 S_central 1316 899 1743 2.074 0.521 0.112 0.026 8 1.5 S_cingul-Marginalis 436 302 711 2.498 0.691 0.126 0.041 3 0.8 S_circular_insula_ant 1345 935 2068 2.588 0.779 0.100 0.023 7 1.3 S_circular_insula_inf 1791 1225 2373 2.234 0.464 0.103 0.025 9 1.9 S_circular_insula_sup 682 480 1314 2.689 0.397 0.133 0.042 9 1.1 S_collat_transv_ant 330 206 350 1.739 0.485 0.147 0.059 5 0.8 S_collat_transv_post 1759 1206 2465 2.028 0.505 0.138 0.048 19 3.5 S_front_inf 1862 1270 2277 1.801 0.443 0.133 0.043 19 3.3 S_front_middle 2641 1828 3647 2.073 0.424 0.127 0.042 24 4.6 S_front_sup 448 292 433 1.694 0.510 0.116 0.180 7 0.8 S_interm_prim-Jensen 2772 1902 3914 1.986 0.462 0.133 0.038 28 4.5 S_intrapariet_and_P_trans 654 464 729 1.707 0.484 0.136 0.037 6 0.9 S_oc_middle_and_Lunatus 1120 763 1271 1.770 0.405 0.130 0.034 10 1.6 S_oc_sup_and_transversal 727 498 937 2.152 0.377 0.126 0.033 6 0.9 S_occipital_ant 835 574 1212 2.419 0.552 0.121 0.033 6 1.2 S_oc-temp_lat 2212 1556 3033 2.196 0.507 0.135 0.043 23 4.0 S_oc-temp_med_and_Lingual 375 253 594 2.273 0.790 0.152 0.044 5 0.8 S_orbital_lateral 850 573 1047 2.037 0.568 0.138 0.051 11 2.0 S_orbital_med-olfact 1125 760 1815 2.537 0.647 0.155 0.059 14 2.6 S_orbital-H_Shaped 1401 911 1627 2.085 0.505 0.126 0.035 13 2.1 S_parieto_occipital 1402 803 1338 2.064 0.919 0.157 0.064 33 3.1 S_pericallosal 3188 2114 3731 1.888 0.431 0.116 0.030 23 4.0 S_postcentral 1954 1327 2893 2.238 0.442 0.126 0.041 18 3.3 S_precentral-inf-part 1422 915 1735 2.093 0.507 0.125 0.043 12 2.5 S_precentral-sup-part 632 411 927 2.233 0.928 0.165 0.066 12 1.5 S_suborbital 809 558 1167 2.034 0.403 0.146 0.047 11 1.6 S_subparietal 1139 779 2063 2.839 0.725 0.141 0.044 14 2.0 S_temporal_inf 4752 3227 7268 2.280 0.532 0.114 0.034 40 5.7 S_temporal_sup 238 163 303 2.303 0.418 0.127 0.031 2 0.3 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Mon Nov 17 17:52:41 EST 2025 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 PBRHOPE_HOPE086_PETMR lh ../surf/lh.sphere.reg /usr/local/freesurfer/stable5_3_0/average/lh.DKTatlas40.gcs ../label/lh.aparc.DKTatlas40.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/stable5_3_0/average/lh.DKTatlas40.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.007 0 singular and 293 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1253 labels changed using aseg relabeling using gibbs priors... 000: 2657 changed, 126893 examined... 001: 665 changed, 11123 examined... 002: 164 changed, 3571 examined... 003: 59 changed, 928 examined... 004: 23 changed, 337 examined... 005: 5 changed, 137 examined... 006: 1 changed, 33 examined... 007: 1 changed, 6 examined... 008: 0 changed, 8 examined... 146 labels changed using aseg 000: 58 total segments, 25 labels (219 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 48 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 631 vertices marked for relabeling... 631 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas40.annot... classification took 0 minutes and 40 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Mon Nov 17 17:53:21 EST 2025 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/scripts mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab PBRHOPE_HOPE086_PETMR lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot. reading volume /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/wm.mgz... reading input surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.white... reading input pial surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.pial... reading input white surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /Applications/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas40.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 1446 989 2471 2.532 0.620 0.170 0.063 37 3.6 caudalanteriorcingulate 3619 2406 5895 2.225 0.539 0.146 0.061 51 9.0 caudalmiddlefrontal 2695 1510 2997 1.854 0.440 0.152 0.078 60 9.1 cuneus 399 256 1332 3.704 0.862 0.118 0.038 3 0.7 entorhinal 4602 3092 8430 2.452 0.551 0.152 0.057 80 10.5 fusiform 5852 3862 9094 2.148 0.532 0.131 0.053 99 9.5 inferiorparietal 4022 2709 9387 2.906 0.698 0.156 0.068 76 11.7 inferiortemporal 1618 1011 2181 2.088 0.678 0.164 0.116 99 5.1 isthmuscingulate 7240 4542 9861 1.992 0.514 0.149 0.057 172 17.5 lateraloccipital 3851 2522 6525 2.369 0.669 0.171 0.086 78 13.5 lateralorbitofrontal 4010 2506 5302 1.975 0.623 0.160 0.072 76 12.5 lingual 2341 1525 3977 2.177 0.748 0.157 0.082 54 8.1 medialorbitofrontal 5161 3493 12178 2.835 0.716 0.147 0.077 140 12.2 middletemporal 1212 793 2020 2.233 0.616 0.107 0.038 10 2.1 parahippocampal 2324 1457 3413 2.146 0.453 0.145 0.117 127 9.6 paracentral 1829 1204 3172 2.368 0.527 0.149 0.057 27 4.5 parsopercularis 821 574 1536 2.268 0.739 0.157 0.058 12 2.2 parsorbitalis 1683 1155 2801 2.254 0.584 0.149 0.055 25 3.9 parstriangularis 1580 1049 1357 1.393 0.345 0.157 0.074 26 4.7 pericalcarine 7231 4531 9376 1.864 0.544 0.132 0.061 139 16.9 postcentral 2147 1397 3329 2.199 0.557 0.164 0.063 40 5.5 posteriorcingulate 7967 4817 12596 2.396 0.571 0.133 0.065 132 21.0 precentral 5444 3647 8767 2.166 0.545 0.155 0.063 106 14.1 precuneus 1372 924 2823 2.688 0.749 0.175 0.076 31 4.6 rostralanteriorcingulate 5539 3745 9517 2.159 0.574 0.164 0.097 109 14.9 rostralmiddlefrontal 10498 7160 19554 2.366 0.573 0.164 0.115 585 41.4 superiorfrontal 6111 3939 8769 2.003 0.477 0.132 0.046 84 12.6 superiorparietal 6378 4260 12690 2.609 0.740 0.137 0.063 110 15.7 superiortemporal 6018 3963 10262 2.300 0.607 0.144 0.053 109 12.1 supramarginal 731 405 1022 2.270 0.431 0.129 0.057 8 1.7 transversetemporal 2860 1890 5537 2.771 0.842 0.123 0.058 57 7.8 insula #-------------------------------------------- #@# Tessellate rh Mon Nov 17 17:53:32 EST 2025 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 2 found - 2 modified | TOTAL: 3 pass 2 (xy-): 0 found - 2 modified | TOTAL: 3 pass 1 (yz+): 1 found - 1 modified | TOTAL: 4 pass 2 (yz+): 0 found - 1 modified | TOTAL: 4 pass 1 (yz-): 5 found - 5 modified | TOTAL: 9 pass 2 (yz-): 0 found - 5 modified | TOTAL: 9 pass 1 (xz+): 2 found - 2 modified | TOTAL: 11 pass 2 (xz+): 0 found - 2 modified | TOTAL: 11 pass 1 (xz-): 2 found - 2 modified | TOTAL: 13 pass 2 (xz-): 0 found - 2 modified | TOTAL: 13 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 (++): 3 found - 3 modified | TOTAL: 3 pass 2 (++): 0 found - 3 modified | TOTAL: 3 pass 1 (+-): 0 found - 0 modified | TOTAL: 3 pass 1 (--): 3 found - 3 modified | TOTAL: 6 pass 2 (--): 0 found - 3 modified | TOTAL: 6 pass 1 (-+): 1 found - 1 modified | TOTAL: 7 pass 2 (-+): 0 found - 1 modified | TOTAL: 7 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 = 20 (out of 260154: 0.007688) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 10: 552 vertices, 637 faces slice 20: 6731 vertices, 7021 faces slice 30: 16473 vertices, 16880 faces slice 40: 28528 vertices, 28933 faces slice 50: 40114 vertices, 40485 faces slice 60: 50639 vertices, 51015 faces slice 70: 61763 vertices, 62161 faces slice 80: 72098 vertices, 72487 faces slice 90: 82647 vertices, 83027 faces slice 100: 92066 vertices, 92446 faces slice 110: 101231 vertices, 101587 faces slice 120: 109850 vertices, 110167 faces slice 130: 117130 vertices, 117377 faces slice 140: 122850 vertices, 123085 faces slice 150: 127066 vertices, 127221 faces slice 160: 127930 vertices, 127988 faces slice 170: 127930 vertices, 127988 faces slice 180: 127930 vertices, 127988 faces slice 190: 127930 vertices, 127988 faces slice 200: 127930 vertices, 127988 faces slice 210: 127930 vertices, 127988 faces slice 220: 127930 vertices, 127988 faces slice 230: 127930 vertices, 127988 faces slice 240: 127930 vertices, 127988 faces slice 250: 127930 vertices, 127988 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 127922 voxel in cpt #1: X=-60 [v=127922,e=383946,f=255964] located at (31.663115, -54.518677, 25.065735) 8 voxel in cpt #2: X=2 [v=8,e=18,f=12] located at (8.000000, -69.000000, 15.000000) For the whole surface: X=-58 [v=127930,e=383964,f=255976] 2 components have been found keeping component #1 with 127922 vertices done #-------------------------------------------- #@# Smooth1 rh Mon Nov 17 17:53:37 EST 2025 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 rh Mon Nov 17 17:53:40 EST 2025 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/scripts avg radius = 46.3 mm, total surface area = 67140 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.3 minutes Not saving sulc step 000: RMS=0.103 (target=0.015) step 005: RMS=0.077 (target=0.015) step 010: RMS=0.059 (target=0.015) step 015: RMS=0.050 (target=0.015) step 020: RMS=0.044 (target=0.015) step 025: RMS=0.040 (target=0.015) step 030: RMS=0.036 (target=0.015) step 035: RMS=0.033 (target=0.015) step 040: RMS=0.031 (target=0.015) step 045: RMS=0.030 (target=0.015) step 050: RMS=0.030 (target=0.015) step 055: RMS=0.030 (target=0.015) step 060: RMS=0.029 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere rh Mon Nov 17 17:54:01 EST 2025 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.01 +- 0.58 (0.00-->7.38) (max @ vno 101831 --> 101862) face area 0.03 +- 0.04 (-0.08-->1.00) scaling brain by 0.349... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=174.540, avgs=0 005/300: dt: 0.9000, rms radial error=174.287, avgs=0 010/300: dt: 0.9000, rms radial error=173.744, avgs=0 015/300: dt: 0.9000, rms radial error=173.030, avgs=0 020/300: dt: 0.9000, rms radial error=172.213, avgs=0 025/300: dt: 0.9000, rms radial error=171.338, avgs=0 030/300: dt: 0.9000, rms radial error=170.429, avgs=0 035/300: dt: 0.9000, rms radial error=169.502, avgs=0 040/300: dt: 0.9000, rms radial error=168.566, avgs=0 045/300: dt: 0.9000, rms radial error=167.627, avgs=0 050/300: dt: 0.9000, rms radial error=166.689, avgs=0 055/300: dt: 0.9000, rms radial error=165.754, avgs=0 060/300: dt: 0.9000, rms radial error=164.823, avgs=0 065/300: dt: 0.9000, rms radial error=163.896, avgs=0 070/300: dt: 0.9000, rms radial error=162.975, avgs=0 075/300: dt: 0.9000, rms radial error=162.059, avgs=0 080/300: dt: 0.9000, rms radial error=161.148, avgs=0 085/300: dt: 0.9000, rms radial error=160.242, avgs=0 090/300: dt: 0.9000, rms radial error=159.342, avgs=0 095/300: dt: 0.9000, rms radial error=158.446, avgs=0 100/300: dt: 0.9000, rms radial error=157.555, avgs=0 105/300: dt: 0.9000, rms radial error=156.670, avgs=0 110/300: dt: 0.9000, rms radial error=155.790, avgs=0 115/300: dt: 0.9000, rms radial error=154.915, avgs=0 120/300: dt: 0.9000, rms radial error=154.045, avgs=0 125/300: dt: 0.9000, rms radial error=153.181, avgs=0 130/300: dt: 0.9000, rms radial error=152.322, avgs=0 135/300: dt: 0.9000, rms radial error=151.470, avgs=0 140/300: dt: 0.9000, rms radial error=150.623, avgs=0 145/300: dt: 0.9000, rms radial error=149.780, avgs=0 150/300: dt: 0.9000, rms radial error=148.942, avgs=0 155/300: dt: 0.9000, rms radial error=148.109, avgs=0 160/300: dt: 0.9000, rms radial error=147.280, avgs=0 165/300: dt: 0.9000, rms radial error=146.456, avgs=0 170/300: dt: 0.9000, rms radial error=145.636, avgs=0 175/300: dt: 0.9000, rms radial error=144.820, avgs=0 180/300: dt: 0.9000, rms radial error=144.009, avgs=0 185/300: dt: 0.9000, rms radial error=143.203, avgs=0 190/300: dt: 0.9000, rms radial error=142.401, avgs=0 195/300: dt: 0.9000, rms radial error=141.603, avgs=0 200/300: dt: 0.9000, rms radial error=140.810, avgs=0 205/300: dt: 0.9000, rms radial error=140.021, avgs=0 210/300: dt: 0.9000, rms radial error=139.236, avgs=0 215/300: dt: 0.9000, rms radial error=138.457, avgs=0 220/300: dt: 0.9000, rms radial error=137.682, avgs=0 225/300: dt: 0.9000, rms radial error=136.911, avgs=0 230/300: dt: 0.9000, rms radial error=136.144, avgs=0 235/300: dt: 0.9000, rms radial error=135.382, avgs=0 240/300: dt: 0.9000, rms radial error=134.623, avgs=0 245/300: dt: 0.9000, rms radial error=133.869, avgs=0 250/300: dt: 0.9000, rms radial error=133.119, avgs=0 255/300: dt: 0.9000, rms radial error=132.373, avgs=0 260/300: dt: 0.9000, rms radial error=131.631, avgs=0 265/300: dt: 0.9000, rms radial error=130.893, avgs=0 270/300: dt: 0.9000, rms radial error=130.159, avgs=0 275/300: dt: 0.9000, rms radial error=129.429, avgs=0 280/300: dt: 0.9000, rms radial error=128.703, avgs=0 285/300: dt: 0.9000, rms radial error=127.982, avgs=0 290/300: dt: 0.9000, rms radial error=127.264, avgs=0 295/300: dt: 0.9000, rms radial error=126.550, avgs=0 300/300: dt: 0.9000, rms radial error=125.840, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 14381.90 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00014 epoch 2 (K=40.0), pass 1, starting sse = 2237.57 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00024 epoch 3 (K=160.0), pass 1, starting sse = 210.27 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.11/11 = 0.01017 epoch 4 (K=640.0), pass 1, starting sse = 12.55 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.15/17 = 0.00899 final writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.05 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology rh Mon Nov 17 17:56:46 EST 2025 cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 PBRHOPE_HOPE086_PETMR 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 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ before topology correction, eno=-60 (nv=127922, nf=255964, ne=383946, g=31) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 11 iterations marking ambiguous vertices... 3881 ambiguous faces found in tessellation segmenting defects... 51 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 50 into 47 50 defects to be corrected 0 vertices coincident reading input surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.5313 (-4.7656) -vertex loglikelihood: -6.2147 (-3.1074) -normal dot loglikelihood: -3.6123 (-3.6123) -quad curv loglikelihood: -6.1991 (-3.0996) Total Loglikelihood : -25.5574 CORRECTING DEFECT 0 (vertices=145, convex hull=107) After retessellation of defect 0, euler #=-48 (125487,375348,249813) : difference with theory (-47) = 1 CORRECTING DEFECT 1 (vertices=289, convex hull=212) After retessellation of defect 1, euler #=-47 (125611,375818,250160) : difference with theory (-46) = 1 CORRECTING DEFECT 2 (vertices=48, convex hull=58) After retessellation of defect 2, euler #=-46 (125623,375874,250205) : difference with theory (-45) = 1 CORRECTING DEFECT 3 (vertices=24, convex hull=58) After retessellation of defect 3, euler #=-45 (125639,375943,250259) : difference with theory (-44) = 1 CORRECTING DEFECT 4 (vertices=7, convex hull=19) After retessellation of defect 4, euler #=-44 (125641,375952,250267) : difference with theory (-43) = 1 CORRECTING DEFECT 5 (vertices=65, convex hull=72) After retessellation of defect 5, euler #=-43 (125659,376043,250341) : difference with theory (-42) = 1 CORRECTING DEFECT 6 (vertices=7, convex hull=20) After retessellation of defect 6, euler #=-42 (125660,376049,250347) : difference with theory (-41) = 1 CORRECTING DEFECT 7 (vertices=5, convex hull=24) After retessellation of defect 7, euler #=-41 (125661,376058,250356) : difference with theory (-40) = 1 CORRECTING DEFECT 8 (vertices=25, convex hull=61) After retessellation of defect 8, euler #=-40 (125675,376122,250407) : difference with theory (-39) = 1 CORRECTING DEFECT 9 (vertices=9, convex hull=16) After retessellation of defect 9, euler #=-39 (125677,376130,250414) : difference with theory (-38) = 1 CORRECTING DEFECT 10 (vertices=6, convex hull=24) After retessellation of defect 10, euler #=-38 (125678,376141,250425) : difference with theory (-37) = 1 CORRECTING DEFECT 11 (vertices=96, convex hull=111) After retessellation of defect 11, euler #=-37 (125723,376329,250569) : difference with theory (-36) = 1 CORRECTING DEFECT 12 (vertices=21, convex hull=17) Warning - incorrect dp selected!!!!(-92.629865 >= -92.629866 ) After retessellation of defect 12, euler #=-36 (125725,376339,250578) : difference with theory (-35) = 1 CORRECTING DEFECT 13 (vertices=19, convex hull=22) Warning - incorrect dp selected!!!!(-90.757672 >= -90.757681 ) After retessellation of defect 13, euler #=-35 (125727,376352,250590) : difference with theory (-34) = 1 CORRECTING DEFECT 14 (vertices=25, convex hull=41) After retessellation of defect 14, euler #=-34 (125735,376392,250623) : difference with theory (-33) = 1 CORRECTING DEFECT 15 (vertices=259, convex hull=149) After retessellation of defect 15, euler #=-33 (125752,376506,250721) : difference with theory (-32) = 1 CORRECTING DEFECT 16 (vertices=26, convex hull=21) After retessellation of defect 16, euler #=-32 (125754,376521,250735) : difference with theory (-31) = 1 CORRECTING DEFECT 17 (vertices=53, convex hull=32) After retessellation of defect 17, euler #=-31 (125760,376549,250758) : difference with theory (-30) = 1 CORRECTING DEFECT 18 (vertices=44, convex hull=78) After retessellation of defect 18, euler #=-30 (125772,376619,250817) : difference with theory (-29) = 1 CORRECTING DEFECT 19 (vertices=59, convex hull=83) After retessellation of defect 19, euler #=-29 (125802,376745,250914) : difference with theory (-28) = 1 CORRECTING DEFECT 20 (vertices=21, convex hull=59) After retessellation of defect 20, euler #=-28 (125811,376795,250956) : difference with theory (-27) = 1 CORRECTING DEFECT 21 (vertices=48, convex hull=31) After retessellation of defect 21, euler #=-27 (125818,376824,250979) : difference with theory (-26) = 1 CORRECTING DEFECT 22 (vertices=37, convex hull=70) After retessellation of defect 22, euler #=-26 (125839,376914,251049) : difference with theory (-25) = 1 CORRECTING DEFECT 23 (vertices=29, convex hull=71) After retessellation of defect 23, euler #=-25 (125854,376987,251108) : difference with theory (-24) = 1 CORRECTING DEFECT 24 (vertices=56, convex hull=39) After retessellation of defect 24, euler #=-24 (125859,377016,251133) : difference with theory (-23) = 1 CORRECTING DEFECT 25 (vertices=25, convex hull=49) After retessellation of defect 25, euler #=-23 (125869,377063,251171) : difference with theory (-22) = 1 CORRECTING DEFECT 26 (vertices=52, convex hull=72) After retessellation of defect 26, euler #=-22 (125887,377143,251234) : difference with theory (-21) = 1 CORRECTING DEFECT 27 (vertices=31, convex hull=30) After retessellation of defect 27, euler #=-21 (125893,377172,251258) : difference with theory (-20) = 1 CORRECTING DEFECT 28 (vertices=98, convex hull=29) After retessellation of defect 28, euler #=-20 (125902,377212,251290) : difference with theory (-19) = 1 CORRECTING DEFECT 29 (vertices=37, convex hull=31) After retessellation of defect 29, euler #=-19 (125908,377239,251312) : difference with theory (-18) = 1 CORRECTING DEFECT 30 (vertices=44, convex hull=35) After retessellation of defect 30, euler #=-18 (125913,377266,251335) : difference with theory (-17) = 1 CORRECTING DEFECT 31 (vertices=37, convex hull=30) After retessellation of defect 31, euler #=-17 (125917,377290,251356) : difference with theory (-16) = 1 CORRECTING DEFECT 32 (vertices=16, convex hull=32) After retessellation of defect 32, euler #=-16 (125921,377312,251375) : difference with theory (-15) = 1 CORRECTING DEFECT 33 (vertices=67, convex hull=38) After retessellation of defect 33, euler #=-15 (125927,377340,251398) : difference with theory (-14) = 1 CORRECTING DEFECT 34 (vertices=75, convex hull=86) After retessellation of defect 34, euler #=-14 (125954,377459,251491) : difference with theory (-13) = 1 CORRECTING DEFECT 35 (vertices=46, convex hull=61) After retessellation of defect 35, euler #=-13 (125958,377497,251526) : difference with theory (-12) = 1 CORRECTING DEFECT 36 (vertices=47, convex hull=92) After retessellation of defect 36, euler #=-12 (125990,377634,251632) : difference with theory (-11) = 1 CORRECTING DEFECT 37 (vertices=38, convex hull=50) After retessellation of defect 37, euler #=-11 (125999,377683,251673) : difference with theory (-10) = 1 CORRECTING DEFECT 38 (vertices=31, convex hull=51) After retessellation of defect 38, euler #=-10 (126015,377751,251726) : difference with theory (-9) = 1 CORRECTING DEFECT 39 (vertices=13, convex hull=31) After retessellation of defect 39, euler #=-9 (126016,377764,251739) : difference with theory (-8) = 1 CORRECTING DEFECT 40 (vertices=5, convex hull=26) After retessellation of defect 40, euler #=-8 (126016,377770,251746) : difference with theory (-7) = 1 CORRECTING DEFECT 41 (vertices=40, convex hull=72) After retessellation of defect 41, euler #=-7 (126034,377856,251815) : difference with theory (-6) = 1 CORRECTING DEFECT 42 (vertices=78, convex hull=76) After retessellation of defect 42, euler #=-6 (126065,377982,251911) : difference with theory (-5) = 1 CORRECTING DEFECT 43 (vertices=54, convex hull=96) After retessellation of defect 43, euler #=-5 (126081,378070,251984) : difference with theory (-4) = 1 CORRECTING DEFECT 44 (vertices=41, convex hull=80) After retessellation of defect 44, euler #=-4 (126101,378162,252057) : difference with theory (-3) = 1 CORRECTING DEFECT 45 (vertices=6, convex hull=14) After retessellation of defect 45, euler #=-3 (126102,378169,252064) : difference with theory (-2) = 1 CORRECTING DEFECT 46 (vertices=24, convex hull=55) After retessellation of defect 46, euler #=-2 (126117,378237,252118) : difference with theory (-1) = 1 CORRECTING DEFECT 47 (vertices=89, convex hull=113) After retessellation of defect 47, euler #=0 (126136,378350,252214) : difference with theory (0) = 0 CORRECTING DEFECT 48 (vertices=24, convex hull=81) After retessellation of defect 48, euler #=1 (126146,378408,252263) : difference with theory (1) = 0 CORRECTING DEFECT 49 (vertices=28, convex hull=60) After retessellation of defect 49, euler #=2 (126155,378459,252306) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.23 (0.14-->8.45) (max @ vno 52045 --> 53094) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.23 (0.14-->8.45) (max @ vno 52045 --> 53094) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 199 mutations (37.3%), 334 crossovers (62.7%), 147 vertices were eliminated building final representation... 1767 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=126155, nf=252306, ne=378459, g=0) writing corrected surface to /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 18.5 minutes 0 defective edges removing intersecting faces 000: 263 intersecting 001: 23 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 126155 - 378459 + 252306 = 2 --> 0 holes F =2V-4: 252306 = 252310-4 (0) 2E=3F: 756918 = 756918 (0) total defect index = 0 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 32 intersecting 001: 3 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Mon Nov 17 18:15:20 EST 2025 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs PBRHOPE_HOPE086_PETMR rh only generating white matter surface not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/filled.mgz... reading volume /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/brain.finalsurfs.mgz... reading volume /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/wm.mgz... 10910 bright wm thresholded. 1793 bright non-wm voxels segmented. reading original surface position from /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.orig... computing class statistics... border white: 244849 voxels (1.46%) border gray 269780 voxels (1.61%) WM (93.0): 94.1 +- 7.4 [70.0 --> 110.0] GM (83.0) : 80.3 +- 11.3 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 62.7 (was 70) setting MAX_BORDER_WHITE to 109.4 (was 105) setting MIN_BORDER_WHITE to 74.0 (was 85) setting MAX_CSF to 51.5 (was 40) setting MAX_GRAY to 94.6 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 68.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 40.2 (was 40) repositioning cortical surface to gray/white boundary reading volume /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.02-->4.17) (max @ vno 23230 --> 125526) face area 0.28 +- 0.12 (0.00-->2.52) mean absolute distance = 0.83 +- 1.14 3897 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=102, GM=74 mean inside = 93.2, mean outside = 77.5 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group mean border=83.9, 67 (67) missing vertices, mean dist 0.1 [0.9 (%41.0)->0.8 (%59.0))] %42 local maxima, %52 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=r440-, 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 0.91 +- 0.26 (0.06-->4.46) (max @ vno 23230 --> 125526) face area 0.28 +- 0.13 (0.00-->2.09) mean absolute distance = 0.47 +- 0.86 4461 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4159250.5, rms=8.88 001: dt: 0.5000, sse=4976264.5, rms=6.028 (0.000%) 002: dt: 0.5000, sse=5295711.5, rms=4.381 (0.000%) 003: dt: 0.5000, sse=5636741.0, rms=3.548 (0.000%) 004: dt: 0.5000, sse=5823491.5, rms=3.110 (0.000%) 005: dt: 0.5000, sse=5967811.0, rms=2.912 (0.000%) 006: dt: 0.5000, sse=6013644.5, rms=2.793 (0.000%) rms = 2.75, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=6046907.0, rms=2.753 (0.000%) 008: dt: 0.2500, sse=3770889.5, rms=1.936 (0.000%) 009: dt: 0.2500, sse=3511992.5, rms=1.766 (0.000%) rms = 1.73, time step reduction 2 of 3 to 0.125... 010: dt: 0.2500, sse=3411933.0, rms=1.728 (0.000%) rms = 1.70, time step reduction 3 of 3 to 0.062... 011: dt: 0.1250, sse=3357916.5, rms=1.696 (0.000%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=85.9, 40 (5) missing vertices, mean dist -0.3 [0.6 (%62.2)->0.3 (%37.8))] %52 local maxima, %42 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=r440-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.08-->4.49) (max @ vno 23230 --> 125526) face area 0.34 +- 0.16 (0.00-->2.57) mean absolute distance = 0.37 +- 0.55 3619 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3727354.2, rms=3.74 012: dt: 0.5000, sse=4084224.2, rms=2.434 (0.000%) 013: dt: 0.5000, sse=4546376.0, rms=2.263 (0.000%) 014: dt: 0.5000, sse=4781948.5, rms=2.180 (0.000%) rms = 2.35, time step reduction 1 of 3 to 0.250... 015: dt: 0.2500, sse=3997673.8, rms=1.687 (0.000%) 016: dt: 0.2500, sse=3725011.5, rms=1.470 (0.000%) rms = 1.43, time step reduction 2 of 3 to 0.125... 017: dt: 0.2500, sse=3630481.5, rms=1.430 (0.000%) rms = 1.41, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=3583509.8, rms=1.408 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=88.2, 50 (4) missing vertices, mean dist -0.2 [0.4 (%66.3)->0.2 (%33.7))] %69 local maxima, %26 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=r440-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.08-->4.44) (max @ vno 23230 --> 125526) face area 0.33 +- 0.16 (0.00-->2.46) mean absolute distance = 0.30 +- 0.43 3205 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3780060.0, rms=3.30 019: dt: 0.5000, sse=4030431.2, rms=2.067 (0.000%) rms = 2.05, time step reduction 1 of 3 to 0.250... 020: dt: 0.5000, sse=4422270.5, rms=2.054 (0.000%) 021: dt: 0.2500, sse=3876077.2, rms=1.398 (0.000%) 022: dt: 0.2500, sse=3777432.5, rms=1.307 (0.000%) rms = 1.31, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=3718805.5, rms=1.306 (0.000%) rms = 1.29, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=3686023.8, rms=1.287 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=89.3, 57 (4) missing vertices, mean dist -0.1 [0.3 (%57.8)->0.2 (%42.2))] %77 local maxima, %18 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=r440-, 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=3717342.5, rms=1.90 025: dt: 0.5000, sse=4582050.5, rms=1.460 (0.000%) rms = 1.81, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=4205335.5, rms=1.129 (0.000%) 027: dt: 0.2500, sse=4035612.5, rms=1.062 (0.000%) rms = 1.03, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=4080929.8, rms=1.025 (0.000%) rms = 1.02, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=4073693.5, rms=1.019 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group generating cortex label... 14 non-cortical segments detected only using segment with 1668 vertices erasing segment 1 (vno[0] = 91427) erasing segment 2 (vno[0] = 94942) erasing segment 3 (vno[0] = 95848) erasing segment 4 (vno[0] = 95859) erasing segment 5 (vno[0] = 95866) erasing segment 6 (vno[0] = 95906) erasing segment 7 (vno[0] = 96723) erasing segment 8 (vno[0] = 97657) erasing segment 9 (vno[0] = 98404) erasing segment 10 (vno[0] = 98461) erasing segment 11 (vno[0] = 99301) erasing segment 12 (vno[0] = 102955) erasing segment 13 (vno[0] = 103826) writing cortex label to /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/label/rh.cortex.label... writing curvature file /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.curv writing smoothed area to rh.area writing curvature file /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.area vertex spacing 0.88 +- 0.25 (0.05-->4.18) (max @ vno 23230 --> 125526) face area 0.33 +- 0.16 (0.00-->2.65) refinement took 3.2 minutes #-------------------------------------------- #@# Smooth2 rh Mon Nov 17 18:18:33 EST 2025 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 rh Mon Nov 17 18:18:36 EST 2025 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 46.4 mm, total surface area = 74671 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.115 (target=0.015) step 005: RMS=0.080 (target=0.015) step 010: RMS=0.060 (target=0.015) step 015: RMS=0.048 (target=0.015) step 020: RMS=0.040 (target=0.015) step 025: RMS=0.034 (target=0.015) step 030: RMS=0.028 (target=0.015) step 035: RMS=0.024 (target=0.015) step 040: RMS=0.020 (target=0.015) step 045: RMS=0.018 (target=0.015) step 050: RMS=0.017 (target=0.015) step 055: RMS=0.016 (target=0.015) step 060: RMS=0.015 (target=0.015) inflation complete. inflation took 0.4 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 144 vertices thresholded to be in k1 ~ [-0.22 0.31], k2 ~ [-0.10 0.07] total integrated curvature = 0.533*4pi (6.692) --> 0 handles ICI = 1.4, FI = 7.9, variation=138.890 107 vertices thresholded to be in [-0.01 0.02] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 129 vertices thresholded to be in [-0.14 0.15] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.017, std = 0.021 done. #----------------------------------------- #@# Curvature Stats rh Mon Nov 17 18:19:51 EST 2025 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm PBRHOPE_HOPE086_PETMR 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 [ PBRHOPE_HOPE086_PETMR/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 [ 239 ] Gb_filter = 0 WARN: S lookup min: -0.500594 WARN: S explicit min: 0.000000 vertex = 414 #-------------------------------------------- #@# Sphere rh Mon Nov 17 18:19:55 EST 2025 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... scaling brain by 0.329... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=r440-, 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 %19.05 pass 1: epoch 2 of 3 starting distance error %19.02 unfolding complete - removing small folds... starting distance error %18.95 removing remaining folds... final distance error %18.97 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/rh.sphere spherical transformation took 0.43 hours #-------------------------------------------- #@# Surf Reg rh Mon Nov 17 18:45:42 EST 2025 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/scripts mris_register -curv ../surf/rh.sphere /usr/local/freesurfer/stable5_3_0/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /usr/local/freesurfer/stable5_3_0/average/rh.average.curvature.filled.buckner40.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=r440-, 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=r440-, 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 = 0.584 curvature mean = 0.028, std = 0.934 curvature mean = 0.027, std = 0.865 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 0.00, -16.00) sse = 281635.1, tmin=0.6190 d=16.00 min @ (-4.00, -4.00, 4.00) sse = 234191.1, tmin=1.8574 d=8.00 min @ (2.00, 0.00, 0.00) sse = 231697.3, tmin=2.5179 d=4.00 min @ (-1.00, 0.00, 0.00) sse = 230876.1, tmin=3.1819 d=2.00 min @ (0.50, 0.00, -0.50) sse = 230624.0, tmin=3.8476 d=1.00 min @ (-0.25, 0.00, 0.25) sse = 230462.9, tmin=4.4996 d=0.50 min @ (0.00, 0.00, -0.12) sse = 230450.0, tmin=5.1430 tol=1.0e+00, sigma=0.5, host=r440-, 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 5.14 min curvature mean = -0.006, std = 0.960 curvature mean = 0.011, std = 0.944 curvature mean = -0.010, std = 0.972 curvature mean = 0.004, std = 0.976 curvature mean = -0.011, std = 0.974 curvature mean = 0.001, std = 0.990 2 Reading smoothwm curvature mean = -0.030, std = 1.187 curvature mean = 0.004, std = 0.071 curvature mean = 0.015, std = 0.091 curvature mean = 0.003, std = 0.086 curvature mean = 0.006, std = 0.140 curvature mean = 0.003, std = 0.092 curvature mean = 0.003, std = 0.182 curvature mean = 0.003, std = 0.096 curvature mean = 0.000, std = 0.247 MRISregister() return, current seed 0 writing registered surface to ../surf/rh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white rh Mon Nov 17 19:01:46 EST 2025 mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white... writing curvature file ../surf/rh.jacobian_white #-------------------------------------------- #@# AvgCurv rh Mon Nov 17 19:01:48 EST 2025 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/scripts mrisp_paint -a 5 /usr/local/freesurfer/stable5_3_0/average/rh.average.curvature.filled.buckner40.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 /usr/local/freesurfer/stable5_3_0/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc rh Mon Nov 17 19:01:49 EST 2025 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 PBRHOPE_HOPE086_PETMR rh ../surf/rh.sphere.reg /usr/local/freesurfer/stable5_3_0/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/stable5_3_0/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.006 0 singular and 311 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1123 labels changed using aseg relabeling using gibbs priors... 000: 2814 changed, 126155 examined... 001: 627 changed, 12031 examined... 002: 175 changed, 3526 examined... 003: 57 changed, 1044 examined... 004: 15 changed, 335 examined... 005: 4 changed, 93 examined... 006: 2 changed, 28 examined... 007: 1 changed, 12 examined... 008: 0 changed, 7 examined... 232 labels changed using aseg 000: 116 total segments, 69 labels (323 vertices) changed 001: 50 total segments, 3 labels (6 vertices) changed 002: 47 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 43 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1447 vertices marked for relabeling... 1447 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 40 seconds. #-------------------------------------------- #@# Make Pial Surf rh Mon Nov 17 19:02:30 EST 2025 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs PBRHOPE_HOPE086_PETMR rh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/filled.mgz... reading volume /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/brain.finalsurfs.mgz... reading volume /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/wm.mgz... 10910 bright wm thresholded. 1793 bright non-wm voxels segmented. reading original surface position from /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.orig... computing class statistics... border white: 244849 voxels (1.46%) border gray 269780 voxels (1.61%) WM (93.0): 94.1 +- 7.4 [70.0 --> 110.0] GM (83.0) : 80.3 +- 11.3 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 62.7 (was 70) setting MAX_BORDER_WHITE to 109.4 (was 105) setting MIN_BORDER_WHITE to 74.0 (was 85) setting MAX_CSF to 51.5 (was 40) setting MAX_GRAY to 94.6 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 68.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 40.2 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=102, GM=74 mean inside = 93.2, mean outside = 77.5 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.02-->4.17) (max @ vno 23230 --> 125526) face area 0.28 +- 0.12 (0.00-->2.52) mean absolute distance = 0.83 +- 1.14 3932 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 1 with 99 points - only 0.00% unknown deleting segment 2 with 64 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 6 points - only 0.00% unknown mean border=83.9, 67 (67) missing vertices, mean dist 0.1 [0.9 (%41.0)->0.8 (%59.0))] %43 local maxima, %52 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=r440-, 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 0.91 +- 0.26 (0.06-->4.46) (max @ vno 23230 --> 125526) face area 0.28 +- 0.13 (0.00-->2.09) mean absolute distance = 0.47 +- 0.86 4473 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4162667.0, rms=8.88 001: dt: 0.5000, sse=4982458.5, rms=6.026 (0.000%) 002: dt: 0.5000, sse=5302398.0, rms=4.379 (0.000%) 003: dt: 0.5000, sse=5645599.0, rms=3.546 (0.000%) 004: dt: 0.5000, sse=5829745.0, rms=3.109 (0.000%) 005: dt: 0.5000, sse=5977226.5, rms=2.911 (0.000%) 006: dt: 0.5000, sse=6021494.0, rms=2.792 (0.000%) rms = 2.75, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=6056009.5, rms=2.751 (0.000%) 008: dt: 0.2500, sse=3775685.5, rms=1.936 (0.000%) 009: dt: 0.2500, sse=3517135.0, rms=1.765 (0.000%) rms = 1.73, time step reduction 2 of 3 to 0.125... 010: dt: 0.2500, sse=3416642.5, rms=1.728 (0.000%) rms = 1.70, time step reduction 3 of 3 to 0.062... 011: dt: 0.1250, sse=3362479.5, rms=1.696 (0.000%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 2 with 2 points - only 0.00% unknown deleting segment 3 with 9 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 3 points - only 0.00% unknown deleting segment 5 with 68 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 8 with 5 points - only 0.00% unknown deleting segment 9 with 50 points - only 26.00% unknown deleting segment 11 with 6 points - only 0.00% unknown removing 3 vertex label from ripped group mean border=85.9, 43 (5) missing vertices, mean dist -0.3 [0.6 (%62.2)->0.3 (%37.8))] %52 local maxima, %42 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=r440-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.08-->4.49) (max @ vno 23230 --> 125526) face area 0.34 +- 0.16 (0.00-->2.57) mean absolute distance = 0.37 +- 0.55 3630 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3736561.8, rms=3.74 012: dt: 0.5000, sse=4094296.2, rms=2.435 (0.000%) 013: dt: 0.5000, sse=4557461.5, rms=2.263 (0.000%) 014: dt: 0.5000, sse=4791543.0, rms=2.181 (0.000%) rms = 2.35, time step reduction 1 of 3 to 0.250... 015: dt: 0.2500, sse=4004758.5, rms=1.688 (0.000%) 016: dt: 0.2500, sse=3731789.5, rms=1.470 (0.000%) rms = 1.43, time step reduction 2 of 3 to 0.125... 017: dt: 0.2500, sse=3637267.0, rms=1.430 (0.000%) rms = 1.41, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=3589071.0, rms=1.407 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group deleting segment 1 with 2 points - only 0.00% unknown deleting segment 2 with 16 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 3 with 4 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 3 points - only 0.00% unknown deleting segment 5 with 88 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 6 with 1 points - only 0.00% unknown deleting segment 7 with 57 points - only 0.00% unknown deleting segment 9 with 36 points - only 30.56% unknown removing 3 vertex label from ripped group removing 2 vertex label from ripped group deleting segment 11 with 2 points - only 0.00% unknown deleting segment 12 with 8 points - only 0.00% unknown mean border=88.2, 50 (4) missing vertices, mean dist -0.2 [0.4 (%66.3)->0.2 (%33.7))] %69 local maxima, %26 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=r440-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.08-->4.44) (max @ vno 23230 --> 125526) face area 0.33 +- 0.16 (0.00-->2.46) mean absolute distance = 0.30 +- 0.43 3219 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3786189.8, rms=3.30 019: dt: 0.5000, sse=4036507.2, rms=2.067 (0.000%) rms = 2.05, time step reduction 1 of 3 to 0.250... 020: dt: 0.5000, sse=4424250.0, rms=2.054 (0.000%) 021: dt: 0.2500, sse=3880226.8, rms=1.400 (0.000%) 022: dt: 0.2500, sse=3781876.0, rms=1.306 (0.000%) rms = 1.30, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=3724745.2, rms=1.302 (0.000%) rms = 1.28, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=3689319.8, rms=1.280 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... deleting segment 1 with 153 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 3 points - only 0.00% unknown deleting segment 4 with 9 points - only 0.00% unknown deleting segment 5 with 56 points - only 0.00% unknown deleting segment 7 with 36 points - only 30.56% unknown removing 3 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 13 points - only 0.00% unknown mean border=89.3, 54 (4) missing vertices, mean dist -0.1 [0.3 (%57.8)->0.2 (%42.2))] %77 local maxima, %18 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=r440-, 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 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=3721539.8, rms=1.90 025: dt: 0.5000, sse=4593661.0, rms=1.455 (0.000%) rms = 1.81, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=4216601.0, rms=1.125 (0.000%) 027: dt: 0.2500, sse=4047530.2, rms=1.062 (0.000%) rms = 1.03, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=4093378.8, rms=1.030 (0.000%) rms = 1.02, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=4086233.2, rms=1.021 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group smoothing surface for 5 iterations... mean border=62.6, 114 (114) missing vertices, mean dist 1.8 [0.1 (%0.0)->2.2 (%100.0))] %32 local maxima, %45 large gradients and %17 min vals, 816 gradients ignored tol=1.0e-04, sigma=2.0, host=r440-, 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=20152162.0, rms=27.27 001: dt: 0.5000, sse=16146970.0, rms=23.986 (0.000%) 002: dt: 0.5000, sse=13044114.0, rms=21.116 (0.000%) 003: dt: 0.5000, sse=10891048.0, rms=18.684 (0.000%) 004: dt: 0.5000, sse=9525546.0, rms=16.565 (0.000%) 005: dt: 0.5000, sse=8454034.0, rms=14.682 (0.000%) 006: dt: 0.5000, sse=7639971.0, rms=13.003 (0.000%) 007: dt: 0.5000, sse=7038895.5, rms=11.463 (0.000%) 008: dt: 0.5000, sse=6610371.0, rms=10.035 (0.000%) 009: dt: 0.5000, sse=6288542.0, rms=8.659 (0.000%) 010: dt: 0.5000, sse=6120574.5, rms=7.402 (0.000%) 011: dt: 0.5000, sse=6004100.0, rms=6.364 (0.000%) 012: dt: 0.5000, sse=6013389.5, rms=5.603 (0.000%) 013: dt: 0.5000, sse=6054071.0, rms=5.111 (0.000%) 014: dt: 0.5000, sse=6114887.5, rms=4.796 (0.000%) 015: dt: 0.5000, sse=6120028.0, rms=4.584 (0.000%) 016: dt: 0.5000, sse=6173811.0, rms=4.443 (0.000%) 017: dt: 0.5000, sse=6189508.0, rms=4.336 (0.000%) 018: dt: 0.5000, sse=6210073.5, rms=4.260 (0.000%) 019: dt: 0.5000, sse=6193129.5, rms=4.204 (0.000%) rms = 4.18, time step reduction 1 of 3 to 0.250... 020: dt: 0.5000, sse=6213325.5, rms=4.175 (0.000%) 021: dt: 0.2500, sse=4140291.5, rms=3.204 (0.000%) 022: dt: 0.2500, sse=3915943.8, rms=2.938 (0.000%) rms = 2.90, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=3785783.8, rms=2.904 (0.000%) 024: dt: 0.1250, sse=3555753.5, rms=2.672 (0.000%) rms = 2.64, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=3520863.0, rms=2.644 (0.000%) positioning took 1.7 minutes mean border=59.5, 726 (17) missing vertices, mean dist 0.2 [0.2 (%40.0)->0.5 (%60.0))] %47 local maxima, %35 large gradients and %13 min vals, 344 gradients ignored tol=1.0e-04, sigma=1.0, host=r440-, 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=4315946.5, rms=5.63 026: dt: 0.5000, sse=4461803.0, rms=4.441 (0.000%) 027: dt: 0.5000, sse=5611790.5, rms=4.385 (0.000%) 028: dt: 0.5000, sse=5539128.0, rms=4.300 (0.000%) rms = 4.34, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=4494018.5, rms=3.304 (0.000%) 030: dt: 0.2500, sse=4273093.5, rms=2.939 (0.000%) 031: dt: 0.2500, sse=4172669.2, rms=2.850 (0.000%) rms = 2.83, time step reduction 2 of 3 to 0.125... 032: dt: 0.2500, sse=4174402.2, rms=2.832 (0.000%) 033: dt: 0.1250, sse=3968989.5, rms=2.594 (0.000%) rms = 2.56, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=3942908.2, rms=2.559 (0.000%) positioning took 0.6 minutes mean border=57.6, 858 (13) missing vertices, mean dist 0.1 [0.2 (%38.0)->0.4 (%62.0))] %57 local maxima, %25 large gradients and %13 min vals, 344 gradients ignored tol=1.0e-04, sigma=0.5, host=r440-, 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=4133516.5, rms=3.71 rms = 3.94, time step reduction 1 of 3 to 0.250... 035: dt: 0.2500, sse=3959380.5, rms=3.104 (0.000%) 036: dt: 0.2500, sse=3937909.5, rms=2.722 (0.000%) 037: dt: 0.2500, sse=4047786.2, rms=2.608 (0.000%) rms = 2.58, time step reduction 2 of 3 to 0.125... 038: dt: 0.2500, sse=4106618.2, rms=2.583 (0.000%) 039: dt: 0.1250, sse=3970758.8, rms=2.443 (0.000%) rms = 2.41, time step reduction 3 of 3 to 0.062... 040: dt: 0.1250, sse=3972841.0, rms=2.411 (0.000%) positioning took 0.4 minutes mean border=56.7, 1590 (12) missing vertices, mean dist 0.1 [0.2 (%43.2)->0.3 (%56.8))] %62 local maxima, %19 large gradients and %12 min vals, 301 gradients ignored tol=1.0e-04, sigma=0.2, host=r440-, 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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=4011535.2, rms=2.75 rms = 3.30, time step reduction 1 of 3 to 0.250... 041: dt: 0.2500, sse=3931855.2, rms=2.472 (0.000%) 042: dt: 0.2500, sse=4038413.0, rms=2.356 (0.000%) rms = 2.33, time step reduction 2 of 3 to 0.125... 043: dt: 0.2500, sse=4089853.8, rms=2.325 (0.000%) 044: dt: 0.1250, sse=4028267.5, rms=2.232 (0.000%) rms = 2.22, time step reduction 3 of 3 to 0.062... 045: dt: 0.1250, sse=4027603.2, rms=2.215 (0.000%) positioning took 0.4 minutes writing curvature file /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.area.pial vertex spacing 0.99 +- 0.40 (0.05-->6.84) (max @ vno 89548 --> 88626) face area 0.39 +- 0.28 (0.00-->5.67) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 126155 vertices processed 25000 of 126155 vertices processed 50000 of 126155 vertices processed 75000 of 126155 vertices processed 100000 of 126155 vertices processed 125000 of 126155 vertices processed 0 of 126155 vertices processed 25000 of 126155 vertices processed 50000 of 126155 vertices processed 75000 of 126155 vertices processed 100000 of 126155 vertices processed 125000 of 126155 vertices processed thickness calculation complete, 345:755 truncations. 37149 vertices at 0 distance 87064 vertices at 1 distance 71683 vertices at 2 distance 29831 vertices at 3 distance 9489 vertices at 4 distance 2760 vertices at 5 distance 903 vertices at 6 distance 364 vertices at 7 distance 152 vertices at 8 distance 81 vertices at 9 distance 37 vertices at 10 distance 19 vertices at 11 distance 15 vertices at 12 distance 13 vertices at 13 distance 20 vertices at 14 distance 15 vertices at 15 distance 9 vertices at 16 distance 5 vertices at 17 distance 8 vertices at 18 distance 3 vertices at 19 distance 0 vertices at 20 distance writing curvature file /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.thickness positioning took 7.0 minutes #-------------------------------------------- #@# Surf Volume rh Mon Nov 17 19:09:29 EST 2025 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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_calc -o rh.volume rh.area.mid mul rh.thickness Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# WM/GM Contrast rh Mon Nov 17 19:09:30 EST 2025 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/scripts pctsurfcon --s PBRHOPE_HOPE086_PETMR --rh-only Log file is /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/scripts/pctsurfcon.log Mon Nov 17 19:09:30 EST 2025 setenv SUBJECTS_DIR /autofs/space/hope_002/users/PBR28_HOPE/data/fs cd /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/scripts /usr/local/freesurfer/stable5_3_0/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux r440-30.nmr.mgh.harvard.edu 4.18.0-553.79.1.el8_10.x86_64 #1 SMP Wed Oct 15 12:48:32 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 mri_vol2surf --mov /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/tmp.pctsurfcon.2564588/rh.wm.mgh --regheader PBRHOPE_HOPE086_PETMR --cortex srcvol = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 INFO: changing type to float Done loading volume Computing registration from header. Using /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/orig.mgz as target reference. Loading label /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/label/rh.cortex.label Reading surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 = 67433 Masking with /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/label/rh.cortex.label Writing to /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/tmp.pctsurfcon.2564588/rh.wm.mgh Dim: 126155 1 1 mri_vol2surf --mov /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/tmp.pctsurfcon.2564588/rh.gm.mgh --projfrac 0.3 --regheader PBRHOPE_HOPE086_PETMR --cortex srcvol = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 INFO: changing type to float Done loading volume Computing registration from header. Using /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/orig.mgz as target reference. Loading label /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/label/rh.cortex.label Reading surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.white Done reading source surface Reading thickness /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 = 81820 Masking with /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/label/rh.cortex.label Writing to /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/tmp.pctsurfcon.2564588/rh.gm.mgh Dim: 126155 1 1 mri_concat /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/tmp.pctsurfcon.2564588/rh.wm.mgh /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/tmp.pctsurfcon.2564588/rh.gm.mgh --paired-diff-norm --mul 100 --o /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.w-g.pct.mgh mri_segstats --in /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.w-g.pct.mgh --annot PBRHOPE_HOPE086_PETMR rh aparc --sum /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/stats/rh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --in /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.w-g.pct.mgh --annot PBRHOPE_HOPE086_PETMR rh aparc --sum /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/stats/rh.w-g.pct.stats --snr sysname Linux hostname r440-30.nmr.mgh.harvard.edu machine x86_64 user ek657 UseRobust 0 Constructing seg from annotation Reading annotation reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Seg base 2000 Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.w-g.pct.mgh Vertex Area is 0.646856 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 2000 unknown 0 0.000 1 2001 bankssts 1228 857.213 2 2002 caudalanteriorcingulate 875 614.886 3 2003 caudalmiddlefrontal 2958 1947.172 4 2004 corpuscallosum 0 0.000 5 2005 cuneus 2043 1195.501 6 2006 entorhinal 433 277.957 7 2007 fusiform 4131 2751.982 8 2008 inferiorparietal 6941 4443.257 9 2009 inferiortemporal 4367 2786.315 10 2010 isthmuscingulate 1308 857.741 11 2011 lateraloccipital 5836 3435.308 12 2012 lateralorbitofrontal 3693 2392.044 13 2013 lingual 4584 2832.234 14 2014 medialorbitofrontal 2878 1846.728 15 2015 middletemporal 4692 3076.586 16 2016 parahippocampal 903 612.238 17 2017 paracentral 1695 1079.281 18 2018 parsopercularis 1634 1062.056 19 2019 parsorbitalis 1155 761.273 20 2020 parstriangularis 2215 1492.464 21 2021 pericalcarine 1858 1270.516 22 2022 postcentral 6410 3974.404 23 2023 posteriorcingulate 1739 1136.281 24 2024 precentral 7520 4612.694 25 2025 precuneus 5268 3559.572 26 2026 rostralanteriorcingulate 738 484.426 27 2027 rostralmiddlefrontal 7385 4992.022 28 2028 superiorfrontal 9398 6414.531 29 2029 superiorparietal 8376 5315.301 30 2030 superiortemporal 4491 3042.212 31 2031 supramarginal 6463 4124.816 32 2032 frontalpole 327 225.668 33 2033 temporalpole 632 410.666 34 2034 transversetemporal 566 310.929 35 2035 insula 3157 2116.071 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats rh Mon Nov 17 19:09:36 EST 2025 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/scripts mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab PBRHOPE_HOPE086_PETMR rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/wm.mgz... reading input surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.white... reading input pial surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.pial... reading input white surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/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 1228 857 1945 2.349 0.525 0.119 0.030 10 1.4 bankssts 875 615 1363 2.018 0.638 0.166 0.051 22 2.1 caudalanteriorcingulate 2958 1947 4955 2.333 0.594 0.155 0.076 53 9.1 caudalmiddlefrontal 2043 1196 2304 1.769 0.409 0.154 0.069 35 5.9 cuneus 433 278 1611 3.539 0.971 0.109 0.050 6 0.8 entorhinal 4131 2752 8227 2.559 0.698 0.139 0.051 61 8.8 fusiform 6941 4443 11585 2.365 0.606 0.138 0.046 97 13.3 inferiorparietal 4367 2786 9459 2.935 0.734 0.152 0.071 82 12.5 inferiortemporal 1308 858 2029 2.239 0.555 0.155 0.061 24 3.2 isthmuscingulate 5836 3435 7742 2.111 0.519 0.138 0.133 120 16.5 lateraloccipital 3693 2392 6627 2.444 0.807 0.170 0.116 170 18.6 lateralorbitofrontal 4584 2832 6088 1.994 0.628 0.157 0.166 110 14.7 lingual 2878 1847 4307 1.948 0.722 0.163 0.148 151 23.4 medialorbitofrontal 4692 3077 10567 2.926 0.637 0.138 0.062 72 9.5 middletemporal 903 612 1602 2.383 0.608 0.112 0.031 9 1.2 parahippocampal 1695 1079 2566 2.181 0.555 0.134 0.048 19 3.6 paracentral 1634 1062 2396 2.020 0.535 0.125 0.037 16 2.5 parsopercularis 1155 761 2151 2.227 0.809 0.175 0.087 27 4.1 parsorbitalis 2215 1492 3658 2.126 0.543 0.157 0.060 37 5.3 parstriangularis 1858 1271 1803 1.530 0.438 0.187 0.079 64 6.9 pericalcarine 6410 3974 8516 1.903 0.520 0.121 0.059 107 12.8 postcentral 1739 1136 2813 2.252 0.594 0.175 0.074 38 5.1 posteriorcingulate 7520 4613 11814 2.385 0.608 0.136 0.086 226 26.0 precentral 5268 3560 7949 2.116 0.578 0.149 0.052 77 11.4 precuneus 738 484 1411 2.402 0.795 0.171 0.083 21 2.6 rostralanteriorcingulate 7385 4992 12199 2.073 0.575 0.174 0.080 168 25.0 rostralmiddlefrontal 9398 6415 17909 2.370 0.594 0.175 0.092 237 34.9 superiorfrontal 8376 5315 12275 2.042 0.480 0.129 0.046 112 15.2 superiorparietal 4491 3042 8813 2.561 0.653 0.125 0.043 50 7.9 superiortemporal 6463 4125 10314 2.302 0.517 0.137 0.621 423 16.0 supramarginal 327 226 883 2.713 0.509 0.241 0.157 18 1.9 frontalpole 632 411 2582 4.182 0.626 0.176 0.128 27 4.3 temporalpole 566 311 796 2.279 0.476 0.131 0.046 6 1.1 transversetemporal 3157 2116 6257 2.882 0.892 0.134 0.057 43 6.9 insula #----------------------------------------- #@# Cortical Parc 2 rh Mon Nov 17 19:09:47 EST 2025 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 PBRHOPE_HOPE086_PETMR rh ../surf/rh.sphere.reg /usr/local/freesurfer/stable5_3_0/average/rh.destrieux.simple.2009-07-29.gcs ../label/rh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/stable5_3_0/average/rh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 1.9 0.2 using min determinant for regularization = 0.000 0 singular and 851 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 47 labels changed using aseg relabeling using gibbs priors... 000: 9289 changed, 126155 examined... 001: 2237 changed, 35243 examined... 002: 685 changed, 11443 examined... 003: 281 changed, 3770 examined... 004: 162 changed, 1604 examined... 005: 86 changed, 926 examined... 006: 51 changed, 484 examined... 007: 26 changed, 268 examined... 008: 11 changed, 131 examined... 009: 5 changed, 67 examined... 010: 2 changed, 30 examined... 011: 1 changed, 10 examined... 012: 1 changed, 6 examined... 013: 2 changed, 7 examined... 014: 2 changed, 11 examined... 015: 1 changed, 9 examined... 016: 0 changed, 6 examined... 34 labels changed using aseg 000: 297 total segments, 210 labels (2384 vertices) changed 001: 99 total segments, 12 labels (25 vertices) changed 002: 87 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 140 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1010 vertices marked for relabeling... 1010 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 46 seconds. #----------------------------------------- #@# Parcellation Stats 2 rh Mon Nov 17 19:10:33 EST 2025 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/scripts mris_anatomical_stats -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 PBRHOPE_HOPE086_PETMR rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/wm.mgz... reading input surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.white... reading input pial surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.pial... reading input white surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.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 700 492 1429 2.323 0.724 0.226 0.122 28 3.7 G_and_S_frontomargin 962 613 1605 2.224 0.447 0.130 0.044 15 1.8 G_and_S_occipital_inf 1239 692 1900 2.284 0.556 0.136 0.135 49 3.2 G_and_S_paracentral 1362 912 2257 2.230 0.580 0.143 0.054 20 2.1 G_and_S_subcentral 865 573 1643 2.252 0.518 0.202 0.123 33 4.0 G_and_S_transv_frontopol 2455 1671 4031 2.116 0.693 0.159 0.067 54 7.0 G_and_S_cingul-Ant 1338 949 2191 2.144 0.579 0.156 0.062 27 3.7 G_and_S_cingul-Mid-Ant 1473 1008 2524 2.289 0.522 0.166 0.063 27 3.7 G_and_S_cingul-Mid-Post 526 334 1086 2.619 0.432 0.198 0.087 14 1.9 G_cingul-Post-dorsal 332 189 607 2.586 0.506 0.158 0.066 8 0.9 G_cingul-Post-ventral 1866 1069 2090 1.758 0.426 0.158 0.072 36 5.4 G_cuneus 1056 669 1964 2.332 0.470 0.148 0.057 16 2.5 G_front_inf-Opercular 398 267 733 2.109 0.698 0.210 0.112 13 2.0 G_front_inf-Orbital 1234 809 2401 2.322 0.479 0.167 0.071 26 3.4 G_front_inf-Triangul 3914 2555 7972 2.398 0.547 0.188 0.105 113 17.9 G_front_middle 5961 3994 12895 2.527 0.582 0.193 0.114 192 27.5 G_front_sup 411 288 972 3.077 0.803 0.152 0.095 10 1.7 G_Ins_lg_and_S_cent_ins 596 355 1815 3.569 0.697 0.157 0.075 13 1.8 G_insular_short 1543 914 2734 2.423 0.501 0.135 0.360 64 7.7 G_occipital_middle 1926 1066 2647 2.182 0.527 0.133 0.057 29 4.0 G_occipital_sup 1633 1016 3586 2.635 0.667 0.162 0.074 39 5.1 G_oc-temp_lat-fusifor 2860 1724 4040 2.038 0.708 0.178 0.244 118 12.1 G_oc-temp_med-Lingual 1222 779 2752 2.820 0.925 0.125 0.056 20 2.4 G_oc-temp_med-Parahip 2693 1721 5879 2.588 0.770 0.188 0.123 159 15.0 G_orbital 3135 1789 5818 2.502 0.558 0.150 1.212 307 9.1 G_pariet_inf-Angular 3176 2004 6054 2.485 0.510 0.151 0.083 143 9.7 G_pariet_inf-Supramar 2746 1739 4815 2.219 0.461 0.141 0.059 49 6.2 G_parietal_sup 2534 1416 3497 1.944 0.436 0.122 0.091 68 7.1 G_postcentral 2921 1510 5465 2.696 0.515 0.150 0.121 151 17.2 G_precentral 2894 1906 4908 2.155 0.517 0.156 0.061 53 7.7 G_precuneus 836 513 1528 2.224 0.635 0.211 0.335 106 17.1 G_rectus 510 311 635 1.894 1.027 0.153 0.128 20 2.7 G_subcallosal 447 241 647 2.285 0.472 0.120 0.045 4 0.9 G_temp_sup-G_T_transv 1550 1008 3661 2.694 0.590 0.149 0.065 29 4.2 G_temp_sup-Lateral 664 439 1808 3.454 0.986 0.104 0.034 5 0.9 G_temp_sup-Plan_polar 671 464 1126 2.227 0.552 0.110 0.028 5 0.7 G_temp_sup-Plan_tempo 2402 1456 5862 3.013 0.772 0.163 0.093 57 9.0 G_temporal_inf 2854 1813 7106 3.005 0.645 0.152 0.079 56 7.2 G_temporal_middle 369 260 426 1.846 0.504 0.120 0.027 2 0.4 Lat_Fis-ant-Horizont 175 110 249 2.054 0.659 0.116 0.027 1 0.2 Lat_Fis-ant-Vertical 1776 1185 2152 2.098 0.487 0.122 0.040 15 2.6 Lat_Fis-post 3519 2024 4025 1.829 0.471 0.147 0.058 53 8.5 Pole_occipital 1725 1137 6189 3.652 0.779 0.160 0.097 46 7.3 Pole_temporal 2233 1600 2549 1.746 0.564 0.163 0.056 35 5.8 S_calcarine 3172 2176 3653 1.867 0.640 0.121 0.042 27 6.2 S_central 1113 767 1502 1.925 0.408 0.134 0.043 11 1.9 S_cingul-Marginalis 607 424 1139 2.974 0.694 0.140 0.080 8 1.8 S_circular_insula_ant 927 671 1549 2.684 0.654 0.099 0.022 5 0.8 S_circular_insula_inf 1361 916 1860 2.254 0.521 0.111 0.029 8 1.6 S_circular_insula_sup 791 560 1647 2.981 0.531 0.124 0.032 7 1.0 S_collat_transv_ant 561 365 697 1.961 0.446 0.152 0.055 7 1.2 S_collat_transv_post 1752 1205 1995 1.731 0.478 0.134 0.041 16 2.8 S_front_inf 1832 1243 2458 1.895 0.488 0.147 0.054 24 3.8 S_front_middle 2456 1698 3476 2.001 0.454 0.133 0.048 26 4.7 S_front_sup 761 524 907 2.067 0.415 0.111 0.026 4 0.9 S_interm_prim-Jensen 3294 2192 4153 1.915 0.474 0.126 0.038 35 4.9 S_intrapariet_and_P_trans 436 283 520 2.074 0.461 0.143 0.037 6 0.7 S_oc_middle_and_Lunatus 1367 899 1708 2.074 0.539 0.122 0.032 12 1.8 S_oc_sup_and_transversal 654 463 838 2.169 0.575 0.122 0.027 4 0.8 S_occipital_ant 1147 794 1735 2.442 0.485 0.124 0.034 9 1.6 S_oc-temp_lat 1605 1142 2400 2.332 0.442 0.110 0.025 10 1.8 S_oc-temp_med_and_Lingual 366 255 435 1.576 0.455 0.164 0.060 6 0.8 S_orbital_lateral 872 566 987 1.671 0.644 0.108 0.063 9 2.3 S_orbital_med-olfact 1054 706 1656 2.327 0.649 0.163 0.077 18 3.1 S_orbital-H_Shaped 1662 1105 2145 2.172 0.626 0.130 0.040 16 2.7 S_parieto_occipital 1353 852 1223 1.823 0.566 0.161 0.058 28 3.1 S_pericallosal 2548 1727 3165 1.955 0.444 0.117 0.032 19 3.3 S_postcentral 1469 978 2084 2.269 0.589 0.133 0.036 15 2.4 S_precentral-inf-part 1295 902 1750 2.178 0.481 0.123 0.034 9 1.9 S_precentral-sup-part 255 171 269 1.427 0.461 0.112 0.029 2 0.3 S_suborbital 1012 697 1329 1.856 0.528 0.151 0.055 15 2.1 S_subparietal 1134 773 1709 2.653 0.647 0.127 0.029 9 1.5 S_temporal_inf 5053 3475 7782 2.385 0.576 0.118 0.033 45 6.7 S_temporal_sup 286 200 471 2.385 0.507 0.149 0.036 3 0.4 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 rh Mon Nov 17 19:10:46 EST 2025 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 PBRHOPE_HOPE086_PETMR rh ../surf/rh.sphere.reg /usr/local/freesurfer/stable5_3_0/average/rh.DKTatlas40.gcs ../label/rh.aparc.DKTatlas40.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/stable5_3_0/average/rh.DKTatlas40.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.008 0 singular and 237 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1417 labels changed using aseg relabeling using gibbs priors... 000: 2706 changed, 126155 examined... 001: 675 changed, 11452 examined... 002: 181 changed, 3571 examined... 003: 80 changed, 1012 examined... 004: 36 changed, 441 examined... 005: 26 changed, 213 examined... 006: 12 changed, 136 examined... 007: 11 changed, 67 examined... 008: 9 changed, 69 examined... 009: 7 changed, 44 examined... 010: 5 changed, 36 examined... 011: 6 changed, 29 examined... 012: 5 changed, 38 examined... 013: 2 changed, 26 examined... 014: 3 changed, 11 examined... 015: 1 changed, 16 examined... 016: 4 changed, 10 examined... 017: 3 changed, 16 examined... 018: 2 changed, 14 examined... 019: 1 changed, 10 examined... 020: 1 changed, 7 examined... 021: 0 changed, 7 examined... 340 labels changed using aseg 000: 65 total segments, 32 labels (477 vertices) changed 001: 34 total segments, 1 labels (2 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 43 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 604 vertices marked for relabeling... 604 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas40.annot... classification took 0 minutes and 40 seconds. #----------------------------------------- #@# Parcellation Stats 3 rh Mon Nov 17 19:11:26 EST 2025 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/scripts mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas40.stats -b -a ../label/rh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab PBRHOPE_HOPE086_PETMR rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot. reading volume /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/wm.mgz... reading input surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.white... reading input pial surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.pial... reading input white surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /Applications/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas40.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 877 618 1364 2.011 0.636 0.167 0.051 22 2.1 caudalanteriorcingulate 2952 1945 4761 2.293 0.570 0.151 0.071 51 8.6 caudalmiddlefrontal 2444 1443 2692 1.763 0.415 0.151 0.064 40 6.6 cuneus 445 285 1654 3.524 0.955 0.110 0.049 7 0.8 entorhinal 3724 2481 7019 2.485 0.607 0.140 0.050 56 8.1 fusiform 6715 4276 10980 2.338 0.593 0.139 0.048 99 13.5 inferiorparietal 4725 3033 10760 2.977 0.769 0.151 0.070 84 13.2 inferiortemporal 1313 863 2028 2.226 0.554 0.155 0.061 24 3.2 isthmuscingulate 6052 3583 7992 2.104 0.518 0.137 0.129 125 16.7 lateraloccipital 3711 2438 6937 2.424 0.793 0.177 0.115 179 18.9 lateralorbitofrontal 4585 2828 6087 1.995 0.630 0.157 0.166 110 14.7 lingual 2421 1532 3812 2.013 0.780 0.170 0.171 147 22.9 medialorbitofrontal 5480 3630 11830 2.858 0.660 0.135 0.057 79 10.4 middletemporal 915 625 1578 2.357 0.594 0.114 0.031 9 1.2 parahippocampal 1788 1146 2732 2.184 0.548 0.135 0.048 21 3.8 paracentral 1808 1177 2718 2.056 0.550 0.129 0.039 20 2.9 parsopercularis 1239 804 2361 2.378 0.784 0.169 0.086 27 4.1 parsorbitalis 2286 1545 3644 2.067 0.537 0.158 0.061 39 5.5 parstriangularis 1865 1277 1815 1.530 0.438 0.188 0.079 65 6.8 pericalcarine 7006 4362 9407 1.919 0.522 0.123 0.058 115 14.0 postcentral 1783 1162 2892 2.264 0.591 0.176 0.081 42 5.7 posteriorcingulate 7231 4402 11423 2.400 0.618 0.136 0.088 223 25.7 precentral 5355 3584 8252 2.141 0.573 0.148 0.053 80 11.8 precuneus 842 558 1495 2.297 0.831 0.169 0.080 22 2.8 rostralanteriorcingulate 5260 3519 8684 2.079 0.597 0.173 0.083 115 17.9 rostralmiddlefrontal 11970 8181 22192 2.304 0.599 0.173 0.087 296 42.3 superiorfrontal 7329 4675 10873 2.054 0.473 0.129 0.046 98 13.2 superiorparietal 6256 4167 13246 2.749 0.830 0.134 0.630 333 15.5 superiortemporal 5969 3838 9596 2.300 0.512 0.132 0.061 171 13.2 supramarginal 560 306 787 2.283 0.477 0.131 0.046 6 1.1 transversetemporal 2991 2027 5903 2.816 0.855 0.133 0.058 41 7.1 insula #-------------------------------------------- #@# Cortical ribbon mask Mon Nov 17 19:11:37 EST 2025 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon PBRHOPE_HOPE086_PETMR SUBJECTS_DIR is /autofs/space/hope_002/users/PBR28_HOPE/data/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 = 41 writing volume /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/ribbon.mgz writing ribbon files #-------------------------------------------- #@# ASeg Stats Mon Nov 17 19:21:08 EST 2025 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR 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 /usr/local/freesurfer/stable5_3_0/ASegStatsLUT.txt --subject PBRHOPE_HOPE086_PETMR $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 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 /usr/local/freesurfer/stable5_3_0/ASegStatsLUT.txt --subject PBRHOPE_HOPE086_PETMR sysname Linux hostname r440-30.nmr.mgh.harvard.edu machine x86_64 user ek657 UseRobust 0 atlas_icv (eTIV) = 1604328 mm^3 (det: 1.214281 ) Computing euler number orig.nofix lheno = -86, rheno = -60 orig.nofix lhholes = 44, rhholes = 31 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 196949.034 196818.000 diff= 131.0 pctdiff= 0.067 rhCtxGM: 196504.325 196174.000 diff= 330.3 pctdiff= 0.168 lhCtxWM: 210405.640 211342.000 diff= -936.4 pctdiff=-0.445 rhCtxWM: 206980.728 207069.000 diff= -88.3 pctdiff=-0.043 SubCortGMVol 51165.000 SupraTentVol 895622.727 (895248.000) diff=374.727 pctdiff=0.042 SupraTentVolNotVent 862975.727 (862601.000) diff=374.727 pctdiff=0.043 BrainSegVol 1024892.000 (1022460.000) diff=2432.000 pctdiff=0.237 BrainSegVolNotVent 988794.000 (988099.727) diff=694.273 pctdiff=0.070 BrainSegVolNotVent 988794.000 CerebellumVol 126062.000 VentChorVol 32647.000 3rd4th5thCSF 3451.000 CSFVol 1080.000, OptChiasmVol 70.000 MaskVol 1508600.000 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 3 4 Left-Lateral-Ventricle 14739 14739.029 4 5 Left-Inf-Lat-Vent 252 252.387 5 7 Left-Cerebellum-White-Matter 11822 11822.182 6 8 Left-Cerebellum-Cortex 48437 48436.922 7 10 Left-Thalamus-Proper 7787 7786.560 8 11 Left-Caudate 3329 3329.042 9 12 Left-Putamen 4198 4197.674 10 13 Left-Pallidum 856 856.092 11 14 3rd-Ventricle 783 782.831 12 15 4th-Ventricle 1851 1850.521 13 16 Brain-Stem 22719 22719.072 14 17 Left-Hippocampus 3358 3358.216 15 18 Left-Amygdala 1393 1393.106 16 24 CSF 1095 1095.324 17 26 Left-Accumbens-area 375 374.760 18 28 Left-VentralDC 3441 3441.428 19 30 Left-vessel 21 21.366 20 31 Left-choroid-plexus 1636 1635.950 23 43 Right-Lateral-Ventricle 13628 13628.335 24 44 Right-Inf-Lat-Vent 114 113.593 25 46 Right-Cerebellum-White-Matter 9943 9942.604 26 47 Right-Cerebellum-Cortex 57086 57086.270 27 49 Right-Thalamus-Proper 6974 6973.532 28 50 Right-Caudate 3716 3716.010 29 51 Right-Putamen 4199 4199.002 30 52 Right-Pallidum 1152 1152.035 31 53 Right-Hippocampus 3699 3699.443 32 54 Right-Amygdala 1512 1511.583 33 58 Right-Accumbens-area 513 512.813 34 60 Right-VentralDC 3486 3486.397 35 62 Right-vessel 37 37.070 36 63 Right-choroid-plexus 2323 2322.871 37 72 5th-Ventricle 3 3.443 38 77 WM-hypointensities 1698 1698.380 39 78 Left-WM-hypointensities 0 0.000 40 79 Right-WM-hypointensities 0 0.000 41 80 non-WM-hypointensities 52 51.821 42 81 Left-non-WM-hypointensities 0 0.000 43 82 Right-non-WM-hypointensities 0 0.000 44 85 Optic-Chiasm 69 69.020 45 251 CC_Posterior 1148 1148.320 46 252 CC_Mid_Posterior 430 429.557 47 253 CC_Central 419 418.739 48 254 CC_Mid_Anterior 588 587.867 49 255 CC_Anterior 1051 1051.046 Reporting on 45 segmentations mri_segstats done #----------------------------------------- #@# AParc-to-ASeg Mon Nov 17 19:23:33 EST 2025 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR mri_aparc2aseg --s PBRHOPE_HOPE086_PETMR --volmask SUBJECTS_DIR /autofs/space/hope_002/users/PBR28_HOPE/data/fs subject PBRHOPE_HOPE086_PETMR outvol /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.white Reading lh pial surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.pial Loading lh annotations from /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Reading rh white surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.white Reading rh pial surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.pial Loading rh annotations from /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- 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 = 391478 Used brute-force search on 0 voxels Writing output aseg to /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/aparc+aseg.mgz /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR mri_aparc2aseg --s PBRHOPE_HOPE086_PETMR --volmask --a2009s SUBJECTS_DIR /autofs/space/hope_002/users/PBR28_HOPE/data/fs subject PBRHOPE_HOPE086_PETMR outvol /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.white Reading lh pial surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.pial Loading lh annotations from /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/label/lh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Reading rh white surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.white Reading rh pial surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.pial Loading rh annotations from /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/label/rh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- 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 = 391478 Used brute-force search on 0 voxels Writing output aseg to /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# WMParc Mon Nov 17 19:25:14 EST 2025 /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR mri_aparc2aseg --s PBRHOPE_HOPE086_PETMR --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /autofs/space/hope_002/users/PBR28_HOPE/data/fs subject PBRHOPE_HOPE086_PETMR outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/aparc+aseg.mgz Reading lh white surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.white Reading lh pial surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.pial Loading lh annotations from /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Reading rh white surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.white Reading rh pial surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.pial Loading rh annotations from /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/ribbon.mgz Loading filled from /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/filled.mgz Ripping vertices labeled as unkown Ripped 8292 vertices from left hemi Ripped 8258 vertices from right hemi Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/aseg.mgz Loading Ctx Seg File /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/aparc+aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- 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 = 807698 Used brute-force search on 292 voxels Fixing Parahip LH WM Found 10 clusters 0 k 273.000000 1 k 1.000000 2 k 6.000000 3 k 1279.000000 4 k 2.000000 5 k 2.000000 6 k 4.000000 7 k 16.000000 8 k 7.000000 9 k 1.000000 Fixing Parahip RH WM Found 2 clusters 0 k 16.000000 1 k 1262.000000 Writing output aseg to mri/wmparc.mgz /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR 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 PBRHOPE_HOPE086_PETMR --surf-wm-vol --ctab /usr/local/freesurfer/stable5_3_0/WMParcStatsLUT.txt --etiv $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 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 PBRHOPE_HOPE086_PETMR --surf-wm-vol --ctab /usr/local/freesurfer/stable5_3_0/WMParcStatsLUT.txt --etiv sysname Linux hostname r440-30.nmr.mgh.harvard.edu machine x86_64 user ek657 UseRobust 0 atlas_icv (eTIV) = 1604328 mm^3 (det: 1.214281 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 196949.034 196818.000 diff= 131.0 pctdiff= 0.067 rhCtxGM: 196504.325 196174.000 diff= 330.3 pctdiff= 0.168 lhCtxWM: 210405.640 211342.000 diff= -936.4 pctdiff=-0.445 rhCtxWM: 206980.728 207069.000 diff= -88.3 pctdiff=-0.043 SubCortGMVol 51165.000 SupraTentVol 895622.727 (895248.000) diff=374.727 pctdiff=0.042 SupraTentVolNotVent 862975.727 (862601.000) diff=374.727 pctdiff=0.043 BrainSegVol 1024892.000 (1022460.000) diff=2432.000 pctdiff=0.237 BrainSegVolNotVent 988794.000 (988099.727) diff=694.273 pctdiff=0.070 BrainSegVolNotVent 988794.000 CerebellumVol 126062.000 VentChorVol 32647.000 3rd4th5thCSF 3451.000 CSFVol 1080.000, OptChiasmVol 70.000 MaskVol 1508600.000 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 0 3000 wm-lh-unknown 0 0.000 1 3001 wm-lh-bankssts 2069 2069.350 2 3002 wm-lh-caudalanteriorcingulate 2756 2756.317 3 3003 wm-lh-caudalmiddlefrontal 6549 6548.601 4 3004 wm-lh-corpuscallosum 0 0.000 5 3005 wm-lh-cuneus 2075 2074.961 6 3006 wm-lh-entorhinal 468 467.711 7 3007 wm-lh-fusiform 6937 6936.993 8 3008 wm-lh-inferiorparietal 9497 9496.906 9 3009 wm-lh-inferiortemporal 5654 5653.979 10 3010 wm-lh-isthmuscingulate 3986 3985.690 11 3011 wm-lh-lateraloccipital 8858 8858.109 12 3012 wm-lh-lateralorbitofrontal 6249 6248.604 13 3013 wm-lh-lingual 4709 4708.911 14 3014 wm-lh-medialorbitofrontal 3279 3278.637 15 3015 wm-lh-middletemporal 4562 4562.025 16 3016 wm-lh-parahippocampal 1371 1371.406 17 3017 wm-lh-paracentral 3851 3850.526 18 3018 wm-lh-parsopercularis 3375 3374.933 19 3019 wm-lh-parsorbitalis 701 701.189 20 3020 wm-lh-parstriangularis 2398 2397.693 21 3021 wm-lh-pericalcarine 2603 2602.510 22 3022 wm-lh-postcentral 7038 7038.124 23 3023 wm-lh-posteriorcingulate 4935 4934.993 24 3024 wm-lh-precentral 12858 12857.659 25 3025 wm-lh-precuneus 8662 8662.148 26 3026 wm-lh-rostralanteriorcingulate 2385 2384.598 27 3027 wm-lh-rostralmiddlefrontal 11505 11504.924 28 3028 wm-lh-superiorfrontal 14758 14758.396 29 3029 wm-lh-superiorparietal 11369 11368.958 30 3030 wm-lh-superiortemporal 6916 6915.607 31 3031 wm-lh-supramarginal 9096 9095.800 32 3032 wm-lh-frontalpole 125 125.274 33 3033 wm-lh-temporalpole 551 551.392 34 3034 wm-lh-transversetemporal 792 791.765 35 3035 wm-lh-insula 9434 9433.553 36 3100 wm-lh-Unknown 0 0.000 37 3101 wm-lh-Corpus_callosum 0 0.000 38 3102 wm-lh-G_and_S_Insula_ONLY_AVERAGE 0 0.000 39 3103 wm-lh-G_cingulate-Isthmus 0 0.000 40 3104 wm-lh-G_cingulate-Main_part 0 0.000 41 3105 wm-lh-G_cuneus 0 0.000 42 3106 wm-lh-G_frontal_inf-Opercular_part 0 0.000 43 3107 wm-lh-G_frontal_inf-Orbital_part 0 0.000 44 3108 wm-lh-G_frontal_inf-Triangular_part 0 0.000 45 3109 wm-lh-G_frontal_middle 0 0.000 46 3110 wm-lh-G_frontal_superior 0 0.000 47 3111 wm-lh-G_frontomarginal 0 0.000 48 3112 wm-lh-G_insular_long 0 0.000 49 3113 wm-lh-G_insular_short 0 0.000 50 3114 wm-lh-G_and_S_occipital_inferior 0 0.000 51 3115 wm-lh-G_occipital_middle 0 0.000 52 3116 wm-lh-G_occipital_superior 0 0.000 53 3117 wm-lh-G_occipit-temp_lat-Or_fusiform 0 0.000 54 3118 wm-lh-G_occipit-temp_med-Lingual_part 0 0.000 55 3119 wm-lh-G_occipit-temp_med-Parahippocampal_part 0 0.000 56 3120 wm-lh-G_orbital 0 0.000 57 3121 wm-lh-G_paracentral 0 0.000 58 3122 wm-lh-G_parietal_inferior-Angular_part 0 0.000 59 3123 wm-lh-G_parietal_inferior-Supramarginal_part 0 0.000 60 3124 wm-lh-G_parietal_superior 0 0.000 61 3125 wm-lh-G_postcentral 0 0.000 62 3126 wm-lh-G_precentral 0 0.000 63 3127 wm-lh-G_precuneus 0 0.000 64 3128 wm-lh-G_rectus 0 0.000 65 3129 wm-lh-G_subcallosal 0 0.000 66 3130 wm-lh-G_subcentral 0 0.000 67 3131 wm-lh-G_temporal_inferior 0 0.000 68 3132 wm-lh-G_temporal_middle 0 0.000 69 3133 wm-lh-G_temp_sup-G_temp_transv_and_interm_S 0 0.000 70 3134 wm-lh-G_temp_sup-Lateral_aspect 0 0.000 71 3135 wm-lh-G_temp_sup-Planum_polare 0 0.000 72 3136 wm-lh-G_temp_sup-Planum_tempolare 0 0.000 73 3137 wm-lh-G_and_S_transverse_frontopolar 0 0.000 74 3138 wm-lh-Lat_Fissure-ant_sgt-ramus_horizontal 0 0.000 75 3139 wm-lh-Lat_Fissure-ant_sgt-ramus_vertical 0 0.000 76 3140 wm-lh-Lat_Fissure-post_sgt 0 0.000 77 3141 wm-lh-Medial_wall 0 0.000 78 3142 wm-lh-Pole_occipital 0 0.000 79 3143 wm-lh-Pole_temporal 0 0.000 80 3144 wm-lh-S_calcarine 0 0.000 81 3145 wm-lh-S_central 0 0.000 82 3146 wm-lh-S_central_insula 0 0.000 83 3147 wm-lh-S_cingulate-Main_part_and_Intracingulate 0 0.000 84 3148 wm-lh-S_cingulate-Marginalis_part 0 0.000 85 3149 wm-lh-S_circular_insula_anterior 0 0.000 86 3150 wm-lh-S_circular_insula_inferior 0 0.000 87 3151 wm-lh-S_circular_insula_superior 0 0.000 88 3152 wm-lh-S_collateral_transverse_ant 0 0.000 89 3153 wm-lh-S_collateral_transverse_post 0 0.000 90 3154 wm-lh-S_frontal_inferior 0 0.000 91 3155 wm-lh-S_frontal_middle 0 0.000 92 3156 wm-lh-S_frontal_superior 0 0.000 93 3157 wm-lh-S_frontomarginal 0 0.000 94 3158 wm-lh-S_intermedius_primus-Jensen 0 0.000 95 3159 wm-lh-S_intraparietal-and_Parietal_transverse 0 0.000 96 3160 wm-lh-S_occipital_anterior 0 0.000 97 3161 wm-lh-S_occipital_middle_and_Lunatus 0 0.000 98 3162 wm-lh-S_occipital_superior_and_transversalis 0 0.000 99 3163 wm-lh-S_occipito-temporal_lateral 0 0.000 100 3164 wm-lh-S_occipito-temporal_medial_and_S_Lingual 0 0.000 101 3165 wm-lh-S_orbital-H_shapped 0 0.000 102 3166 wm-lh-S_orbital_lateral 0 0.000 103 3167 wm-lh-S_orbital_medial-Or_olfactory 0 0.000 104 3168 wm-lh-S_paracentral 0 0.000 105 3169 wm-lh-S_parieto_occipital 0 0.000 106 3170 wm-lh-S_pericallosal 0 0.000 107 3171 wm-lh-S_postcentral 0 0.000 108 3172 wm-lh-S_precentral-Inferior-part 0 0.000 109 3173 wm-lh-S_precentral-Superior-part 0 0.000 110 3174 wm-lh-S_subcentral_ant 0 0.000 111 3175 wm-lh-S_subcentral_post 0 0.000 112 3176 wm-lh-S_suborbital 0 0.000 113 3177 wm-lh-S_subparietal 0 0.000 114 3178 wm-lh-S_supracingulate 0 0.000 115 3179 wm-lh-S_temporal_inferior 0 0.000 116 3180 wm-lh-S_temporal_superior 0 0.000 117 3181 wm-lh-S_temporal_transverse 0 0.000 118 4000 wm-rh-unknown 0 0.000 119 4001 wm-rh-bankssts 2578 2578.279 120 4002 wm-rh-caudalanteriorcingulate 2698 2698.122 121 4003 wm-rh-caudalmiddlefrontal 5670 5669.939 122 4004 wm-rh-corpuscallosum 0 0.000 123 4005 wm-rh-cuneus 2027 2027.484 124 4006 wm-rh-entorhinal 497 496.646 125 4007 wm-rh-fusiform 5602 5602.277 126 4008 wm-rh-inferiorparietal 10523 10523.017 127 4009 wm-rh-inferiortemporal 5501 5500.833 128 4010 wm-rh-isthmuscingulate 3510 3510.319 129 4011 wm-rh-lateraloccipital 7542 7541.954 130 4012 wm-rh-lateralorbitofrontal 6424 6423.971 131 4013 wm-rh-lingual 5747 5746.956 132 4014 wm-rh-medialorbitofrontal 3274 3274.488 133 4015 wm-rh-middletemporal 5782 5782.395 134 4016 wm-rh-parahippocampal 1358 1357.597 135 4017 wm-rh-paracentral 3403 3402.890 136 4018 wm-rh-parsopercularis 2571 2571.448 137 4019 wm-rh-parsorbitalis 1196 1195.591 138 4020 wm-rh-parstriangularis 3460 3459.772 139 4021 wm-rh-pericalcarine 3000 2999.877 140 4022 wm-rh-postcentral 7369 7368.791 141 4023 wm-rh-posteriorcingulate 4254 4253.954 142 4024 wm-rh-precentral 12743 12743.141 143 4025 wm-rh-precuneus 9065 9064.617 144 4026 wm-rh-rostralanteriorcingulate 1706 1705.727 145 4027 wm-rh-rostralmiddlefrontal 10663 10663.374 146 4028 wm-rh-superiorfrontal 14992 14992.078 147 4029 wm-rh-superiorparietal 11557 11557.413 148 4030 wm-rh-superiortemporal 5777 5777.454 149 4031 wm-rh-supramarginal 9870 9870.178 150 4032 wm-rh-frontalpole 219 219.446 151 4033 wm-rh-temporalpole 570 569.842 152 4034 wm-rh-transversetemporal 515 514.508 153 4035 wm-rh-insula 9197 9197.396 154 4100 wm-rh-Unknown 0 0.000 155 4101 wm-rh-Corpus_callosum 0 0.000 156 4102 wm-rh-G_and_S_Insula_ONLY_AVERAGE 0 0.000 157 4103 wm-rh-G_cingulate-Isthmus 0 0.000 158 4104 wm-rh-G_cingulate-Main_part 0 0.000 159 4105 wm-rh-G_cuneus 0 0.000 160 4106 wm-rh-G_frontal_inf-Opercular_part 0 0.000 161 4107 wm-rh-G_frontal_inf-Orbital_part 0 0.000 162 4108 wm-rh-G_frontal_inf-Triangular_part 0 0.000 163 4109 wm-rh-G_frontal_middle 0 0.000 164 4110 wm-rh-G_frontal_superior 0 0.000 165 4111 wm-rh-G_frontomarginal 0 0.000 166 4112 wm-rh-G_insular_long 0 0.000 167 4113 wm-rh-G_insular_short 0 0.000 168 4114 wm-rh-G_and_S_occipital_inferior 0 0.000 169 4115 wm-rh-G_occipital_middle 0 0.000 170 4116 wm-rh-G_occipital_superior 0 0.000 171 4117 wm-rh-G_occipit-temp_lat-Or_fusiform 0 0.000 172 4118 wm-rh-G_occipit-temp_med-Lingual_part 0 0.000 173 4119 wm-rh-G_occipit-temp_med-Parahippocampal_part 0 0.000 174 4120 wm-rh-G_orbital 0 0.000 175 4121 wm-rh-G_paracentral 0 0.000 176 4122 wm-rh-G_parietal_inferior-Angular_part 0 0.000 177 4123 wm-rh-G_parietal_inferior-Supramarginal_part 0 0.000 178 4124 wm-rh-G_parietal_superior 0 0.000 179 4125 wm-rh-G_postcentral 0 0.000 180 4126 wm-rh-G_precentral 0 0.000 181 4127 wm-rh-G_precuneus 0 0.000 182 4128 wm-rh-G_rectus 0 0.000 183 4129 wm-rh-G_subcallosal 0 0.000 184 4130 wm-rh-G_subcentral 0 0.000 185 4131 wm-rh-G_temporal_inferior 0 0.000 186 4132 wm-rh-G_temporal_middle 0 0.000 187 4133 wm-rh-G_temp_sup-G_temp_transv_and_interm_S 0 0.000 188 4134 wm-rh-G_temp_sup-Lateral_aspect 0 0.000 189 4135 wm-rh-G_temp_sup-Planum_polare 0 0.000 190 4136 wm-rh-G_temp_sup-Planum_tempolare 0 0.000 191 4137 wm-rh-G_and_S_transverse_frontopolar 0 0.000 192 4138 wm-rh-Lat_Fissure-ant_sgt-ramus_horizontal 0 0.000 193 4139 wm-rh-Lat_Fissure-ant_sgt-ramus_vertical 0 0.000 194 4140 wm-rh-Lat_Fissure-post_sgt 0 0.000 195 4141 wm-rh-Medial_wall 0 0.000 196 4142 wm-rh-Pole_occipital 0 0.000 197 4143 wm-rh-Pole_temporal 0 0.000 198 4144 wm-rh-S_calcarine 0 0.000 199 4145 wm-rh-S_central 0 0.000 200 4146 wm-rh-S_central_insula 0 0.000 201 4147 wm-rh-S_cingulate-Main_part_and_Intracingulate 0 0.000 202 4148 wm-rh-S_cingulate-Marginalis_part 0 0.000 203 4149 wm-rh-S_circular_insula_anterior 0 0.000 204 4150 wm-rh-S_circular_insula_inferior 0 0.000 205 4151 wm-rh-S_circular_insula_superior 0 0.000 206 4152 wm-rh-S_collateral_transverse_ant 0 0.000 207 4153 wm-rh-S_collateral_transverse_post 0 0.000 208 4154 wm-rh-S_frontal_inferior 0 0.000 209 4155 wm-rh-S_frontal_middle 0 0.000 210 4156 wm-rh-S_frontal_superior 0 0.000 211 4157 wm-rh-S_frontomarginal 0 0.000 212 4158 wm-rh-S_intermedius_primus-Jensen 0 0.000 213 4159 wm-rh-S_intraparietal-and_Parietal_transverse 0 0.000 214 4160 wm-rh-S_occipital_anterior 0 0.000 215 4161 wm-rh-S_occipital_middle_and_Lunatus 0 0.000 216 4162 wm-rh-S_occipital_superior_and_transversalis 0 0.000 217 4163 wm-rh-S_occipito-temporal_lateral 0 0.000 218 4164 wm-rh-S_occipito-temporal_medial_and_S_Lingual 0 0.000 219 4165 wm-rh-S_orbital-H_shapped 0 0.000 220 4166 wm-rh-S_orbital_lateral 0 0.000 221 4167 wm-rh-S_orbital_medial-Or_olfactory 0 0.000 222 4168 wm-rh-S_paracentral 0 0.000 223 4169 wm-rh-S_parieto_occipital 0 0.000 224 4170 wm-rh-S_pericallosal 0 0.000 225 4171 wm-rh-S_postcentral 0 0.000 226 4172 wm-rh-S_precentral-Inferior-part 0 0.000 227 4173 wm-rh-S_precentral-Superior-part 0 0.000 228 4174 wm-rh-S_subcentral_ant 0 0.000 229 4175 wm-rh-S_subcentral_post 0 0.000 230 4176 wm-rh-S_suborbital 0 0.000 231 4177 wm-rh-S_subparietal 0 0.000 232 4178 wm-rh-S_supracingulate 0 0.000 233 4179 wm-rh-S_temporal_inferior 0 0.000 234 4180 wm-rh-S_temporal_superior 0 0.000 235 4181 wm-rh-S_temporal_transverse 0 0.000 236 5001 Left-UnsegmentedWhiteMatter 29272 29271.889 237 5002 Right-UnsegmentedWhiteMatter 27991 27991.361 238 13100 wm_lh_Unknown 0 0.000 239 13101 wm_lh_G_and_S_frontomargin 0 0.000 240 13102 wm_lh_G_and_S_occipital_inf 0 0.000 241 13103 wm_lh_G_and_S_paracentral 0 0.000 242 13104 wm_lh_G_and_S_subcentral 0 0.000 243 13105 wm_lh_G_and_S_transv_frontopol 0 0.000 244 13106 wm_lh_G_and_S_cingul-Ant 0 0.000 245 13107 wm_lh_G_and_S_cingul-Mid-Ant 0 0.000 246 13108 wm_lh_G_and_S_cingul-Mid-Post 0 0.000 247 13109 wm_lh_G_cingul-Post-dorsal 0 0.000 248 13110 wm_lh_G_cingul-Post-ventral 0 0.000 249 13111 wm_lh_G_cuneus 0 0.000 250 13112 wm_lh_G_front_inf-Opercular 0 0.000 251 13113 wm_lh_G_front_inf-Orbital 0 0.000 252 13114 wm_lh_G_front_inf-Triangul 0 0.000 253 13115 wm_lh_G_front_middle 0 0.000 254 13116 wm_lh_G_front_sup 0 0.000 255 13117 wm_lh_G_Ins_lg_and_S_cent_ins 0 0.000 256 13118 wm_lh_G_insular_short 0 0.000 257 13119 wm_lh_G_occipital_middle 0 0.000 258 13120 wm_lh_G_occipital_sup 0 0.000 259 13121 wm_lh_G_oc-temp_lat-fusifor 0 0.000 260 13122 wm_lh_G_oc-temp_med-Lingual 0 0.000 261 13123 wm_lh_G_oc-temp_med-Parahip 0 0.000 262 13124 wm_lh_G_orbital 0 0.000 263 13125 wm_lh_G_pariet_inf-Angular 0 0.000 264 13126 wm_lh_G_pariet_inf-Supramar 0 0.000 265 13127 wm_lh_G_parietal_sup 0 0.000 266 13128 wm_lh_G_postcentral 0 0.000 267 13129 wm_lh_G_precentral 0 0.000 268 13130 wm_lh_G_precuneus 0 0.000 269 13131 wm_lh_G_rectus 0 0.000 270 13132 wm_lh_G_subcallosal 0 0.000 271 13133 wm_lh_G_temp_sup-G_T_transv 0 0.000 272 13134 wm_lh_G_temp_sup-Lateral 0 0.000 273 13135 wm_lh_G_temp_sup-Plan_polar 0 0.000 274 13136 wm_lh_G_temp_sup-Plan_tempo 0 0.000 275 13137 wm_lh_G_temporal_inf 0 0.000 276 13138 wm_lh_G_temporal_middle 0 0.000 277 13139 wm_lh_Lat_Fis-ant-Horizont 0 0.000 278 13140 wm_lh_Lat_Fis-ant-Vertical 0 0.000 279 13141 wm_lh_Lat_Fis-post 0 0.000 280 13142 wm_lh_Medial_wall 0 0.000 281 13143 wm_lh_Pole_occipital 0 0.000 282 13144 wm_lh_Pole_temporal 0 0.000 283 13145 wm_lh_S_calcarine 0 0.000 284 13146 wm_lh_S_central 0 0.000 285 13147 wm_lh_S_cingul-Marginalis 0 0.000 286 13148 wm_lh_S_circular_insula_ant 0 0.000 287 13149 wm_lh_S_circular_insula_inf 0 0.000 288 13150 wm_lh_S_circular_insula_sup 0 0.000 289 13151 wm_lh_S_collat_transv_ant 0 0.000 290 13152 wm_lh_S_collat_transv_post 0 0.000 291 13153 wm_lh_S_front_inf 0 0.000 292 13154 wm_lh_S_front_middle 0 0.000 293 13155 wm_lh_S_front_sup 0 0.000 294 13156 wm_lh_S_interm_prim-Jensen 0 0.000 295 13157 wm_lh_S_intrapariet_and_P_trans 0 0.000 296 13158 wm_lh_S_oc_middle_and_Lunatus 0 0.000 297 13159 wm_lh_S_oc_sup_and_transversal 0 0.000 298 13160 wm_lh_S_occipital_ant 0 0.000 299 13161 wm_lh_S_oc-temp_lat 0 0.000 300 13162 wm_lh_S_oc-temp_med_and_Lingual 0 0.000 301 13163 wm_lh_S_orbital_lateral 0 0.000 302 13164 wm_lh_S_orbital_med-olfact 0 0.000 303 13165 wm_lh_S_orbital-H_Shaped 0 0.000 304 13166 wm_lh_S_parieto_occipital 0 0.000 305 13167 wm_lh_S_pericallosal 0 0.000 306 13168 wm_lh_S_postcentral 0 0.000 307 13169 wm_lh_S_precentral-inf-part 0 0.000 308 13170 wm_lh_S_precentral-sup-part 0 0.000 309 13171 wm_lh_S_suborbital 0 0.000 310 13172 wm_lh_S_subparietal 0 0.000 311 13173 wm_lh_S_temporal_inf 0 0.000 312 13174 wm_lh_S_temporal_sup 0 0.000 313 13175 wm_lh_S_temporal_transverse 0 0.000 314 14100 wm_rh_Unknown 0 0.000 315 14101 wm_rh_G_and_S_frontomargin 0 0.000 316 14102 wm_rh_G_and_S_occipital_inf 0 0.000 317 14103 wm_rh_G_and_S_paracentral 0 0.000 318 14104 wm_rh_G_and_S_subcentral 0 0.000 319 14105 wm_rh_G_and_S_transv_frontopol 0 0.000 320 14106 wm_rh_G_and_S_cingul-Ant 0 0.000 321 14107 wm_rh_G_and_S_cingul-Mid-Ant 0 0.000 322 14108 wm_rh_G_and_S_cingul-Mid-Post 0 0.000 323 14109 wm_rh_G_cingul-Post-dorsal 0 0.000 324 14110 wm_rh_G_cingul-Post-ventral 0 0.000 325 14111 wm_rh_G_cuneus 0 0.000 326 14112 wm_rh_G_front_inf-Opercular 0 0.000 327 14113 wm_rh_G_front_inf-Orbital 0 0.000 328 14114 wm_rh_G_front_inf-Triangul 0 0.000 329 14115 wm_rh_G_front_middle 0 0.000 330 14116 wm_rh_G_front_sup 0 0.000 331 14117 wm_rh_G_Ins_lg_and_S_cent_ins 0 0.000 332 14118 wm_rh_G_insular_short 0 0.000 333 14119 wm_rh_G_occipital_middle 0 0.000 334 14120 wm_rh_G_occipital_sup 0 0.000 335 14121 wm_rh_G_oc-temp_lat-fusifor 0 0.000 336 14122 wm_rh_G_oc-temp_med-Lingual 0 0.000 337 14123 wm_rh_G_oc-temp_med-Parahip 0 0.000 338 14124 wm_rh_G_orbital 0 0.000 339 14125 wm_rh_G_pariet_inf-Angular 0 0.000 340 14126 wm_rh_G_pariet_inf-Supramar 0 0.000 341 14127 wm_rh_G_parietal_sup 0 0.000 342 14128 wm_rh_G_postcentral 0 0.000 343 14129 wm_rh_G_precentral 0 0.000 344 14130 wm_rh_G_precuneus 0 0.000 345 14131 wm_rh_G_rectus 0 0.000 346 14132 wm_rh_G_subcallosal 0 0.000 347 14133 wm_rh_G_temp_sup-G_T_transv 0 0.000 348 14134 wm_rh_G_temp_sup-Lateral 0 0.000 349 14135 wm_rh_G_temp_sup-Plan_polar 0 0.000 350 14136 wm_rh_G_temp_sup-Plan_tempo 0 0.000 351 14137 wm_rh_G_temporal_inf 0 0.000 352 14138 wm_rh_G_temporal_middle 0 0.000 353 14139 wm_rh_Lat_Fis-ant-Horizont 0 0.000 354 14140 wm_rh_Lat_Fis-ant-Vertical 0 0.000 355 14141 wm_rh_Lat_Fis-post 0 0.000 356 14142 wm_rh_Medial_wall 0 0.000 357 14143 wm_rh_Pole_occipital 0 0.000 358 14144 wm_rh_Pole_temporal 0 0.000 359 14145 wm_rh_S_calcarine 0 0.000 360 14146 wm_rh_S_central 0 0.000 361 14147 wm_rh_S_cingul-Marginalis 0 0.000 362 14148 wm_rh_S_circular_insula_ant 0 0.000 363 14149 wm_rh_S_circular_insula_inf 0 0.000 364 14150 wm_rh_S_circular_insula_sup 0 0.000 365 14151 wm_rh_S_collat_transv_ant 0 0.000 366 14152 wm_rh_S_collat_transv_post 0 0.000 367 14153 wm_rh_S_front_inf 0 0.000 368 14154 wm_rh_S_front_middle 0 0.000 369 14155 wm_rh_S_front_sup 0 0.000 370 14156 wm_rh_S_interm_prim-Jensen 0 0.000 371 14157 wm_rh_S_intrapariet_and_P_trans 0 0.000 372 14158 wm_rh_S_oc_middle_and_Lunatus 0 0.000 373 14159 wm_rh_S_oc_sup_and_transversal 0 0.000 374 14160 wm_rh_S_occipital_ant 0 0.000 375 14161 wm_rh_S_oc-temp_lat 0 0.000 376 14162 wm_rh_S_oc-temp_med_and_Lingual 0 0.000 377 14163 wm_rh_S_orbital_lateral 0 0.000 378 14164 wm_rh_S_orbital_med-olfact 0 0.000 379 14165 wm_rh_S_orbital-H_Shaped 0 0.000 380 14166 wm_rh_S_parieto_occipital 0 0.000 381 14167 wm_rh_S_pericallosal 0 0.000 382 14168 wm_rh_S_postcentral 0 0.000 383 14169 wm_rh_S_precentral-inf-part 0 0.000 384 14170 wm_rh_S_precentral-sup-part 0 0.000 385 14171 wm_rh_S_suborbital 0 0.000 386 14172 wm_rh_S_subparietal 0 0.000 387 14173 wm_rh_S_temporal_inf 0 0.000 388 14174 wm_rh_S_temporal_sup 0 0.000 389 14175 wm_rh_S_temporal_transverse 0 0.000 Reporting on 70 segmentations mri_segstats done /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/label #-------------------------------------------- #@# BA Labels lh Mon Nov 17 19:31:48 EST 2025 INFO: fsaverage subject does not have perirhinal labels! cd /autofs/space/hope_002/users/PBR28_HOPE/data/fs; rm -Rf fsaverage; cd - INFO: Creating symlink to fsaverage subject... cd /autofs/space/hope_002/users/PBR28_HOPE/data/fs; ln -s /usr/local/freesurfer/stable5_3_0/subjects/fsaverage; cd - mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA1.label --trgsubject PBRHOPE_HOPE086_PETMR --trglabel ./lh.BA1.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE086_PETMR trglabel = ./lh.BA1.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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 126893 Number of reverse mapping hits = 347 Checking for and removing duplicates Writing label file ./lh.BA1.label 4476 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA2.label --trgsubject PBRHOPE_HOPE086_PETMR --trglabel ./lh.BA2.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA2.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE086_PETMR trglabel = ./lh.BA2.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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 126893 Number of reverse mapping hits = 648 Checking for and removing duplicates Writing label file ./lh.BA2.label 8557 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA3a.label --trgsubject PBRHOPE_HOPE086_PETMR --trglabel ./lh.BA3a.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA3a.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE086_PETMR trglabel = ./lh.BA3a.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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 126893 Number of reverse mapping hits = 170 Checking for and removing duplicates Writing label file ./lh.BA3a.label 4247 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA3b.label --trgsubject PBRHOPE_HOPE086_PETMR --trglabel ./lh.BA3b.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA3b.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE086_PETMR trglabel = ./lh.BA3b.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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 126893 Number of reverse mapping hits = 414 Checking for and removing duplicates Writing label file ./lh.BA3b.label 6397 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA4a.label --trgsubject PBRHOPE_HOPE086_PETMR --trglabel ./lh.BA4a.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA4a.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE086_PETMR trglabel = ./lh.BA4a.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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 126893 Number of reverse mapping hits = 524 Checking for and removing duplicates Writing label file ./lh.BA4a.label 6308 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA4p.label --trgsubject PBRHOPE_HOPE086_PETMR --trglabel ./lh.BA4p.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA4p.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE086_PETMR trglabel = ./lh.BA4p.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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 126893 Number of reverse mapping hits = 298 Checking for and removing duplicates Writing label file ./lh.BA4p.label 4368 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA6.label --trgsubject PBRHOPE_HOPE086_PETMR --trglabel ./lh.BA6.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA6.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE086_PETMR trglabel = ./lh.BA6.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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 126893 Number of reverse mapping hits = 1410 Checking for and removing duplicates Writing label file ./lh.BA6.label 14999 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA44.label --trgsubject PBRHOPE_HOPE086_PETMR --trglabel ./lh.BA44.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA44.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE086_PETMR trglabel = ./lh.BA44.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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 126893 Number of reverse mapping hits = 395 Checking for and removing duplicates Writing label file ./lh.BA44.label 4576 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA45.label --trgsubject PBRHOPE_HOPE086_PETMR --trglabel ./lh.BA45.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA45.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE086_PETMR trglabel = ./lh.BA45.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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 126893 Number of reverse mapping hits = 363 Checking for and removing duplicates Writing label file ./lh.BA45.label 3785 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.V1.label --trgsubject PBRHOPE_HOPE086_PETMR --trglabel ./lh.V1.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.V1.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE086_PETMR trglabel = ./lh.V1.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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 126893 Number of reverse mapping hits = 1065 Checking for and removing duplicates Writing label file ./lh.V1.label 5706 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.V2.label --trgsubject PBRHOPE_HOPE086_PETMR --trglabel ./lh.V2.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.V2.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE086_PETMR trglabel = ./lh.V2.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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 126893 Number of reverse mapping hits = 2560 Checking for and removing duplicates Writing label file ./lh.V2.label 10674 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.MT.label --trgsubject PBRHOPE_HOPE086_PETMR --trglabel ./lh.MT.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.MT.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE086_PETMR trglabel = ./lh.MT.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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 126893 Number of reverse mapping hits = 444 Checking for and removing duplicates Writing label file ./lh.MT.label 2462 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.perirhinal.label --trgsubject PBRHOPE_HOPE086_PETMR --trglabel ./lh.perirhinal.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.perirhinal.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE086_PETMR trglabel = ./lh.perirhinal.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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 126893 Number of reverse mapping hits = 76 Checking for and removing duplicates Writing label file ./lh.perirhinal.label 1275 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA1.thresh.label --trgsubject PBRHOPE_HOPE086_PETMR --trglabel ./lh.BA1.thresh.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA1.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE086_PETMR trglabel = ./lh.BA1.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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 126893 Number of reverse mapping hits = 67 Checking for and removing duplicates Writing label file ./lh.BA1.thresh.label 1081 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA2.thresh.label --trgsubject PBRHOPE_HOPE086_PETMR --trglabel ./lh.BA2.thresh.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA2.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE086_PETMR trglabel = ./lh.BA2.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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 126893 Number of reverse mapping hits = 197 Checking for and removing duplicates Writing label file ./lh.BA2.thresh.label 2289 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA3a.thresh.label --trgsubject PBRHOPE_HOPE086_PETMR --trglabel ./lh.BA3a.thresh.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA3a.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE086_PETMR trglabel = ./lh.BA3a.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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 126893 Number of reverse mapping hits = 32 Checking for and removing duplicates Writing label file ./lh.BA3a.thresh.label 1536 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA3b.thresh.label --trgsubject PBRHOPE_HOPE086_PETMR --trglabel ./lh.BA3b.thresh.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA3b.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE086_PETMR trglabel = ./lh.BA3b.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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 126893 Number of reverse mapping hits = 115 Checking for and removing duplicates Writing label file ./lh.BA3b.thresh.label 2111 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA4a.thresh.label --trgsubject PBRHOPE_HOPE086_PETMR --trglabel ./lh.BA4a.thresh.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA4a.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE086_PETMR trglabel = ./lh.BA4a.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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 126893 Number of reverse mapping hits = 166 Checking for and removing duplicates Writing label file ./lh.BA4a.thresh.label 2485 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA4p.thresh.label --trgsubject PBRHOPE_HOPE086_PETMR --trglabel ./lh.BA4p.thresh.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA4p.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE086_PETMR trglabel = ./lh.BA4p.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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 126893 Number of reverse mapping hits = 72 Checking for and removing duplicates Writing label file ./lh.BA4p.thresh.label 1621 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA6.thresh.label --trgsubject PBRHOPE_HOPE086_PETMR --trglabel ./lh.BA6.thresh.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA6.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE086_PETMR trglabel = ./lh.BA6.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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 126893 Number of reverse mapping hits = 684 Checking for and removing duplicates Writing label file ./lh.BA6.thresh.label 7719 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA44.thresh.label --trgsubject PBRHOPE_HOPE086_PETMR --trglabel ./lh.BA44.thresh.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA44.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE086_PETMR trglabel = ./lh.BA44.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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 126893 Number of reverse mapping hits = 116 Checking for and removing duplicates Writing label file ./lh.BA44.thresh.label 2028 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA45.thresh.label --trgsubject PBRHOPE_HOPE086_PETMR --trglabel ./lh.BA45.thresh.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.BA45.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE086_PETMR trglabel = ./lh.BA45.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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 126893 Number of reverse mapping hits = 133 Checking for and removing duplicates Writing label file ./lh.BA45.thresh.label 1284 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.V1.thresh.label --trgsubject PBRHOPE_HOPE086_PETMR --trglabel ./lh.V1.thresh.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.V1.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE086_PETMR trglabel = ./lh.V1.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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 126893 Number of reverse mapping hits = 695 Checking for and removing duplicates Writing label file ./lh.V1.thresh.label 4100 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.V2.thresh.label --trgsubject PBRHOPE_HOPE086_PETMR --trglabel ./lh.V2.thresh.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.V2.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE086_PETMR trglabel = ./lh.V2.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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 126893 Number of reverse mapping hits = 1134 Checking for and removing duplicates Writing label file ./lh.V2.thresh.label 4468 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.MT.thresh.label --trgsubject PBRHOPE_HOPE086_PETMR --trglabel ./lh.MT.thresh.label --hemi lh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/lh.MT.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE086_PETMR trglabel = ./lh.MT.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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 126893 Number of reverse mapping hits = 81 Checking for and removing duplicates Writing label file ./lh.MT.thresh.label 594 mri_label2label: Done mris_label2annot --s PBRHOPE_HOPE086_PETMR --hemi lh --ctab /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --l lh.perirhinal.label --a BA --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt Number of ctab entries 14 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/label cmdline mris_label2annot --s PBRHOPE_HOPE086_PETMR --hemi lh --ctab /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --l lh.perirhinal.label --a BA --maxstatwinner --noverbose sysname Linux hostname r440-30.nmr.mgh.harvard.edu machine x86_64 user ek657 subject PBRHOPE_HOPE086_PETMR hemi lh SUBJECTS_DIR /autofs/space/hope_002/users/PBR28_HOPE/data/fs ColorTable /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt AnnotName BA nlables 13 LabelThresh 0 0.000000 Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.orig 1 1530880 BA1 2 16749699 BA2 3 16711680 BA3a 4 3368703 BA3b 5 1376196 BA4a 6 13382655 BA4p 7 10036737 BA6 8 2490521 BA44 9 39283 BA45 10 3993 V1 11 8508928 V2 12 10027163 MT 13 16422433 perirhinal Mapping unhit to unknown Found 87217 unhit vertices Writing annot to /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/label/lh.BA.annot mris_label2annot --s PBRHOPE_HOPE086_PETMR --hemi lh --ctab /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt --l lh.BA1.thresh.label --l lh.BA2.thresh.label --l lh.BA3a.thresh.label --l lh.BA3b.thresh.label --l lh.BA4a.thresh.label --l lh.BA4p.thresh.label --l lh.BA6.thresh.label --l lh.BA44.thresh.label --l lh.BA45.thresh.label --l lh.V1.thresh.label --l lh.V2.thresh.label --l lh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt Number of ctab entries 14 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/label cmdline mris_label2annot --s PBRHOPE_HOPE086_PETMR --hemi lh --ctab /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt --l lh.BA1.thresh.label --l lh.BA2.thresh.label --l lh.BA3a.thresh.label --l lh.BA3b.thresh.label --l lh.BA4a.thresh.label --l lh.BA4p.thresh.label --l lh.BA6.thresh.label --l lh.BA44.thresh.label --l lh.BA45.thresh.label --l lh.V1.thresh.label --l lh.V2.thresh.label --l lh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose sysname Linux hostname r440-30.nmr.mgh.harvard.edu machine x86_64 user ek657 subject PBRHOPE_HOPE086_PETMR hemi lh SUBJECTS_DIR /autofs/space/hope_002/users/PBR28_HOPE/data/fs ColorTable /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt AnnotName BA.thresh nlables 12 LabelThresh 0 0.000000 Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.orig 1 1530880 BA1 2 16749699 BA2 3 16711680 BA3a 4 3368703 BA3b 5 1376196 BA4a 6 13382655 BA4p 7 10036737 BA6 8 2490521 BA44 9 39283 BA45 10 3993 V1 11 8508928 V2 12 10027163 MT Mapping unhit to unknown Found 104205 unhit vertices Writing annot to /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/label/lh.BA.thresh.annot mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab PBRHOPE_HOPE086_PETMR lh white computing statistics for each annotation in ./lh.BA.annot. reading volume /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/wm.mgz... reading input surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.white... reading input pial surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.pial... reading input white surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt) Saving annotation colortable ./BA.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 1179 627 1548 1.918 0.475 0.154 0.084 29 4.8 BA1 4303 2795 5747 1.958 0.507 0.124 0.038 44 7.0 BA2 935 665 899 1.751 0.489 0.147 0.051 8 1.9 BA3a 2480 1572 3088 1.733 0.601 0.137 0.083 76 6.4 BA3b 1656 886 2548 2.472 0.569 0.150 0.179 151 9.2 BA4a 1211 761 1831 2.464 0.555 0.124 0.043 10 2.4 BA4p 9508 6024 17211 2.434 0.574 0.154 0.118 532 38.9 BA6 2160 1458 3900 2.356 0.494 0.142 0.056 30 5.2 BA44 2464 1710 4256 2.191 0.595 0.158 0.058 39 5.9 BA45 3025 1894 2954 1.515 0.431 0.155 0.075 51 9.3 V1 7863 4759 9855 1.914 0.539 0.158 0.066 140 22.4 V2 2010 1324 3048 2.139 0.428 0.143 0.054 91 4.9 MT 882 571 2398 3.120 1.052 0.126 0.051 12 2.0 perirhinal mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab PBRHOPE_HOPE086_PETMR lh white computing statistics for each annotation in ./lh.BA.thresh.annot. reading volume /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/wm.mgz... reading input surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.white... reading input pial surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.pial... reading input white surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt) Saving annotation colortable ./BA.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 743 345 892 1.905 0.480 0.157 0.091 20 3.1 BA1 1756 1099 2381 1.950 0.442 0.116 0.035 17 2.5 BA2 762 547 681 1.663 0.427 0.153 0.053 7 1.7 BA3a 1486 958 1435 1.433 0.396 0.116 0.047 12 2.3 BA3b 1580 851 2529 2.534 0.568 0.145 0.171 146 8.0 BA4a 1001 643 1463 2.443 0.570 0.128 0.049 9 2.2 BA4p 5435 3322 9590 2.442 0.616 0.149 0.143 438 24.0 BA6 1265 858 2424 2.438 0.444 0.154 0.069 21 3.8 BA44 997 677 1834 2.206 0.564 0.164 0.061 18 2.6 BA45 3302 2041 3306 1.542 0.425 0.157 0.075 57 10.6 V1 3876 2354 4595 1.854 0.535 0.169 0.071 79 11.4 V2 485 337 612 1.901 0.398 0.137 0.039 5 0.7 MT #-------------------------------------------- #@# BA Labels rh Mon Nov 17 19:34:24 EST 2025 mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA1.label --trgsubject PBRHOPE_HOPE086_PETMR --trglabel ./rh.BA1.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA1.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE086_PETMR trglabel = ./rh.BA1.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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 126155 Number of reverse mapping hits = 357 Checking for and removing duplicates Writing label file ./rh.BA1.label 4319 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA2.label --trgsubject PBRHOPE_HOPE086_PETMR --trglabel ./rh.BA2.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA2.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE086_PETMR trglabel = ./rh.BA2.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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 126155 Number of reverse mapping hits = 430 Checking for and removing duplicates Writing label file ./rh.BA2.label 7117 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA3a.label --trgsubject PBRHOPE_HOPE086_PETMR --trglabel ./rh.BA3a.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA3a.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE086_PETMR trglabel = ./rh.BA3a.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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 126155 Number of reverse mapping hits = 139 Checking for and removing duplicates Writing label file ./rh.BA3a.label 4119 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA3b.label --trgsubject PBRHOPE_HOPE086_PETMR --trglabel ./rh.BA3b.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA3b.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE086_PETMR trglabel = ./rh.BA3b.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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 126155 Number of reverse mapping hits = 323 Checking for and removing duplicates Writing label file ./rh.BA3b.label 4845 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA4a.label --trgsubject PBRHOPE_HOPE086_PETMR --trglabel ./rh.BA4a.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA4a.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE086_PETMR trglabel = ./rh.BA4a.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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 126155 Number of reverse mapping hits = 415 Checking for and removing duplicates Writing label file ./rh.BA4a.label 6162 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA4p.label --trgsubject PBRHOPE_HOPE086_PETMR --trglabel ./rh.BA4p.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA4p.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE086_PETMR trglabel = ./rh.BA4p.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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 126155 Number of reverse mapping hits = 279 Checking for and removing duplicates Writing label file ./rh.BA4p.label 4752 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA6.label --trgsubject PBRHOPE_HOPE086_PETMR --trglabel ./rh.BA6.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA6.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE086_PETMR trglabel = ./rh.BA6.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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 126155 Number of reverse mapping hits = 1038 Checking for and removing duplicates Writing label file ./rh.BA6.label 13294 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA44.label --trgsubject PBRHOPE_HOPE086_PETMR --trglabel ./rh.BA44.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA44.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE086_PETMR trglabel = ./rh.BA44.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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 126155 Number of reverse mapping hits = 625 Checking for and removing duplicates Writing label file ./rh.BA44.label 7537 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA45.label --trgsubject PBRHOPE_HOPE086_PETMR --trglabel ./rh.BA45.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA45.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE086_PETMR trglabel = ./rh.BA45.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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 126155 Number of reverse mapping hits = 1048 Checking for and removing duplicates Writing label file ./rh.BA45.label 6403 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.V1.label --trgsubject PBRHOPE_HOPE086_PETMR --trglabel ./rh.V1.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.V1.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE086_PETMR trglabel = ./rh.V1.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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 126155 Number of reverse mapping hits = 1329 Checking for and removing duplicates Writing label file ./rh.V1.label 6056 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.V2.label --trgsubject PBRHOPE_HOPE086_PETMR --trglabel ./rh.V2.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.V2.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE086_PETMR trglabel = ./rh.V2.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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 126155 Number of reverse mapping hits = 2598 Checking for and removing duplicates Writing label file ./rh.V2.label 10614 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.MT.label --trgsubject PBRHOPE_HOPE086_PETMR --trglabel ./rh.MT.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.MT.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE086_PETMR trglabel = ./rh.MT.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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 126155 Number of reverse mapping hits = 98 Checking for and removing duplicates Writing label file ./rh.MT.label 2030 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.perirhinal.label --trgsubject PBRHOPE_HOPE086_PETMR --trglabel ./rh.perirhinal.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.perirhinal.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE086_PETMR trglabel = ./rh.perirhinal.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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 126155 Number of reverse mapping hits = 23 Checking for and removing duplicates Writing label file ./rh.perirhinal.label 775 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA1.thresh.label --trgsubject PBRHOPE_HOPE086_PETMR --trglabel ./rh.BA1.thresh.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA1.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE086_PETMR trglabel = ./rh.BA1.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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 126155 Number of reverse mapping hits = 88 Checking for and removing duplicates Writing label file ./rh.BA1.thresh.label 964 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA2.thresh.label --trgsubject PBRHOPE_HOPE086_PETMR --trglabel ./rh.BA2.thresh.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA2.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE086_PETMR trglabel = ./rh.BA2.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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 126155 Number of reverse mapping hits = 131 Checking for and removing duplicates Writing label file ./rh.BA2.thresh.label 2819 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA3a.thresh.label --trgsubject PBRHOPE_HOPE086_PETMR --trglabel ./rh.BA3a.thresh.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA3a.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE086_PETMR trglabel = ./rh.BA3a.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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 126155 Number of reverse mapping hits = 28 Checking for and removing duplicates Writing label file ./rh.BA3a.thresh.label 1726 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA3b.thresh.label --trgsubject PBRHOPE_HOPE086_PETMR --trglabel ./rh.BA3b.thresh.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA3b.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE086_PETMR trglabel = ./rh.BA3b.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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 126155 Number of reverse mapping hits = 198 Checking for and removing duplicates Writing label file ./rh.BA3b.thresh.label 2381 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA4a.thresh.label --trgsubject PBRHOPE_HOPE086_PETMR --trglabel ./rh.BA4a.thresh.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA4a.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE086_PETMR trglabel = ./rh.BA4a.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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 126155 Number of reverse mapping hits = 61 Checking for and removing duplicates Writing label file ./rh.BA4a.thresh.label 1449 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA4p.thresh.label --trgsubject PBRHOPE_HOPE086_PETMR --trglabel ./rh.BA4p.thresh.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA4p.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE086_PETMR trglabel = ./rh.BA4p.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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 126155 Number of reverse mapping hits = 83 Checking for and removing duplicates Writing label file ./rh.BA4p.thresh.label 1572 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA6.thresh.label --trgsubject PBRHOPE_HOPE086_PETMR --trglabel ./rh.BA6.thresh.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA6.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE086_PETMR trglabel = ./rh.BA6.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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 126155 Number of reverse mapping hits = 592 Checking for and removing duplicates Writing label file ./rh.BA6.thresh.label 7551 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA44.thresh.label --trgsubject PBRHOPE_HOPE086_PETMR --trglabel ./rh.BA44.thresh.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA44.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE086_PETMR trglabel = ./rh.BA44.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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 126155 Number of reverse mapping hits = 65 Checking for and removing duplicates Writing label file ./rh.BA44.thresh.label 1077 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA45.thresh.label --trgsubject PBRHOPE_HOPE086_PETMR --trglabel ./rh.BA45.thresh.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.BA45.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE086_PETMR trglabel = ./rh.BA45.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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 126155 Number of reverse mapping hits = 209 Checking for and removing duplicates Writing label file ./rh.BA45.thresh.label 1387 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.V1.thresh.label --trgsubject PBRHOPE_HOPE086_PETMR --trglabel ./rh.V1.thresh.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.V1.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE086_PETMR trglabel = ./rh.V1.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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 126155 Number of reverse mapping hits = 805 Checking for and removing duplicates Writing label file ./rh.V1.thresh.label 4037 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.V2.thresh.label --trgsubject PBRHOPE_HOPE086_PETMR --trglabel ./rh.V2.thresh.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.V2.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE086_PETMR trglabel = ./rh.V2.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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 126155 Number of reverse mapping hits = 1479 Checking for and removing duplicates Writing label file ./rh.V2.thresh.label 4916 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.MT.thresh.label --trgsubject PBRHOPE_HOPE086_PETMR --trglabel ./rh.MT.thresh.label --hemi rh --regmethod surface srclabel = /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/label/rh.MT.thresh.label srcsubject = fsaverage trgsubject = PBRHOPE_HOPE086_PETMR trglabel = ./rh.MT.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 /autofs/space/hope_002/users/PBR28_HOPE/data/fs FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.white Reading target registration /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/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 126155 Number of reverse mapping hits = 10 Checking for and removing duplicates Writing label file ./rh.MT.thresh.label 278 mri_label2label: Done mris_label2annot --s PBRHOPE_HOPE086_PETMR --hemi rh --ctab /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt --l rh.BA1.label --l rh.BA2.label --l rh.BA3a.label --l rh.BA3b.label --l rh.BA4a.label --l rh.BA4p.label --l rh.BA6.label --l rh.BA44.label --l rh.BA45.label --l rh.V1.label --l rh.V2.label --l rh.MT.label --l rh.perirhinal.label --a BA --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt Number of ctab entries 14 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/label cmdline mris_label2annot --s PBRHOPE_HOPE086_PETMR --hemi rh --ctab /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt --l rh.BA1.label --l rh.BA2.label --l rh.BA3a.label --l rh.BA3b.label --l rh.BA4a.label --l rh.BA4p.label --l rh.BA6.label --l rh.BA44.label --l rh.BA45.label --l rh.V1.label --l rh.V2.label --l rh.MT.label --l rh.perirhinal.label --a BA --maxstatwinner --noverbose sysname Linux hostname r440-30.nmr.mgh.harvard.edu machine x86_64 user ek657 subject PBRHOPE_HOPE086_PETMR hemi rh SUBJECTS_DIR /autofs/space/hope_002/users/PBR28_HOPE/data/fs ColorTable /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt AnnotName BA nlables 13 LabelThresh 0 0.000000 Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.orig 1 1530880 BA1 2 16749699 BA2 3 16711680 BA3a 4 3368703 BA3b 5 1376196 BA4a 6 13382655 BA4p 7 10036737 BA6 8 2490521 BA44 9 39283 BA45 10 3993 V1 11 8508928 V2 12 10027163 MT 13 16422433 perirhinal Mapping unhit to unknown Found 87322 unhit vertices Writing annot to /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/label/rh.BA.annot mris_label2annot --s PBRHOPE_HOPE086_PETMR --hemi rh --ctab /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt --l rh.BA1.thresh.label --l rh.BA2.thresh.label --l rh.BA3a.thresh.label --l rh.BA3b.thresh.label --l rh.BA4a.thresh.label --l rh.BA4p.thresh.label --l rh.BA6.thresh.label --l rh.BA44.thresh.label --l rh.BA45.thresh.label --l rh.V1.thresh.label --l rh.V2.thresh.label --l rh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt Number of ctab entries 14 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/label cmdline mris_label2annot --s PBRHOPE_HOPE086_PETMR --hemi rh --ctab /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt --l rh.BA1.thresh.label --l rh.BA2.thresh.label --l rh.BA3a.thresh.label --l rh.BA3b.thresh.label --l rh.BA4a.thresh.label --l rh.BA4p.thresh.label --l rh.BA6.thresh.label --l rh.BA44.thresh.label --l rh.BA45.thresh.label --l rh.V1.thresh.label --l rh.V2.thresh.label --l rh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose sysname Linux hostname r440-30.nmr.mgh.harvard.edu machine x86_64 user ek657 subject PBRHOPE_HOPE086_PETMR hemi rh SUBJECTS_DIR /autofs/space/hope_002/users/PBR28_HOPE/data/fs ColorTable /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt AnnotName BA.thresh nlables 12 LabelThresh 0 0.000000 Loading /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.orig 1 1530880 BA1 2 16749699 BA2 3 16711680 BA3a 4 3368703 BA3b 5 1376196 BA4a 6 13382655 BA4p 7 10036737 BA6 8 2490521 BA44 9 39283 BA45 10 3993 V1 11 8508928 V2 12 10027163 MT Mapping unhit to unknown Found 104229 unhit vertices Writing annot to /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/label/rh.BA.thresh.annot mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab PBRHOPE_HOPE086_PETMR rh white computing statistics for each annotation in ./rh.BA.annot. reading volume /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/wm.mgz... reading input surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.white... reading input pial surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.pial... reading input white surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt) Saving annotation colortable ./BA.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 1039 513 1439 2.069 0.415 0.146 0.170 55 4.5 BA1 3296 2209 4432 1.963 0.435 0.111 0.031 23 4.3 BA2 972 689 911 1.608 0.416 0.142 0.055 11 2.6 BA3a 2168 1339 2510 1.675 0.479 0.115 0.041 24 4.0 BA3b 1476 754 2447 2.773 0.428 0.138 0.169 114 7.8 BA4a 1198 782 1819 2.439 0.554 0.126 0.051 13 2.4 BA4p 7616 4932 14127 2.452 0.577 0.165 0.098 208 31.6 BA6 3226 2149 5058 2.179 0.608 0.135 0.043 38 5.7 BA44 4484 2971 7650 2.162 0.666 0.158 0.066 79 11.7 BA45 3584 2296 3842 1.606 0.444 0.177 0.079 100 12.7 V1 7960 4769 9808 1.962 0.562 0.152 0.119 157 21.7 V2 1331 863 2009 2.352 0.506 0.135 0.045 19 2.4 MT 483 320 1602 3.285 0.978 0.108 0.044 6 0.8 perirhinal mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab PBRHOPE_HOPE086_PETMR rh white computing statistics for each annotation in ./rh.BA.thresh.annot. reading volume /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/wm.mgz... reading input surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.white... reading input pial surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.pial... reading input white surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /usr/local/freesurfer/stable5_3_0/average/colortable_BA.txt) Saving annotation colortable ./BA.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 708 331 931 2.015 0.394 0.149 0.210 49 3.6 BA1 1918 1270 2627 1.938 0.439 0.102 0.026 12 2.2 BA2 872 623 780 1.590 0.373 0.141 0.056 10 2.4 BA3a 1778 1137 1868 1.561 0.412 0.107 0.036 17 3.0 BA3b 751 363 1330 2.861 0.361 0.137 0.232 57 4.1 BA4a 1007 670 1572 2.457 0.576 0.133 0.055 13 2.4 BA4p 4922 3157 9043 2.455 0.598 0.163 0.102 146 22.2 BA6 728 480 1097 2.024 0.443 0.142 0.049 9 1.5 BA44 1170 766 2236 2.320 0.492 0.164 0.070 22 3.3 BA45 3396 2192 3540 1.583 0.434 0.176 0.077 95 12.1 V1 4501 2694 5253 1.835 0.492 0.161 0.171 107 14.4 V2 175 125 258 2.188 0.410 0.133 0.029 2 0.2 MT /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label lh Mon Nov 17 19:36:57 EST 2025 mris_spherical_average -erode 1 -orig white -t 0.4 -o PBRHOPE_HOPE086_PETMR label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label painting output onto subject PBRHOPE_HOPE086_PETMR. processing subject lh.EC_average... reading output surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.sphere.reg... eroding label 1 times before writing thresholding label stat at 0.400 before writing only 1 subject - copying statistics... writing label with 939 points to lh.entorhinal_exvivo.label... mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label PBRHOPE_HOPE086_PETMR lh white limiting computations to label ./lh.entorhinal_exvivo.label. reading volume /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/wm.mgz... reading input surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.white... reading input pial surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.pial... reading input white surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/lh.white... INFO: assuming MGZ format for volumes. 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 366 211 1059 3.162 1.237 0.157 0.178 15 2.0 ./lh.entorhinal_exvivo.label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label rh Mon Nov 17 19:37:08 EST 2025 mris_spherical_average -erode 1 -orig white -t 0.4 -o PBRHOPE_HOPE086_PETMR label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label painting output onto subject PBRHOPE_HOPE086_PETMR. processing subject rh.EC_average... reading output surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.sphere.reg... eroding label 1 times before writing thresholding label stat at 0.400 before writing only 1 subject - copying statistics... writing label with 679 points to rh.entorhinal_exvivo.label... mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label PBRHOPE_HOPE086_PETMR rh white limiting computations to label ./rh.entorhinal_exvivo.label. reading volume /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/mri/wm.mgz... reading input surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.white... reading input pial surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.pial... reading input white surface /autofs/space/hope_002/users/PBR28_HOPE/data/fs/PBRHOPE_HOPE086_PETMR/surf/rh.white... INFO: assuming MGZ format for volumes. 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 273 165 1011 3.584 0.732 0.123 0.052 5 0.5 ./rh.entorhinal_exvivo.label #------------------------------------------ Started at Mon Nov 17 12:32:23 EST 2025 Ended at Mon Nov 17 19:37:18 EST 2025 #@#%# recon-all-run-time-hours 7.082 recon-all -s PBRHOPE_HOPE086_PETMR finished without error at Mon Nov 17 19:37:18 EST 2025