Sun May 10 20:55:29 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1 /opt/local/freesurfer-6.0/x86_64/bin/recon-all -i /home/server1/data/frames_analysis/subjects/brain/subject7/V1/V1_subject7_t1/V1_subject7_t1.nii.gz -T2 /home/server1/data/frames_analysis/subjects/brain/subject7/V1/V1_subject7_t2/V1_subject7_t2.nii.gz -T2pial -s subject7_V1 -sd /home/server1/data/freesurfer_workingdir/subjects -all -brainstem-structures -parallel -openmp 8 subjid subject7_V1 setenv SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Actual FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 build-stamp.txt: freesurfer-Linux-centos6_x86_64-dev-20150828 Linux frames1.cmrr.umn.edu 3.10.0-1127.el7.x86_64 #1 SMP Tue Mar 31 23:36:51 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 102400 maxlocks unlimited maxsignal 2062670 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 528093384 5267908 58149728 51840 464675748 521373424 Swap: 134217724 0 134217724 ######################################## program versions used $Id: recon-all,v 1.543 2015/08/21 10:57:29 iglesias 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: $ TimeStamp: 2020/05/11-01:55:29-GMT BuildTimeStamp: Aug 28 2015 14:25:09 CVS: $Id: mri_convert.c,v 1.222 2015/06/08 18:22:26 greve Exp $ User: isaaca Machine: frames1.cmrr.umn.edu Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 6.0 $Id: talairach_avi,v 1.11 2015/01/13 20:22:51 nicks Exp $ mri_convert --version dev build (use --all-info flag for full version info) ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2020/05/11-01:55:29-GMT BuildTimeStamp: Aug 28 2015 14:25:09 CVS: $Id: tkregister2.c,v 1.129 2014/02/26 21:31:58 greve Exp $ User: isaaca Machine: frames1.cmrr.umn.edu Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/05/11-01:55:29-GMT BuildTimeStamp: Aug 28 2015 14:25:09 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: isaaca Machine: frames1.cmrr.umn.edu Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/05/11-01:55:29-GMT BuildTimeStamp: Aug 28 2015 14:25:09 CVS: $Id: mri_normalize.c,v 1.85 2015/08/05 19:24:14 fischl Exp $ User: isaaca Machine: frames1.cmrr.umn.edu Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/05/11-01:55:29-GMT BuildTimeStamp: Aug 28 2015 14:25:09 CVS: $Id: mri_watershed.cpp,v 1.101 2015/07/10 18:57:33 greve Exp $ User: isaaca Machine: frames1.cmrr.umn.edu Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/05/11-01:55:29-GMT BuildTimeStamp: Aug 28 2015 14:25:09 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: isaaca Machine: frames1.cmrr.umn.edu Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/05/11-01:55:29-GMT BuildTimeStamp: Aug 28 2015 14:25:09 CVS: $Id: mri_segment.c,v 1.43 2015/02/05 23:34:40 zkaufman Exp $ User: isaaca Machine: frames1.cmrr.umn.edu Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/05/11-01:55:29-GMT BuildTimeStamp: Aug 28 2015 14:25:09 CVS: $Id: mri_label2label.c,v 1.47 2014/12/22 19:59:18 greve Exp $ User: isaaca Machine: frames1.cmrr.umn.edu Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/05/11-01:55:29-GMT BuildTimeStamp: Aug 28 2015 14:25:09 CVS: $Id: mri_em_register.c,v 1.103 2015/08/26 16:51:09 fischl Exp $ User: isaaca Machine: frames1.cmrr.umn.edu Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/05/11-01:55:29-GMT BuildTimeStamp: Aug 28 2015 14:25:09 CVS: $Id: mri_ca_normalize.c,v 1.64 2015/08/26 16:50:50 fischl Exp $ User: isaaca Machine: frames1.cmrr.umn.edu Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/05/11-01:55:29-GMT BuildTimeStamp: Aug 28 2015 14:25:09 CVS: $Id: mri_ca_register.c,v 1.93 2015/06/24 16:03:22 fischl Exp $ User: isaaca Machine: frames1.cmrr.umn.edu Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/05/11-01:55:29-GMT BuildTimeStamp: Aug 28 2015 14:25:09 CVS: $Id: mri_ca_label.c,v 1.109 2015/08/26 16:46:38 fischl Exp $ User: isaaca Machine: frames1.cmrr.umn.edu Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/05/11-01:55:29-GMT BuildTimeStamp: Aug 28 2015 14:25:09 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: isaaca Machine: frames1.cmrr.umn.edu Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/05/11-01:55:29-GMT BuildTimeStamp: Aug 28 2015 14:25:09 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: isaaca Machine: frames1.cmrr.umn.edu Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/05/11-01:55:29-GMT BuildTimeStamp: Aug 28 2015 14:25:09 CVS: $Id: mri_tessellate.c,v 1.38 2014/03/22 00:41:04 greve Exp $ User: isaaca Machine: frames1.cmrr.umn.edu Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/05/11-01:55:29-GMT BuildTimeStamp: Aug 28 2015 14:25:09 CVS: $Id: mri_concatenate_lta.c,v 1.15 2015/08/19 16:35:05 greve Exp $ User: isaaca Machine: frames1.cmrr.umn.edu Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/05/11-01:55:29-GMT BuildTimeStamp: Aug 28 2015 14:25:09 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: isaaca Machine: frames1.cmrr.umn.edu Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/05/11-01:55:29-GMT BuildTimeStamp: Aug 28 2015 14:25:09 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: isaaca Machine: frames1.cmrr.umn.edu Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/05/11-01:55:29-GMT BuildTimeStamp: Aug 28 2015 14:25:09 CVS: $Id: mris_inflate.c,v 1.44 2012/01/05 18:36:17 greve Exp $ User: isaaca Machine: frames1.cmrr.umn.edu Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/05/11-01:55:29-GMT BuildTimeStamp: Aug 28 2015 14:25:09 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: isaaca Machine: frames1.cmrr.umn.edu Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/05/11-01:55:29-GMT BuildTimeStamp: Aug 28 2015 14:25:09 CVS: $Id: mris_sphere.c,v 1.59 2014/11/06 01:38:58 nicks Exp $ User: isaaca Machine: frames1.cmrr.umn.edu Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/05/11-01:55:29-GMT BuildTimeStamp: Aug 28 2015 14:25:09 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: isaaca Machine: frames1.cmrr.umn.edu Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/05/11-01:55:29-GMT BuildTimeStamp: Aug 28 2015 14:25:09 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: isaaca Machine: frames1.cmrr.umn.edu Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/05/11-01:55:29-GMT BuildTimeStamp: Aug 28 2015 14:25:09 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: isaaca Machine: frames1.cmrr.umn.edu Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/05/11-01:55:29-GMT BuildTimeStamp: Aug 28 2015 14:25:09 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: isaaca Machine: frames1.cmrr.umn.edu Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/05/11-01:55:29-GMT BuildTimeStamp: Aug 28 2015 14:25:09 CVS: $Id: mris_make_surfaces.c,v 1.158 2015/08/05 19:26:19 fischl Exp $ User: isaaca Machine: frames1.cmrr.umn.edu Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/05/11-01:55:29-GMT BuildTimeStamp: Aug 28 2015 14:25:09 CVS: $Id: mris_register.c,v 1.61 2013/01/15 17:19:03 greve Exp $ User: isaaca Machine: frames1.cmrr.umn.edu Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2020/05/11-01:55:29-GMT BuildTimeStamp: Aug 28 2015 14:25:09 CVS: $Id: mris_volmask.cpp,v 1.26 2014/11/06 03:40:22 nicks Exp $ User: isaaca Machine: frames1.cmrr.umn.edu Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/05/11-01:55:29-GMT BuildTimeStamp: Aug 28 2015 14:25:09 CVS: $Id: mris_anatomical_stats.c,v 1.78 2015/07/06 21:58:51 greve Exp $ User: isaaca Machine: frames1.cmrr.umn.edu Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/05/11-01:55:29-GMT BuildTimeStamp: Aug 28 2015 14:25:09 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: isaaca Machine: frames1.cmrr.umn.edu Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/05/11-01:55:29-GMT BuildTimeStamp: Aug 28 2015 14:25:09 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: isaaca Machine: frames1.cmrr.umn.edu Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/05/11-01:55:29-GMT BuildTimeStamp: Aug 28 2015 14:25:09 CVS: $Id: mris_calc.c,v 1.53 2015/06/04 20:50:50 nicks Exp $ User: isaaca Machine: frames1.cmrr.umn.edu Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.75 2014/11/18 16:14:42 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/05/11-01:55:29-GMT BuildTimeStamp: Aug 28 2015 14:25:09 CVS: $Id: mri_robust_register.cpp,v 1.75 2014/11/18 16:14:42 mreuter Exp $ User: isaaca Machine: frames1.cmrr.umn.edu Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.48 2013/05/21 18:03:15 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/05/11-01:55:29-GMT BuildTimeStamp: Aug 28 2015 14:25:09 CVS: $Id: mri_robust_template.cpp,v 1.48 2013/05/21 18:03:15 mreuter Exp $ User: isaaca Machine: frames1.cmrr.umn.edu Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/05/11-01:55:29-GMT BuildTimeStamp: Aug 28 2015 14:25:09 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: isaaca Machine: frames1.cmrr.umn.edu Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/05/11-01:55:29-GMT BuildTimeStamp: Aug 28 2015 14:25:09 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: isaaca Machine: frames1.cmrr.umn.edu Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/05/11-01:55:29-GMT BuildTimeStamp: Aug 28 2015 14:25:09 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: isaaca Machine: frames1.cmrr.umn.edu Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/05/11-01:55:29-GMT BuildTimeStamp: Aug 28 2015 14:25:09 CVS: $Id: mri_segstats.c,v 1.117 2015/07/02 15:52:06 fischl Exp $ User: isaaca Machine: frames1.cmrr.umn.edu Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/05/11-01:55:30-GMT BuildTimeStamp: Aug 28 2015 14:25:09 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: isaaca Machine: frames1.cmrr.umn.edu Platform: Linux PlatformVersion: 3.10.0-1127.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /opt/local/freesurfer-6.0/x86_64/average GCA RB_all_2014-08-21.gca GCASkull RB_all_withskull_2014-08-21.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /opt/local/freesurfer-6.0/x86_64/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /home/server1/data/freesurfer_workingdir/subjects/subject7_V1 mri_convert /home/server1/data/frames_analysis/subjects/brain/subject7/V1/V1_subject7_t1/V1_subject7_t1.nii.gz /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/orig/001.mgz mri_convert /home/server1/data/frames_analysis/subjects/brain/subject7/V1/V1_subject7_t1/V1_subject7_t1.nii.gz /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/orig/001.mgz $Id: mri_convert.c,v 1.222 2015/06/08 18:22:26 greve Exp $ reading from /home/server1/data/frames_analysis/subjects/brain/subject7/V1/V1_subject7_t1/V1_subject7_t1.nii.gz... TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998529, -0.0509025, -0.0186871) j_ras = (-0.0472866, 0.986091, -0.159337) k_ras = (-0.0265378, 0.158218, 0.987047) writing to /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/orig/001.mgz... #-------------------------------------------- #@# T2/FLAIR Input Sun May 10 20:55:39 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1 mri_convert --no_scale 1 /home/server1/data/frames_analysis/subjects/brain/subject7/V1/V1_subject7_t2/V1_subject7_t2.nii.gz /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/orig/T2raw.mgz mri_convert --no_scale 1 /home/server1/data/frames_analysis/subjects/brain/subject7/V1/V1_subject7_t2/V1_subject7_t2.nii.gz /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/orig/T2raw.mgz $Id: mri_convert.c,v 1.222 2015/06/08 18:22:26 greve Exp $ reading from /home/server1/data/frames_analysis/subjects/brain/subject7/V1/V1_subject7_t2/V1_subject7_t2.nii.gz... TR=3200.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998529, -0.0509025, -0.0186871) j_ras = (-0.0472866, 0.986091, -0.159337) k_ras = (-0.0265378, 0.158218, 0.987047) writing to /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/orig/T2raw.mgz... #-------------------------------------------- #@# MotionCor Sun May 10 20:55:49 CDT 2020 Found 1 runs /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/orig/001.mgz /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/rawavg.mgz /home/server1/data/freesurfer_workingdir/subjects/subject7_V1 mri_convert /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/rawavg.mgz /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/orig.mgz --conform mri_convert /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/rawavg.mgz /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/orig.mgz --conform $Id: mri_convert.c,v 1.222 2015/06/08 18:22:26 greve Exp $ reading from /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/rawavg.mgz... TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998529, -0.0509025, -0.0186871) j_ras = (-0.0472866, 0.986091, -0.159337) k_ras = (-0.0265378, 0.158218, 0.987047) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/orig.mgz... mri_add_xform_to_header -c /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/talairach.xfm /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/orig.mgz /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Sun May 10 20:56:00 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 200 --stop 1e-4 --shrink 2 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri /opt/local/freesurfer-6.0/x86_64/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 200 --stop 1e-4 --shrink 2 nIters 1 $Id: mri_nu_correct.mni,v 1.23 2015/06/18 00:21:28 nicks Exp $ Linux frames1.cmrr.umn.edu 3.10.0-1127.el7.x86_64 #1 SMP Tue Mar 31 23:36:51 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux Sun May 10 20:56:00 CDT 2020 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 tmpdir is ./tmp.mri_nu_correct.mni.20787 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.20787/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.20787/nu0.mnc -odt float $Id: mri_convert.c,v 1.222 2015/06/08 18:22:26 greve Exp $ reading from orig.mgz... TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 5.12227e-09, 1.86265e-09) j_ras = (0, 0, -1) k_ras = (-1.39698e-09, 1, -2.98023e-08) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.20787/nu0.mnc... -------------------------------------------------------- Iteration 1 Sun May 10 20:56:03 CDT 2020 nu_correct -clobber ./tmp.mri_nu_correct.mni.20787/nu0.mnc ./tmp.mri_nu_correct.mni.20787/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.20787/0/ -iterations 1000 -stop 1e-4 -distance 200 -shrink 2 [isaaca@frames1.cmrr.umn.edu:/home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/] [2020-05-10 20:56:03] running: /opt/local/freesurfer-6.0/x86_64/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 1e-4 -shrink 2 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.20787/0/ ./tmp.mri_nu_correct.mni.20787/nu0.mnc 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Processing:.................................................................................................................................Done Processing:.................................................................................................................................Done Processing:.................................................................................................................................Done Processing:.................................................................................................................................Done Processing:.................................................................................................................................Done Number of iterations: 269 CV of field change: 9.90934e-05 mri_convert ./tmp.mri_nu_correct.mni.20787/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert ./tmp.mri_nu_correct.mni.20787/nu1.mnc orig_nu.mgz --like orig.mgz --conform $Id: mri_convert.c,v 1.222 2015/06/08 18:22:26 greve Exp $ reading from ./tmp.mri_nu_correct.mni.20787/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 5.12227e-09, 1.86265e-09) j_ras = (0, 0, -1) k_ras = (-1.39698e-09, 1, -2.98023e-08) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz... Sun May 10 21:11:37 CDT 2020 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Sun May 10 21:12:06 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7435, pval=0.6675 >= threshold=0.0050) awk -f /opt/local/freesurfer-6.0/x86_64/bin/extract_talairach_avi_QA.awk /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/talairach_avi.log tal_QC_AZS /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/talairach_avi.log TalAviQA: 0.96293 z-score: -3 #-------------------------------------------- #@# Intensity Normalization Sun May 10 21:12:06 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri mri_normalize -g 1 orig_nu.mgz T1.mgz using max gradient = 1.000 reading from orig_nu.mgz... normalizing image... talairach transform 1.08389 0.05556 0.01533 -1.83113; -0.08059 1.01650 0.14314 -26.57138; -0.01748 -0.05352 1.10966 -28.57836; 0.00000 0.00000 0.00000 1.00000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 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 109 gm peak at 84 (84), valley at 56 (56) csf peak at 30, setting threshold to 66 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 78 (78), valley at 58 (58) csf peak at 29, setting threshold to 61 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 43 seconds. #-------------------------------------------- #@# Skull Stripping Sun May 10 21:13:49 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri mri_em_register -skull orig_nu.mgz /opt/local/freesurfer-6.0/x86_64/average/RB_all_withskull_2014-08-21.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 == Number of threads available to mri_em_register for OpenMP = 8 == reading 1 input volumes... logging results to talairach_with_skull.log reading '/opt/local/freesurfer-6.0/x86_64/average/RB_all_withskull_2014-08-21.gca'... average std = 23.5 using min determinant for regularization = 55.2 0 singular and 5018 ill-conditioned covariance matrices regularized reading 'orig_nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 15.9 or > 1063.6 total sample mean = 86.3 (1445 zeros) ************************************************ spacing=8, using 3388 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3388, passno 0, spacing 8 resetting wm mean[0]: 110 --> 118 resetting gm mean[0]: 70 --> 70 input volume #1 is the most T1-like using real data threshold=6.0 skull bounding box = (48, 16, 21) --> (204, 255, 214) using (100, 96, 118) as brain centroid... mean wm in atlas = 118, using box (81,66,94) --> (119, 125,141) to find MRI wm before smoothing, mri peak at 94 after smoothing, mri peak at 95, scaling input intensities by 1.242 scaling channel 0 by 1.24211 initial log_p = -4.632 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.602589 @ (-9.091, 27.273, -9.091) max log p = -4.521068 @ (4.545, -4.545, -4.545) max log p = -4.460949 @ (2.273, -6.818, 2.273) max log p = -4.425831 @ (1.136, 3.409, 3.409) max log p = -4.425831 @ (0.000, 0.000, 0.000) max log p = -4.420122 @ (0.852, -1.420, -1.989) Found translation: (-0.3, 17.9, -9.9): log p = -4.420 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.271, old_max_log_p =-4.420 (thresh=-4.4) 1.14016 0.02206 -0.14816 -2.94105; 0.00000 1.07125 0.11999 -4.13967; 0.15011 -0.16757 1.12538 -25.51943; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.270, old_max_log_p =-4.271 (thresh=-4.3) 1.14016 0.02206 -0.14816 -2.94105; 0.00000 1.15159 0.12898 -6.51209; 0.16136 -0.18014 1.20979 -43.08165; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.181, old_max_log_p =-4.270 (thresh=-4.3) 1.12623 0.04542 -0.06218 -14.29998; -0.03420 1.08054 0.16148 -2.42814; 0.08160 -0.20663 1.14469 -16.44798; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.181, old_max_log_p =-4.181 (thresh=-4.2) 1.12623 0.04542 -0.06218 -14.29998; -0.03420 1.08054 0.16148 -2.42814; 0.08160 -0.20663 1.14469 -16.44798; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.164, old_max_log_p =-4.181 (thresh=-4.2) 1.12897 0.03297 -0.04501 -14.91448; -0.02369 1.07984 0.18025 -4.99037; 0.06394 -0.22578 1.14678 -12.87505; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.164, old_max_log_p =-4.164 (thresh=-4.2) 1.12897 0.03297 -0.04501 -14.91448; -0.02369 1.07984 0.18025 -4.99037; 0.06394 -0.22578 1.14678 -12.87505; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3388 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.12897 0.03297 -0.04501 -14.91448; -0.02369 1.07984 0.18025 -4.99037; 0.06394 -0.22578 1.14678 -12.87505; 0.00000 0.00000 0.00000 1.00000; nsamples 3388 Quasinewton: input matrix 1.12897 0.03297 -0.04501 -14.91448; -0.02369 1.07984 0.18025 -4.99037; 0.06394 -0.22578 1.14678 -12.87505; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.12897 0.03297 -0.04501 -14.91448; -0.02369 1.07984 0.18025 -4.99037; 0.06394 -0.22578 1.14678 -12.87505; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -4.164 (old=-4.632) transform before final EM align: 1.12897 0.03297 -0.04501 -14.91448; -0.02369 1.07984 0.18025 -4.99037; 0.06394 -0.22578 1.14678 -12.87505; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 380366 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.12897 0.03297 -0.04501 -14.91448; -0.02369 1.07984 0.18025 -4.99037; 0.06394 -0.22578 1.14678 -12.87505; 0.00000 0.00000 0.00000 1.00000; nsamples 380366 Quasinewton: input matrix 1.12897 0.03297 -0.04501 -14.91448; -0.02369 1.07984 0.18025 -4.99037; 0.06394 -0.22578 1.14678 -12.87505; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = 4.6 tol 0.000000 final transform: 1.12897 0.03297 -0.04501 -14.91448; -0.02369 1.07984 0.18025 -4.99037; 0.06394 -0.22578 1.14678 -12.87505; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... registration took 12 minutes and 32 seconds. mri_watershed -T1 -brain_atlas /opt/local/freesurfer-6.0/x86_64/average/RB_all_withskull_2014-08-21.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=127 y=92 z=123 r=94 first estimation of the main basin volume: 3541150 voxels Looking for seedpoints 2 found in the cerebellum 16 found in the rest of the brain global maximum in x=107, y=77, z=84, Imax=255 CSF=19, 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=20243009941 voxels, voxel volume =1.000 = 20243009941 mmm3 = 20243009.536 cm3 done. PostAnalyze...Basin Prior 36 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=127,y=99, z=115, r=9253 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=9, CSF_MAX=44 , nb = 44306 RIGHT_CER CSF_MIN=0, CSF_intensity=7, CSF_MAX=82 , nb = -1040007226 LEFT_CER CSF_MIN=0, CSF_intensity=7, CSF_MAX=60 , nb = -1084736698 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=45 , nb = 1064956760 LEFT_BRAIN CSF_MIN=1, CSF_intensity=9, CSF_MAX=41 , nb = 1072597504 OTHER CSF_MIN=0, CSF_intensity=6, CSF_MAX=39 , nb = 1076334780 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 44, 45, 47, 75 after analyzing : 44, 46, 47, 53 RIGHT_CER before analyzing : 82, 66, 61, 85 after analyzing : 46, 66, 66, 70 LEFT_CER before analyzing : 60, 59, 59, 85 after analyzing : 44, 59, 59, 65 RIGHT_BRAIN before analyzing : 45, 46, 48, 75 after analyzing : 45, 47, 48, 54 LEFT_BRAIN before analyzing : 41, 43, 45, 73 after analyzing : 41, 44, 45, 51 OTHER before analyzing : 39, 43, 47, 75 after analyzing : 39, 45, 47, 52 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...70 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.012 curvature mean = 68.768, std = 7.954 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 3.67, sigma = 5.57 after rotation: sse = 3.67, sigma = 5.57 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 4.54, its var is 7.41 before Erosion-Dilatation 2.33% of inacurate vertices after Erosion-Dilatation 2.78% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...45 iterations mri_strip_skull: done peeling brain Brain Size = 1610028 voxels, voxel volume = 1.000 mm3 = 1610028 mmm3 = 1610.028 cm3 ****************************** Saving brainmask.auto.mgz done cp brainmask.auto.mgz brainmask.mgz #-------------------------------------------- #@# Nu Intensity Correction Sun May 10 21:26:42 CDT 2020 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 1 --proto-iters 1000 --distance 200 --stop 1e-4 --shrink 2 --mask brainmask.mgz /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri /opt/local/freesurfer-6.0/x86_64/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 1 --proto-iters 1000 --distance 200 --stop 1e-4 --shrink 2 --mask brainmask.mgz nIters 1 $Id: mri_nu_correct.mni,v 1.23 2015/06/18 00:21:28 nicks Exp $ Linux frames1.cmrr.umn.edu 3.10.0-1127.el7.x86_64 #1 SMP Tue Mar 31 23:36:51 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux Sun May 10 21:26:42 CDT 2020 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 tmpdir is ./tmp.mri_nu_correct.mni.30377 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.30377/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.30377/nu0.mnc -odt float $Id: mri_convert.c,v 1.222 2015/06/08 18:22:26 greve Exp $ reading from orig.mgz... TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 5.12227e-09, 1.86265e-09) j_ras = (0, 0, -1) k_ras = (-1.39698e-09, 1, -2.98023e-08) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.30377/nu0.mnc... /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri mri_binarize --i brainmask.mgz --min 1 --o ./tmp.mri_nu_correct.mni.30377/mask.mgz $Id: mri_binarize.c,v 1.41 2014/08/17 17:47:29 greve Exp $ cwd /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri cmdline mri_binarize --i brainmask.mgz --min 1 --o ./tmp.mri_nu_correct.mni.30377/mask.mgz sysname Linux hostname frames1.cmrr.umn.edu machine x86_64 user isaaca input brainmask.mgz frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.30377/mask.mgz Binarizing based on threshold min 1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 1609937 values in range Counting number of voxels in first frame Found 1609937 voxels in final mask Count: 1609937 1609937.000000 16777216 9.595972 mri_binarize done mri_convert ./tmp.mri_nu_correct.mni.30377/mask.mgz ./tmp.mri_nu_correct.mni.30377/mask.mnc -odt float mri_convert ./tmp.mri_nu_correct.mni.30377/mask.mgz ./tmp.mri_nu_correct.mni.30377/mask.mnc -odt float $Id: mri_convert.c,v 1.222 2015/06/08 18:22:26 greve Exp $ reading from ./tmp.mri_nu_correct.mni.30377/mask.mgz... TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 5.12227e-09, 1.86265e-09) j_ras = (0, 0, -1) k_ras = (-1.39698e-09, 1, -2.98023e-08) changing data type from int to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.30377/mask.mnc... -------------------------------------------------------- Iteration 1 Sun May 10 21:26:50 CDT 2020 nu_correct -clobber ./tmp.mri_nu_correct.mni.30377/nu0.mnc ./tmp.mri_nu_correct.mni.30377/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.30377/0/ -iterations 1000 -stop 1e-4 -distance 200 -shrink 2 -mask ./tmp.mri_nu_correct.mni.30377/mask.mnc [isaaca@frames1.cmrr.umn.edu:/home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/] [2020-05-10 21:26:50] running: /opt/local/freesurfer-6.0/x86_64/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 1e-4 -shrink 2 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -mask ./tmp.mri_nu_correct.mni.30377/mask.mnc -quiet -execute -clobber -nokeeptmp -tmpdir 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Processing:.................................................................................................................................Done Processing:.................................................................................................................................Done Processing:.................................................................................................................................Done Processing:.................................................................................................................................Done Processing:.................................................................................................................................Done Number of iterations: 160 CV of field change: 9.85696e-05 mri_binarize --i ./tmp.mri_nu_correct.mni.30377/nu1.mnc --min -1 --o ./tmp.mri_nu_correct.mni.30377/ones.mgz $Id: mri_binarize.c,v 1.41 2014/08/17 17:47:29 greve Exp $ cwd /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.30377/nu1.mnc --min -1 --o ./tmp.mri_nu_correct.mni.30377/ones.mgz sysname Linux hostname frames1.cmrr.umn.edu machine x86_64 user isaaca input ./tmp.mri_nu_correct.mni.30377/nu1.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.30377/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 16777216 values in range Counting number of voxels in first frame Found 16777216 voxels in final mask Count: 16777216 16777216.000000 16777216 100.000000 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.30377/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.30377/sum.junk --avgwf ./tmp.mri_nu_correct.mni.30377/input.mean.dat $Id: mri_segstats.c,v 1.117 2015/07/02 15:52:06 fischl Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.30377/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.30377/sum.junk --avgwf ./tmp.mri_nu_correct.mni.30377/input.mean.dat sysname Linux hostname frames1.cmrr.umn.edu machine x86_64 user isaaca UseRobust 0 Loading ./tmp.mri_nu_correct.mni.30377/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.30377/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.30377/ones.mgz --i ./tmp.mri_nu_correct.mni.30377/nu1.mnc --sum ./tmp.mri_nu_correct.mni.30377/sum.junk --avgwf ./tmp.mri_nu_correct.mni.30377/output.mean.dat $Id: mri_segstats.c,v 1.117 2015/07/02 15:52:06 fischl Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.30377/ones.mgz --i ./tmp.mri_nu_correct.mni.30377/nu1.mnc --sum ./tmp.mri_nu_correct.mni.30377/sum.junk --avgwf ./tmp.mri_nu_correct.mni.30377/output.mean.dat sysname Linux hostname frames1.cmrr.umn.edu machine x86_64 user isaaca UseRobust 0 Loading ./tmp.mri_nu_correct.mni.30377/ones.mgz Loading ./tmp.mri_nu_correct.mni.30377/nu1.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.30377/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.30377/nu1.mnc ./tmp.mri_nu_correct.mni.30377/nu1.mnc mul .83183884269858483619 Saving result to './tmp.mri_nu_correct.mni.30377/nu1.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.30377/nu1.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.30377/nu1.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.222 2015/06/08 18:22:26 greve Exp $ reading from ./tmp.mri_nu_correct.mni.30377/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 5.12227e-09, 1.86265e-09) j_ras = (0, 0, -1) k_ras = (-1.39698e-09, 1, -2.98023e-08) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 7 seconds. mapping ( 5, 73) to ( 3, 110) Sun May 10 21:35:52 CDT 2020 mri_nu_correct.mni done mri_add_xform_to_header -c /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #------------------------------------- #@# EM Registration Sun May 10 21:35:53 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /opt/local/freesurfer-6.0/x86_64/average/RB_all_2014-08-21.gca transforms/talairach.lta setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 8 == reading 1 input volumes... logging results to talairach.log reading '/opt/local/freesurfer-6.0/x86_64/average/RB_all_2014-08-21.gca'... average std = 5.4 using min determinant for regularization = 2.9 0 singular and 348 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 5.6 or > 725.9 total sample mean = 79.0 (1030 zeros) ************************************************ spacing=8, using 2898 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2898, passno 0, spacing 8 resetting wm mean[0]: 96 --> 104 resetting gm mean[0]: 58 --> 58 input volume #1 is the most T1-like using real data threshold=24.9 skull bounding box = (61, 34, 33) --> (190, 151, 205) using (104, 73, 119) as brain centroid... mean wm in atlas = 104, using box (88,59,98) --> (119, 87,140) to find MRI wm before smoothing, mri peak at 109 after smoothing, mri peak at 109, scaling input intensities by 0.954 scaling channel 0 by 0.954128 initial log_p = -4.267 ************************************************ First Search limited to translation only. ************************************************ max log p = -3.713470 @ (-9.091, 27.273, -9.091) max log p = -3.585701 @ (4.545, -4.545, -4.545) max log p = -3.435289 @ (2.273, -2.273, 2.273) max log p = -3.420139 @ (-1.136, 1.136, 1.136) max log p = -3.402049 @ (1.705, 1.705, 1.705) max log p = -3.402049 @ (0.000, 0.000, 0.000) Found translation: (-1.7, 23.3, -8.5): log p = -3.402 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.402, old_max_log_p =-3.402 (thresh=-3.4) 1.00000 0.00000 0.00000 -1.70455; 0.00000 1.00000 0.00000 23.29545; 0.00000 0.00000 1.00000 -8.52273; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 1 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.350, old_max_log_p =-3.402 (thresh=-3.4) 1.03686 0.00000 -0.03517 -0.58666; 0.00000 1.01875 0.00000 19.61833; 0.03090 0.00000 0.98080 -12.20822; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.344, old_max_log_p =-3.350 (thresh=-3.3) 1.01688 -0.03271 -0.03449 3.21832; 0.03456 1.03730 -0.00117 15.39474; 0.03090 0.00000 0.98080 -12.20822; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.344, old_max_log_p =-3.344 (thresh=-3.3) 1.01688 -0.03271 -0.03449 3.21832; 0.03456 1.03730 -0.00117 15.39474; 0.03090 0.00000 0.98080 -12.20822; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.318, old_max_log_p =-3.344 (thresh=-3.3) 1.01449 -0.03263 -0.03441 3.51049; 0.03494 1.04091 0.00688 13.59387; 0.03073 -0.00852 0.98423 -12.22648; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.317, old_max_log_p =-3.318 (thresh=-3.3) 1.01331 -0.03259 -0.03437 3.65623; 0.03502 1.04335 0.00689 13.34586; 0.03073 -0.00852 0.98423 -12.22648; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2898 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.01331 -0.03259 -0.03437 3.65623; 0.03502 1.04335 0.00689 13.34586; 0.03073 -0.00852 0.98423 -12.22648; 0.00000 0.00000 0.00000 1.00000; nsamples 2898 Quasinewton: input matrix 1.01331 -0.03259 -0.03437 3.65623; 0.03502 1.04335 0.00689 13.34586; 0.03073 -0.00852 0.98423 -12.22648; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.01331 -0.03259 -0.03437 3.65623; 0.03502 1.04335 0.00689 13.34586; 0.03073 -0.00852 0.98423 -12.22648; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.317 (old=-4.267) transform before final EM align: 1.01331 -0.03259 -0.03437 3.65623; 0.03502 1.04335 0.00689 13.34586; 0.03073 -0.00852 0.98423 -12.22648; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 317681 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.01331 -0.03259 -0.03437 3.65623; 0.03502 1.04335 0.00689 13.34586; 0.03073 -0.00852 0.98423 -12.22648; 0.00000 0.00000 0.00000 1.00000; nsamples 317681 Quasinewton: input matrix 1.01331 -0.03259 -0.03437 3.65623; 0.03502 1.04335 0.00689 13.34586; 0.03073 -0.00852 0.98423 -12.22648; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = 3.7 tol 0.000000 final transform: 1.01331 -0.03259 -0.03437 3.65623; 0.03502 1.04335 0.00689 13.34586; 0.03073 -0.00852 0.98423 -12.22648; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... registration took 10 minutes and 12 seconds. #-------------------------------------- #@# CA Normalize Sun May 10 21:46:05 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /opt/local/freesurfer-6.0/x86_64/average/RB_all_2014-08-21.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 '/opt/local/freesurfer-6.0/x86_64/average/RB_all_2014-08-21.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 96 --> 104 resetting gm mean[0]: 58 --> 58 input volume #1 is the most T1-like using real data threshold=24.9 skull bounding box = (61, 34, 33) --> (190, 151, 205) using (104, 73, 119) as brain centroid... mean wm in atlas = 104, using box (88,59,98) --> (119, 87,140) to find MRI wm before smoothing, mri peak at 109 after smoothing, mri peak at 109, scaling input intensities by 0.954 scaling channel 0 by 0.954128 using 248362 sample points... INFO: compute sample coordinates transform 1.01331 -0.03259 -0.03437 3.65623; 0.03502 1.04335 0.00689 13.34586; 0.03073 -0.00852 0.98423 -12.22648; 0.00000 0.00000 0.00000 1.00000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 43167 control points for structure... bounding box (125, 32, 35) --> (194, 146, 206) Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 163.0 0 of 946 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 42457 control points for structure... bounding box (64, 32, 36) --> (130, 148, 207) Right_Cerebral_White_Matter: limiting intensities to 95.0 --> 163.0 0 of 1575 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3111 control points for structure... bounding box (129, 114, 58) --> (178, 154, 113) Left_Cerebellum_White_Matter: limiting intensities to 95.0 --> 163.0 0 of 8 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2755 control points for structure... bounding box (83, 113, 59) --> (128, 155, 116) Right_Cerebellum_White_Matter: limiting intensities to 98.0 --> 163.0 0 of 11 (0.0%) samples deleted finding control points in Brain_Stem.... found 3398 control points for structure... bounding box (113, 107, 93) --> (147, 174, 126) Brain_Stem: limiting intensities to 93.0 --> 163.0 0 of 14 (0.0%) samples deleted using 2554 total control points for intensity normalization... bias field = 0.991 +- 0.039 13 of 2554 control points discarded finding control points in Left_Cerebral_White_Matter.... found 43167 control points for structure... bounding box (125, 32, 35) --> (194, 146, 206) Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 144.0 0 of 881 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 42457 control points for structure... bounding box (64, 32, 36) --> (130, 148, 207) Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 144.0 0 of 1500 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3111 control points for structure... bounding box (129, 114, 58) --> (178, 154, 113) Left_Cerebellum_White_Matter: limiting intensities to 85.0 --> 144.0 5 of 57 (8.8%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2755 control points for structure... bounding box (83, 113, 59) --> (128, 155, 116) Right_Cerebellum_White_Matter: limiting intensities to 85.0 --> 144.0 0 of 29 (0.0%) samples deleted finding control points in Brain_Stem.... found 3398 control points for structure... bounding box (113, 107, 93) --> (147, 174, 126) Brain_Stem: limiting intensities to 84.0 --> 144.0 0 of 81 (0.0%) samples deleted using 2548 total control points for intensity normalization... bias field = 1.025 +- 0.047 17 of 2543 control points discarded finding control points in Left_Cerebral_White_Matter.... found 43167 control points for structure... bounding box (125, 32, 35) --> (194, 146, 206) Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 135.0 0 of 969 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 42457 control points for structure... bounding box (64, 32, 36) --> (130, 148, 207) Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 135.0 0 of 1530 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3111 control points for structure... bounding box (129, 114, 58) --> (178, 154, 113) Left_Cerebellum_White_Matter: limiting intensities to 82.0 --> 135.0 0 of 63 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2755 control points for structure... bounding box (83, 113, 59) --> (128, 155, 116) Right_Cerebellum_White_Matter: limiting intensities to 79.0 --> 135.0 15 of 60 (25.0%) samples deleted finding control points in Brain_Stem.... found 3398 control points for structure... bounding box (113, 107, 93) --> (147, 174, 126) Brain_Stem: limiting intensities to 79.0 --> 135.0 0 of 112 (0.0%) samples deleted using 2734 total control points for intensity normalization... bias field = 1.024 +- 0.042 29 of 2719 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 17 seconds. #-------------------------------------- #@# CA Reg Sun May 10 21:47:22 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /opt/local/freesurfer-6.0/x86_64/average/RB_all_2014-08-21.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_ca_register for OpenMP = 8 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/opt/local/freesurfer-6.0/x86_64/average/RB_all_2014-08-21.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.04 (predicted orig area = 7.7) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=1.020, neg=0, invalid=1235 0001: dt=302.712644, rms=0.894 (12.433%), neg=0, invalid=1235 0002: dt=138.778206, rms=0.834 (6.685%), neg=0, invalid=1235 0003: dt=165.647059, rms=0.820 (1.686%), neg=0, invalid=1235 0004: dt=177.385827, rms=0.812 (1.001%), neg=0, invalid=1235 0005: dt=146.666667, rms=0.806 (0.686%), neg=0, invalid=1235 0006: dt=129.472000, rms=0.802 (0.448%), neg=0, invalid=1235 0007: dt=517.888000, rms=0.796 (0.851%), neg=0, invalid=1235 0008: dt=92.480000, rms=0.792 (0.510%), neg=0, invalid=1235 0009: dt=1479.680000, rms=0.784 (0.951%), neg=0, invalid=1235 0010: dt=92.480000, rms=0.779 (0.586%), neg=0, invalid=1235 0011: dt=517.888000, rms=0.777 (0.322%), neg=0, invalid=1235 0012: dt=73.984000, rms=0.776 (0.063%), neg=0, invalid=1235 0013: dt=73.984000, rms=0.776 (0.020%), neg=0, invalid=1235 0014: dt=73.984000, rms=0.776 (0.039%), neg=0, invalid=1235 0015: dt=73.984000, rms=0.775 (0.066%), neg=0, invalid=1235 0016: dt=73.984000, rms=0.775 (0.101%), neg=0, invalid=1235 0017: dt=73.984000, rms=0.774 (0.128%), neg=0, invalid=1235 0018: dt=73.984000, rms=0.773 (0.145%), neg=0, invalid=1235 0019: dt=73.984000, rms=0.771 (0.147%), neg=0, invalid=1235 0020: dt=73.984000, rms=0.770 (0.138%), neg=0, invalid=1235 0021: dt=73.984000, rms=0.769 (0.131%), neg=0, invalid=1235 0022: dt=73.984000, rms=0.768 (0.122%), neg=0, invalid=1235 0023: dt=73.984000, rms=0.767 (0.116%), neg=0, invalid=1235 0024: dt=2071.552000, rms=0.766 (0.260%), neg=0, invalid=1235 0025: dt=92.480000, rms=0.765 (0.105%), neg=0, invalid=1235 0026: dt=92.480000, rms=0.765 (0.007%), neg=0, invalid=1235 0027: dt=92.480000, rms=0.765 (0.009%), neg=0, invalid=1235 0028: dt=92.480000, rms=0.764 (0.025%), neg=0, invalid=1235 0029: dt=92.480000, rms=0.764 (0.062%), neg=0, invalid=1235 0030: dt=92.480000, rms=0.763 (0.081%), neg=0, invalid=1235 0031: dt=92.480000, rms=0.763 (0.074%), neg=0, invalid=1235 0032: dt=92.480000, rms=0.762 (0.059%), neg=0, invalid=1235 0033: dt=0.000000, rms=0.762 (-0.002%), neg=0, invalid=1235 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.763, neg=0, invalid=1235 0034: dt=369.920000, rms=0.758 (0.591%), neg=0, invalid=1235 0035: dt=92.480000, rms=0.758 (0.044%), neg=0, invalid=1235 0036: dt=92.480000, rms=0.758 (0.012%), neg=0, invalid=1235 0037: dt=92.480000, rms=0.758 (0.006%), neg=0, invalid=1235 0038: dt=92.480000, rms=0.758 (0.021%), neg=0, invalid=1235 0039: dt=92.480000, rms=0.757 (0.058%), neg=0, invalid=1235 0040: dt=92.480000, rms=0.756 (0.097%), neg=0, invalid=1235 0041: dt=92.480000, rms=0.756 (0.103%), neg=0, invalid=1235 0042: dt=92.480000, rms=0.755 (0.087%), neg=0, invalid=1235 0043: dt=0.000000, rms=0.755 (0.001%), neg=0, invalid=1235 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.760, neg=0, invalid=1235 0044: dt=36.288000, rms=0.758 (0.295%), neg=0, invalid=1235 0045: dt=145.152000, rms=0.754 (0.466%), neg=0, invalid=1235 0046: dt=375.142263, rms=0.730 (3.156%), neg=0, invalid=1235 0047: dt=30.839378, rms=0.727 (0.401%), neg=0, invalid=1235 0048: dt=2.268000, rms=0.727 (0.008%), neg=0, invalid=1235 0049: dt=2.268000, rms=0.727 (0.001%), neg=0, invalid=1235 0050: dt=2.268000, rms=0.727 (-0.003%), neg=0, invalid=1235 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.728, neg=0, invalid=1235 0051: dt=91.333333, rms=0.726 (0.304%), neg=0, invalid=1235 0052: dt=331.776000, rms=0.721 (0.646%), neg=0, invalid=1235 0053: dt=36.288000, rms=0.719 (0.306%), neg=0, invalid=1235 0054: dt=62.208000, rms=0.718 (0.100%), neg=0, invalid=1235 0055: dt=62.208000, rms=0.717 (0.117%), neg=0, invalid=1235 0056: dt=62.208000, rms=0.716 (0.191%), neg=0, invalid=1235 0057: dt=62.208000, rms=0.714 (0.275%), neg=0, invalid=1235 0058: dt=62.208000, rms=0.712 (0.306%), neg=0, invalid=1235 0059: dt=62.208000, rms=0.709 (0.332%), neg=0, invalid=1235 0060: dt=62.208000, rms=0.707 (0.340%), neg=0, invalid=1235 0061: dt=62.208000, rms=0.705 (0.319%), neg=0, invalid=1235 0062: dt=62.208000, rms=0.703 (0.297%), neg=0, invalid=1235 0063: dt=62.208000, rms=0.701 (0.277%), neg=0, invalid=1235 0064: dt=62.208000, rms=0.699 (0.271%), neg=0, invalid=1235 0065: dt=62.208000, rms=0.697 (0.253%), neg=0, invalid=1235 0066: dt=62.208000, rms=0.695 (0.237%), neg=0, invalid=1235 0067: dt=62.208000, rms=0.694 (0.210%), neg=0, invalid=1235 0068: dt=62.208000, rms=0.693 (0.188%), neg=0, invalid=1235 0069: dt=62.208000, rms=0.691 (0.164%), neg=0, invalid=1235 0070: dt=62.208000, rms=0.690 (0.139%), neg=0, invalid=1235 0071: dt=62.208000, rms=0.690 (0.121%), neg=0, invalid=1235 0072: dt=62.208000, rms=0.689 (0.108%), neg=0, invalid=1235 0073: dt=103.680000, rms=0.689 (0.014%), neg=0, invalid=1235 0074: dt=103.680000, rms=0.689 (-0.003%), neg=0, invalid=1235 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.711, neg=0, invalid=1235 0075: dt=0.000000, rms=0.710 (0.075%), neg=0, invalid=1235 0076: dt=0.000000, rms=0.710 (-0.000%), neg=0, invalid=1235 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.711, neg=0, invalid=1235 0077: dt=0.000000, rms=0.710 (0.075%), neg=0, invalid=1235 0078: dt=0.000000, rms=0.710 (0.000%), neg=0, invalid=1235 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.775, neg=0, invalid=1235 0079: dt=5.171779, rms=0.758 (2.218%), neg=0, invalid=1235 0080: dt=0.864000, rms=0.758 (0.011%), neg=0, invalid=1235 0081: dt=0.864000, rms=0.758 (-0.007%), neg=0, invalid=1235 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.759, neg=0, invalid=1235 0082: dt=0.000000, rms=0.758 (0.056%), neg=0, invalid=1235 0083: dt=0.000000, rms=0.758 (-0.000%), neg=0, invalid=1235 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.837, neg=0, invalid=1235 0084: dt=1.536000, rms=0.831 (0.760%), neg=0, invalid=1235 0085: dt=1.792000, rms=0.827 (0.456%), neg=0, invalid=1235 0086: dt=0.448000, rms=0.827 (0.048%), neg=0, invalid=1235 0087: dt=0.448000, rms=0.826 (0.010%), neg=0, invalid=1235 0088: dt=0.448000, rms=0.826 (-0.026%), neg=0, invalid=1235 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.827, neg=0, invalid=1235 0089: dt=1.024000, rms=0.826 (0.138%), neg=0, invalid=1235 0090: dt=0.000000, rms=0.826 (-0.001%), neg=0, invalid=1235 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.751, neg=0, invalid=1235 0091: dt=0.880049, rms=0.732 (2.612%), neg=0, invalid=1235 0092: dt=0.096000, rms=0.730 (0.153%), neg=0, invalid=1235 0093: dt=0.096000, rms=0.730 (-0.084%), neg=0, invalid=1235 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.731, neg=0, invalid=1235 0094: dt=0.028000, rms=0.730 (0.076%), neg=0, invalid=1235 0095: dt=0.007000, rms=0.730 (0.001%), neg=0, invalid=1235 0096: dt=0.007000, rms=0.730 (-0.000%), neg=0, invalid=1235 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.17034 (15) mri peak = 0.26576 (20) Left_Lateral_Ventricle (4): linear fit = 1.24 x + 0.0 (2017 voxels, overlap=0.454) Left_Lateral_Ventricle (4): linear fit = 1.24 x + 0.0 (2017 voxels, peak = 19), gca=18.5 gca peak = 0.15472 (13) mri peak = 0.17689 (20) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (1478 voxels, overlap=0.389) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (1478 voxels, peak = 19), gca=19.4 gca peak = 0.25085 (95) mri peak = 0.07692 (93) Right_Pallidum (52): linear fit = 0.98 x + 0.0 (1196 voxels, overlap=0.983) Right_Pallidum (52): linear fit = 0.98 x + 0.0 (1196 voxels, peak = 93), gca=92.6 gca peak = 0.20192 (94) mri peak = 0.09063 (84) Left_Pallidum (13): linear fit = 0.89 x + 0.0 (1009 voxels, overlap=0.041) Left_Pallidum (13): linear fit = 0.89 x + 0.0 (1009 voxels, peak = 84), gca=84.1 gca peak = 0.23749 (55) mri peak = 0.07617 (72) Right_Hippocampus (53): linear fit = 1.26 x + 0.0 (1223 voxels, overlap=0.034) Right_Hippocampus (53): linear fit = 1.26 x + 0.0 (1223 voxels, peak = 70), gca=69.6 gca peak = 0.28812 (57) mri peak = 0.08249 (66) Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (953 voxels, overlap=0.606) Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (953 voxels, peak = 64), gca=63.6 gca peak = 0.13909 (99) mri peak = 0.16597 (101) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (96198 voxels, overlap=0.660) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (96198 voxels, peak = 100), gca=100.5 gca peak = 0.15071 (100) mri peak = 0.13575 (101) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (92046 voxels, overlap=0.677) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (92046 voxels, peak = 102), gca=101.5 gca peak = 0.13362 (57) mri peak = 0.03535 (71) Left_Cerebral_Cortex (3): linear fit = 1.23 x + 0.0 (30274 voxels, overlap=0.316) Left_Cerebral_Cortex (3): linear fit = 1.23 x + 0.0 (30274 voxels, peak = 70), gca=69.8 gca peak = 0.15234 (57) mri peak = 0.04232 (71) Right_Cerebral_Cortex (42): linear fit = 1.25 x + 0.0 (35996 voxels, overlap=0.058) Right_Cerebral_Cortex (42): linear fit = 1.25 x + 0.0 (35996 voxels, peak = 71), gca=71.0 gca peak = 0.15027 (66) mri peak = 0.07970 (73) Right_Caudate (50): linear fit = 1.11 x + 0.0 (730 voxels, overlap=0.319) Right_Caudate (50): linear fit = 1.11 x + 0.0 (730 voxels, peak = 73), gca=72.9 gca peak = 0.16264 (70) mri peak = 0.10787 (79) Left_Caudate (11): linear fit = 1.05 x + 0.0 (1069 voxels, overlap=0.642) Left_Caudate (11): linear fit = 1.05 x + 0.0 (1069 voxels, peak = 74), gca=73.8 gca peak = 0.12236 (58) mri peak = 0.04588 (72) Left_Cerebellum_Cortex (8): linear fit = 1.25 x + 0.0 (23178 voxels, overlap=0.008) Left_Cerebellum_Cortex (8): linear fit = 1.25 x + 0.0 (23178 voxels, peak = 72), gca=72.2 gca peak = 0.12528 (58) mri peak = 0.05145 (74) Right_Cerebellum_Cortex (47): linear fit = 1.29 x + 0.0 (24641 voxels, overlap=0.001) Right_Cerebellum_Cortex (47): linear fit = 1.29 x + 0.0 (24641 voxels, peak = 75), gca=75.1 gca peak = 0.22484 (87) mri peak = 0.07673 (88) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (11703 voxels, overlap=0.715) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (11703 voxels, peak = 89), gca=89.2 gca peak = 0.19967 (86) mri peak = 0.05403 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (9399 voxels, overlap=0.772) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (9399 voxels, peak = 88), gca=88.2 gca peak = 0.25254 (57) mri peak = 0.07634 (72) Left_Amygdala (18): linear fit = 1.25 x + 0.0 (469 voxels, overlap=0.080) Left_Amygdala (18): linear fit = 1.25 x + 0.0 (469 voxels, peak = 72), gca=71.5 gca peak = 0.34306 (56) mri peak = 0.08859 (73) Right_Amygdala (54): linear fit = 1.27 x + 0.0 (584 voxels, overlap=0.037) Right_Amygdala (54): linear fit = 1.27 x + 0.0 (584 voxels, peak = 71), gca=71.4 gca peak = 0.11868 (85) mri peak = 0.08154 (98) Left_Thalamus_Proper (10): linear fit = 1.08 x + 0.0 (6724 voxels, overlap=0.849) Left_Thalamus_Proper (10): linear fit = 1.08 x + 0.0 (6724 voxels, peak = 91), gca=91.4 gca peak = 0.10630 (84) mri peak = 0.06247 (81) Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (4584 voxels, overlap=0.795) Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (4584 voxels, peak = 88), gca=87.8 gca peak = 0.14358 (76) mri peak = 0.04385 (78) Left_Putamen (12): linear fit = 1.09 x + 0.0 (3371 voxels, overlap=0.522) Left_Putamen (12): linear fit = 1.09 x + 0.0 (3371 voxels, peak = 82), gca=82.5 gca peak = 0.12531 (77) mri peak = 0.08831 (78) Right_Putamen (51): linear fit = 1.09 x + 0.0 (3259 voxels, overlap=0.694) Right_Putamen (51): linear fit = 1.09 x + 0.0 (3259 voxels, peak = 84), gca=83.5 gca peak = 0.11986 (81) mri peak = 0.10669 (89) Brain_Stem (16): linear fit = 1.11 x + 0.0 (12935 voxels, overlap=0.365) Brain_Stem (16): linear fit = 1.11 x + 0.0 (12935 voxels, peak = 90), gca=89.5 gca peak = 0.12662 (89) mri peak = 0.10131 (95) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (1144 voxels, overlap=0.588) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (1144 voxels, peak = 96), gca=95.7 gca peak = 0.11568 (91) mri peak = 0.08954 (96) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1509 voxels, overlap=0.617) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1509 voxels, peak = 98), gca=97.8 gca peak = 0.17958 (23) mri peak = 0.13339 (20) Third_Ventricle (14): linear fit = 0.80 x + 0.0 (185 voxels, overlap=0.969) Third_Ventricle (14): linear fit = 0.80 x + 0.0 (185 voxels, peak = 18), gca=18.3 gca peak = 0.13562 (17) mri peak = 0.14936 (24) Fourth_Ventricle (15): linear fit = 1.25 x + 0.0 (369 voxels, overlap=0.494) Fourth_Ventricle (15): linear fit = 1.25 x + 0.0 (369 voxels, peak = 21), gca=21.3 gca peak Unknown = 0.99973 ( 0) gca peak Left_Inf_Lat_Vent = 0.14331 (27) gca peak Left_Thalamus = 0.32757 (93) gca peak CSF = 0.19936 (37) gca peak Left_Accumbens_area = 0.46890 (61) gca peak Left_undetermined = 0.95064 (27) gca peak Left_vessel = 0.46024 (53) gca peak Left_choroid_plexus = 0.12215 (39) gca peak Right_Inf_Lat_Vent = 0.17768 (25) gca peak Right_Accumbens_area = 0.31203 (65) gca peak Right_vessel = 0.44843 (50) gca peak Right_choroid_plexus = 0.10617 (41) gca peak Fifth_Ventricle = 0.69389 (32) gca peak WM_hypointensities = 0.10221 (75) gca peak non_WM_hypointensities = 0.12565 (44) gca peak Optic_Chiasm = 0.29183 (82) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 1.23 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 1.20 x + 0.0 saving intensity scales to talairach.label_intensities.txt ********************* ALLOWING NEGATIVE NODES IN DEFORMATION******************************** **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.749, neg=0, invalid=1235 0097: dt=147.650086, rms=0.724 (3.347%), neg=0, invalid=1235 0098: dt=184.195122, rms=0.718 (0.845%), neg=0, invalid=1235 0099: dt=129.472000, rms=0.716 (0.331%), neg=0, invalid=1235 0100: dt=221.952000, rms=0.714 (0.251%), neg=0, invalid=1235 0101: dt=110.976000, rms=0.713 (0.159%), neg=0, invalid=1235 0102: dt=110.976000, rms=0.712 (0.096%), neg=0, invalid=1235 0103: dt=110.976000, rms=0.711 (0.121%), neg=0, invalid=1235 0104: dt=110.976000, rms=0.710 (0.180%), neg=0, invalid=1235 0105: dt=110.976000, rms=0.709 (0.130%), neg=0, invalid=1235 0106: dt=110.976000, rms=0.708 (0.137%), neg=0, invalid=1235 0107: dt=110.976000, rms=0.707 (0.080%), neg=0, invalid=1235 0108: dt=110.976000, rms=0.707 (0.114%), neg=0, invalid=1235 0109: dt=110.976000, rms=0.706 (0.088%), neg=0, invalid=1235 0110: dt=129.472000, rms=0.706 (0.031%), neg=0, invalid=1235 0111: dt=129.472000, rms=0.705 (0.050%), neg=0, invalid=1235 0112: dt=129.472000, rms=0.705 (0.061%), neg=0, invalid=1235 0113: dt=129.472000, rms=0.704 (0.071%), neg=0, invalid=1235 0114: dt=129.472000, rms=0.704 (0.082%), neg=0, invalid=1235 0115: dt=129.472000, rms=0.703 (0.090%), neg=0, invalid=1235 0116: dt=129.472000, rms=0.703 (0.072%), neg=0, invalid=1235 0117: dt=129.472000, rms=0.702 (0.067%), neg=0, invalid=1235 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.702, neg=0, invalid=1235 0118: dt=295.936000, rms=0.701 (0.271%), neg=0, invalid=1235 0119: dt=110.976000, rms=0.700 (0.068%), neg=0, invalid=1235 0120: dt=110.976000, rms=0.700 (0.031%), neg=0, invalid=1235 0121: dt=110.976000, rms=0.700 (0.038%), neg=0, invalid=1235 0122: dt=110.976000, rms=0.699 (0.058%), neg=0, invalid=1235 0123: dt=110.976000, rms=0.699 (0.050%), neg=0, invalid=1235 0124: dt=110.976000, rms=0.698 (0.059%), neg=0, invalid=1235 0125: dt=110.976000, rms=0.698 (0.059%), neg=0, invalid=1235 0126: dt=369.920000, rms=0.698 (0.025%), neg=0, invalid=1235 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.699, neg=0, invalid=1235 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0127: dt=142.262857, rms=0.692 (1.017%), neg=0, invalid=1235 iter 0, gcam->neg = 5 after 4 iterations, nbhd size=0, neg = 0 0128: dt=112.280702, rms=0.685 (0.999%), neg=0, invalid=1235 iter 0, gcam->neg = 5 after 2 iterations, nbhd size=0, neg = 0 0129: dt=60.160000, rms=0.681 (0.546%), neg=0, invalid=1235 iter 0, gcam->neg = 3 after 3 iterations, nbhd size=0, neg = 0 0130: dt=79.379845, rms=0.679 (0.357%), neg=0, invalid=1235 iter 0, gcam->neg = 5 after 3 iterations, nbhd size=0, neg = 0 0131: dt=66.291169, rms=0.677 (0.341%), neg=0, invalid=1235 iter 0, gcam->neg = 7 after 3 iterations, nbhd size=0, neg = 0 0132: dt=85.508197, rms=0.675 (0.268%), neg=0, invalid=1235 iter 0, gcam->neg = 1 after 3 iterations, nbhd size=0, neg = 0 0133: dt=62.208000, rms=0.673 (0.264%), neg=0, invalid=1235 iter 0, gcam->neg = 4 after 4 iterations, nbhd size=0, neg = 0 0134: dt=100.905109, rms=0.672 (0.213%), neg=0, invalid=1235 iter 0, gcam->neg = 4 after 6 iterations, nbhd size=0, neg = 0 0135: dt=100.905109, rms=0.671 (0.128%), neg=0, invalid=1235 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0136: dt=100.905109, rms=0.666 (0.640%), neg=0, invalid=1235 iter 0, gcam->neg = 7 after 6 iterations, nbhd size=0, neg = 0 0137: dt=100.905109, rms=0.664 (0.321%), neg=0, invalid=1235 iter 0, gcam->neg = 11 after 7 iterations, nbhd size=0, neg = 0 0138: dt=100.905109, rms=0.661 (0.534%), neg=0, invalid=1235 iter 0, gcam->neg = 5 after 8 iterations, nbhd size=0, neg = 0 0139: dt=100.905109, rms=0.658 (0.442%), neg=0, invalid=1235 iter 0, gcam->neg = 5 after 6 iterations, nbhd size=0, neg = 0 0140: dt=100.905109, rms=0.656 (0.213%), neg=0, invalid=1235 iter 0, gcam->neg = 2 after 5 iterations, nbhd size=0, neg = 0 0141: dt=100.905109, rms=0.654 (0.432%), neg=0, invalid=1235 0142: dt=100.905109, rms=0.653 (0.147%), neg=0, invalid=1235 0143: dt=100.905109, rms=0.651 (0.174%), neg=0, invalid=1235 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0144: dt=100.905109, rms=0.650 (0.272%), neg=0, invalid=1235 iter 0, gcam->neg = 4 after 4 iterations, nbhd size=0, neg = 0 0145: dt=100.905109, rms=0.649 (0.083%), neg=0, invalid=1235 iter 0, gcam->neg = 7 after 2 iterations, nbhd size=0, neg = 0 0146: dt=100.905109, rms=0.648 (0.208%), neg=0, invalid=1235 iter 0, gcam->neg = 32 after 8 iterations, nbhd size=0, neg = 0 0147: dt=100.905109, rms=0.647 (0.122%), neg=0, invalid=1235 iter 0, gcam->neg = 31 after 9 iterations, nbhd size=0, neg = 0 0148: dt=100.905109, rms=0.646 (0.087%), neg=0, invalid=1235 0149: dt=36.288000, rms=0.646 (0.089%), neg=0, invalid=1235 0150: dt=145.152000, rms=0.646 (0.044%), neg=0, invalid=1235 0151: dt=145.152000, rms=0.645 (0.041%), neg=0, invalid=1235 0152: dt=145.152000, rms=0.645 (-0.028%), neg=0, invalid=1235 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.646, neg=0, invalid=1235 0153: dt=114.113208, rms=0.643 (0.457%), neg=0, invalid=1235 0154: dt=36.288000, rms=0.642 (0.089%), neg=0, invalid=1235 0155: dt=36.288000, rms=0.642 (0.028%), neg=0, invalid=1235 0156: dt=36.288000, rms=0.642 (0.032%), neg=0, invalid=1235 0157: dt=36.288000, rms=0.642 (0.034%), neg=0, invalid=1235 0158: dt=36.288000, rms=0.641 (0.025%), neg=0, invalid=1235 0159: dt=36.288000, rms=0.641 (0.007%), neg=0, invalid=1235 0160: dt=145.152000, rms=0.641 (0.037%), neg=0, invalid=1235 0161: dt=25.920000, rms=0.641 (0.001%), neg=0, invalid=1235 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.654, neg=0, invalid=1235 0162: dt=6.400000, rms=0.654 (0.098%), neg=0, invalid=1235 0163: dt=2.800000, rms=0.654 (0.009%), neg=0, invalid=1235 0164: dt=2.800000, rms=0.654 (0.002%), neg=0, invalid=1235 0165: dt=2.800000, rms=0.654 (-0.017%), neg=0, invalid=1235 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.654, neg=0, invalid=1235 0166: dt=6.400000, rms=0.654 (0.065%), neg=0, invalid=1235 0167: dt=2.800000, rms=0.654 (0.002%), neg=0, invalid=1235 0168: dt=2.800000, rms=0.654 (-0.001%), neg=0, invalid=1235 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.683, neg=0, invalid=1235 0169: dt=3.572917, rms=0.678 (0.738%), neg=0, invalid=1235 0170: dt=1.008000, rms=0.678 (0.020%), neg=0, invalid=1235 0171: dt=1.008000, rms=0.678 (-0.007%), neg=0, invalid=1235 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.678, neg=0, invalid=1235 0172: dt=0.576000, rms=0.678 (0.046%), neg=0, invalid=1235 0173: dt=0.108000, rms=0.678 (0.001%), neg=0, invalid=1235 0174: dt=0.108000, rms=0.678 (-0.000%), neg=0, invalid=1235 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.712, neg=0, invalid=1235 0175: dt=0.320000, rms=0.711 (0.081%), neg=0, invalid=1235 0176: dt=0.112000, rms=0.711 (0.006%), neg=0, invalid=1235 0177: dt=0.112000, rms=0.711 (0.002%), neg=0, invalid=1235 0178: dt=0.112000, rms=0.711 (-0.012%), neg=0, invalid=1235 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.711, neg=0, invalid=1235 0179: dt=0.384000, rms=0.711 (0.080%), neg=0, invalid=1235 0180: dt=0.192000, rms=0.711 (0.011%), neg=0, invalid=1235 0181: dt=0.192000, rms=0.711 (0.002%), neg=0, invalid=1235 0182: dt=0.192000, rms=0.711 (-0.022%), neg=0, invalid=1235 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.673, neg=0, invalid=1235 iter 0, gcam->neg = 7 after 0 iterations, nbhd size=0, neg = 0 0183: dt=0.819615, rms=0.655 (2.657%), neg=0, invalid=1235 0184: dt=0.080000, rms=0.654 (0.108%), neg=0, invalid=1235 0185: dt=0.080000, rms=0.654 (-0.094%), neg=0, invalid=1235 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.655, neg=0, invalid=1235 0186: dt=0.020000, rms=0.654 (0.053%), neg=0, invalid=1235 0187: dt=0.001250, rms=0.654 (0.000%), neg=0, invalid=1235 0188: dt=0.001250, rms=0.654 (-0.000%), neg=0, invalid=1235 label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.644, neg=0, invalid=1235 0189: dt=129.472000, rms=0.643 (0.124%), neg=0, invalid=1235 0190: dt=129.472000, rms=0.643 (0.030%), neg=0, invalid=1235 0191: dt=129.472000, rms=0.643 (0.020%), neg=0, invalid=1235 0192: dt=129.472000, rms=0.643 (0.014%), neg=0, invalid=1235 0193: dt=129.472000, rms=0.643 (-0.005%), neg=0, invalid=1235 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.643, neg=0, invalid=1235 0194: dt=295.936000, rms=0.641 (0.271%), neg=0, invalid=1235 0195: dt=73.984000, rms=0.641 (0.044%), neg=0, invalid=1235 0196: dt=73.984000, rms=0.641 (0.010%), neg=0, invalid=1235 0197: dt=73.984000, rms=0.641 (0.007%), neg=0, invalid=1235 0198: dt=73.984000, rms=0.641 (0.011%), neg=0, invalid=1235 0199: dt=73.984000, rms=0.640 (0.029%), neg=0, invalid=1235 0200: dt=73.984000, rms=0.640 (0.045%), neg=0, invalid=1235 0201: dt=73.984000, rms=0.640 (0.046%), neg=0, invalid=1235 0202: dt=73.984000, rms=0.640 (0.039%), neg=0, invalid=1235 0203: dt=73.984000, rms=0.640 (0.002%), neg=0, invalid=1235 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.640, neg=0, invalid=1235 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0204: dt=65.240997, rms=0.638 (0.291%), neg=0, invalid=1235 iter 0, gcam->neg = 11 after 5 iterations, nbhd size=0, neg = 0 0205: dt=145.152000, rms=0.634 (0.556%), neg=0, invalid=1235 iter 0, gcam->neg = 4 after 3 iterations, nbhd size=0, neg = 0 0206: dt=124.416000, rms=0.633 (0.235%), neg=0, invalid=1235 iter 0, gcam->neg = 12 after 5 iterations, nbhd size=0, neg = 0 0207: dt=124.416000, rms=0.631 (0.229%), neg=0, invalid=1235 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0208: dt=124.416000, rms=0.629 (0.380%), neg=0, invalid=1235 iter 0, gcam->neg = 6 after 5 iterations, nbhd size=0, neg = 0 0209: dt=124.416000, rms=0.627 (0.361%), neg=0, invalid=1235 iter 0, gcam->neg = 20 after 15 iterations, nbhd size=0, neg = 0 0210: dt=124.416000, rms=0.624 (0.377%), neg=0, invalid=1235 iter 0, gcam->neg = 16 after 9 iterations, nbhd size=0, neg = 0 0211: dt=124.416000, rms=0.623 (0.223%), neg=0, invalid=1235 iter 0, gcam->neg = 11 after 10 iterations, nbhd size=0, neg = 0 0212: dt=124.416000, rms=0.622 (0.110%), neg=0, invalid=1235 iter 0, gcam->neg = 15 after 10 iterations, nbhd size=0, neg = 0 0213: dt=124.416000, rms=0.621 (0.180%), neg=0, invalid=1235 0214: dt=124.416000, rms=0.620 (0.254%), neg=0, invalid=1235 0215: dt=124.416000, rms=0.618 (0.177%), neg=0, invalid=1235 iter 0, gcam->neg = 4 after 4 iterations, nbhd size=0, neg = 0 0216: dt=124.416000, rms=0.618 (0.122%), neg=0, invalid=1235 iter 0, gcam->neg = 14 after 9 iterations, nbhd size=0, neg = 0 0217: dt=124.416000, rms=0.617 (0.126%), neg=0, invalid=1235 iter 0, gcam->neg = 41 after 6 iterations, nbhd size=0, neg = 0 0218: dt=124.416000, rms=0.616 (0.157%), neg=0, invalid=1235 iter 0, gcam->neg = 52 after 8 iterations, nbhd size=0, neg = 0 0219: dt=124.416000, rms=0.615 (0.127%), neg=0, invalid=1235 iter 0, gcam->neg = 28 after 5 iterations, nbhd size=0, neg = 0 0220: dt=124.416000, rms=0.615 (0.044%), neg=0, invalid=1235 iter 0, gcam->neg = 8 after 11 iterations, nbhd size=0, neg = 0 0221: dt=124.416000, rms=0.614 (0.139%), neg=0, invalid=1235 iter 0, gcam->neg = 9 after 7 iterations, nbhd size=0, neg = 0 0222: dt=124.416000, rms=0.613 (0.116%), neg=0, invalid=1235 iter 0, gcam->neg = 13 after 9 iterations, nbhd size=0, neg = 0 0223: dt=124.416000, rms=0.613 (-0.029%), neg=0, invalid=1235 0224: dt=31.104000, rms=0.613 (0.059%), neg=0, invalid=1235 0225: dt=36.288000, rms=0.613 (0.007%), neg=0, invalid=1235 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.613, neg=0, invalid=1235 0226: dt=145.152000, rms=0.609 (0.637%), neg=0, invalid=1235 0227: dt=36.288000, rms=0.609 (0.086%), neg=0, invalid=1235 0228: dt=36.288000, rms=0.608 (0.018%), neg=0, invalid=1235 0229: dt=36.288000, rms=0.608 (0.018%), neg=0, invalid=1235 0230: dt=36.288000, rms=0.608 (0.028%), neg=0, invalid=1235 0231: dt=36.288000, rms=0.608 (0.055%), neg=0, invalid=1235 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0232: dt=36.288000, rms=0.607 (0.072%), neg=0, invalid=1235 0233: dt=36.288000, rms=0.607 (0.065%), neg=0, invalid=1235 0234: dt=145.152000, rms=0.607 (0.032%), neg=0, invalid=1235 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.614, neg=0, invalid=1235 0235: dt=11.200000, rms=0.614 (0.123%), neg=0, invalid=1235 0236: dt=9.600000, rms=0.613 (0.040%), neg=0, invalid=1235 0237: dt=9.600000, rms=0.613 (0.025%), neg=0, invalid=1235 0238: dt=9.600000, rms=0.613 (-0.025%), neg=0, invalid=1235 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.613, neg=0, invalid=1235 0239: dt=29.325648, rms=0.611 (0.332%), neg=0, invalid=1235 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0240: dt=25.600000, rms=0.611 (0.084%), neg=0, invalid=1235 0241: dt=25.600000, rms=0.610 (0.117%), neg=0, invalid=1235 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0242: dt=25.600000, rms=0.609 (0.169%), neg=0, invalid=1235 iter 0, gcam->neg = 2 after 4 iterations, nbhd size=0, neg = 0 0243: dt=25.600000, rms=0.608 (0.221%), neg=0, invalid=1235 0244: dt=25.600000, rms=0.606 (0.302%), neg=0, invalid=1235 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0245: dt=25.600000, rms=0.603 (0.424%), neg=0, invalid=1235 iter 0, gcam->neg = 2 after 3 iterations, nbhd size=0, neg = 0 0246: dt=25.600000, rms=0.600 (0.439%), neg=0, invalid=1235 iter 0, gcam->neg = 10 after 5 iterations, nbhd size=0, neg = 0 0247: dt=25.600000, rms=0.598 (0.344%), neg=0, invalid=1235 iter 0, gcam->neg = 18 after 10 iterations, nbhd size=0, neg = 0 0248: dt=25.600000, rms=0.597 (0.172%), neg=0, invalid=1235 iter 0, gcam->neg = 26 after 11 iterations, nbhd size=0, neg = 0 0249: dt=25.600000, rms=0.597 (0.025%), neg=0, invalid=1235 iter 0, gcam->neg = 41 after 10 iterations, nbhd size=0, neg = 0 0250: dt=25.600000, rms=0.597 (-0.099%), neg=0, invalid=1235 0251: dt=0.000586, rms=0.597 (0.000%), neg=0, invalid=1235 0252: dt=0.000000, rms=0.597 (0.000%), neg=0, invalid=1235 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.608, neg=0, invalid=1235 0253: dt=0.000000, rms=0.608 (0.000%), neg=0, invalid=1235 0254: dt=0.150000, rms=0.608 (-0.047%), neg=0, invalid=1235 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.608, neg=0, invalid=1235 0255: dt=0.000000, rms=0.608 (0.000%), neg=0, invalid=1235 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.630, neg=0, invalid=1235 0256: dt=0.384000, rms=0.629 (0.154%), neg=0, invalid=1235 0257: dt=0.000000, rms=0.629 (0.000%), neg=0, invalid=1235 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.629, neg=0, invalid=1235 0258: dt=0.064000, rms=0.629 (0.003%), neg=0, invalid=1235 0259: dt=0.000000, rms=0.629 (0.000%), neg=0, invalid=1235 0260: dt=0.100000, rms=0.629 (-0.008%), neg=0, invalid=1235 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.601, neg=0, invalid=1235 iter 0, gcam->neg = 77 after 7 iterations, nbhd size=0, neg = 0 0261: dt=0.665094, rms=0.589 (2.083%), neg=0, invalid=1235 0262: dt=0.028000, rms=0.589 (0.026%), neg=0, invalid=1235 0263: dt=0.028000, rms=0.589 (-0.007%), neg=0, invalid=1235 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.589, neg=0, invalid=1235 0264: dt=0.028000, rms=0.589 (0.014%), neg=0, invalid=1235 0265: dt=0.000000, rms=0.589 (0.000%), neg=0, invalid=1235 writing output transformation to transforms/talairach.m3z... GCAMwrite registration took 0 hours, 41 minutes and 10 seconds. #-------------------------------------- #@# Remove Neck Sun May 10 22:28:33 CDT 2020 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /opt/local/freesurfer-6.0/x86_64/average/RB_all_2014-08-21.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/opt/local/freesurfer-6.0/x86_64/average/RB_all_2014-08-21.gca'... reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... setting orig areas to linear transform determinant scaled 7.67 removing structures at least 25 mm from brain... 11050657 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 0 minutes and 40 seconds. #-------------------------------------- #@# SkullLTA Sun May 10 22:29:12 CDT 2020 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /opt/local/freesurfer-6.0/x86_64/average/RB_all_withskull_2014-08-21.gca transforms/talairach_with_skull_2.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 using previously computed transform transforms/talairach.lta == Number of threads available to mri_em_register for OpenMP = 8 == reading 1 input volumes... logging results to talairach_with_skull_2.log reading '/opt/local/freesurfer-6.0/x86_64/average/RB_all_withskull_2014-08-21.gca'... average std = 23.5 using min determinant for regularization = 55.2 0 singular and 5018 ill-conditioned covariance matrices regularized reading 'nu_noneck.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 15.9 or > 1063.6 total sample mean = 86.3 (1445 zeros) ************************************************ spacing=8, using 3388 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3388, passno 0, spacing 8 resetting wm mean[0]: 110 --> 118 resetting gm mean[0]: 70 --> 70 input volume #1 is the most T1-like using real data threshold=13.0 skull bounding box = (42, 18, 17) --> (205, 174, 218) using (96, 70, 118) as brain centroid... mean wm in atlas = 118, using box (76,51,93) --> (116, 89,142) to find MRI wm before smoothing, mri peak at 109 after smoothing, mri peak at 109, scaling input intensities by 1.083 scaling channel 0 by 1.08257 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.041, old_max_log_p =-4.232 (thresh=-4.2) 1.16530 -0.03748 -0.03953 -14.81171; 0.04027 1.19985 0.00793 -3.77614; 0.03269 -0.00906 1.04698 -19.93194; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.041, old_max_log_p =-4.041 (thresh=-4.0) 1.16530 -0.03748 -0.03953 -14.81171; 0.04027 1.19985 0.00793 -3.77614; 0.03269 -0.00906 1.04698 -19.93194; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.970, old_max_log_p =-4.041 (thresh=-4.0) 1.09874 0.07860 -0.04180 -14.26245; -0.07378 1.21904 -0.02395 14.54169; 0.03585 0.02820 1.02703 -20.15535; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.964, old_max_log_p =-3.970 (thresh=-4.0) 1.09874 0.07860 -0.04180 -14.26245; -0.07239 1.19618 -0.02350 16.65952; 0.03585 0.02820 1.02703 -20.15535; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.964, old_max_log_p =-3.964 (thresh=-4.0) 1.09874 0.07860 -0.04180 -14.26245; -0.07239 1.19618 -0.02350 16.65952; 0.03585 0.02820 1.02703 -20.15535; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.952, old_max_log_p =-3.964 (thresh=-4.0) 1.09617 0.07841 -0.04170 -13.93189; -0.07256 1.19898 -0.02356 16.39976; 0.03589 0.02823 1.02823 -20.30593; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.951, old_max_log_p =-3.952 (thresh=-3.9) 1.09617 0.07841 -0.04170 -13.93189; -0.07273 1.20179 -0.02361 16.13938; 0.03589 0.02823 1.02823 -20.30593; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3388 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.09617 0.07841 -0.04170 -13.93189; -0.07273 1.20179 -0.02361 16.13938; 0.03589 0.02823 1.02823 -20.30593; 0.00000 0.00000 0.00000 1.00000; nsamples 3388 Quasinewton: input matrix 1.09617 0.07841 -0.04170 -13.93189; -0.07273 1.20179 -0.02361 16.13938; 0.03589 0.02823 1.02823 -20.30593; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.09617 0.07841 -0.04170 -13.93189; -0.07273 1.20179 -0.02361 16.13938; 0.03589 0.02823 1.02823 -20.30593; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.951 (old=-4.232) transform before final EM align: 1.09617 0.07841 -0.04170 -13.93189; -0.07273 1.20179 -0.02361 16.13938; 0.03589 0.02823 1.02823 -20.30593; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 380366 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.09617 0.07841 -0.04170 -13.93189; -0.07273 1.20179 -0.02361 16.13938; 0.03589 0.02823 1.02823 -20.30593; 0.00000 0.00000 0.00000 1.00000; nsamples 380366 Quasinewton: input matrix 1.09617 0.07841 -0.04170 -13.93189; -0.07273 1.20179 -0.02361 16.13938; 0.03589 0.02823 1.02823 -20.30593; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = 4.3 tol 0.000000 final transform: 1.09617 0.07841 -0.04170 -13.93189; -0.07273 1.20179 -0.02361 16.13938; 0.03589 0.02823 1.02823 -20.30593; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull_2.lta... registration took 14 minutes and 13 seconds. #-------------------------------------- #@# SubCort Seg Sun May 10 22:43:25 CDT 2020 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /opt/local/freesurfer-6.0/x86_64/average/RB_all_2014-08-21.gca aseg.auto_noCCseg.mgz sysname Linux hostname frames1.cmrr.umn.edu machine x86_64 setenv SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects cd /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /opt/local/freesurfer-6.0/x86_64/average/RB_all_2014-08-21.gca aseg.auto_noCCseg.mgz == Number of threads available to mri_ca_label for OpenMP = 8 == relabeling unlikely voxels with window_size = 9 and prior threshold 0.30 using Gibbs prior factor = 0.500 renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes... reading classifier array from /opt/local/freesurfer-6.0/x86_64/average/RB_all_2014-08-21.gca... reading input volume from norm.mgz... average std[0] = 5.4 reading transform from transforms/talairach.m3z... setting orig areas to linear transform determinant scaled 7.67 Atlas used for the 3D morph was /opt/local/freesurfer-6.0/x86_64/average/RB_all_2014-08-21.gca average std = 5.4 using min determinant for regularization = 2.9 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15536 (18) mri peak = 0.29125 (20) Left_Lateral_Ventricle (4): linear fit = 1.18 x + 0.0 (1703 voxels, overlap=0.745) Left_Lateral_Ventricle (4): linear fit = 1.18 x + 0.0 (1703 voxels, peak = 21), gca=21.3 gca peak = 0.20988 (12) mri peak = 0.20000 (20) Right_Lateral_Ventricle (43): linear fit = 1.57 x + 0.0 (1380 voxels, overlap=0.314) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (1380 voxels, peak = 19), gca=18.0 gca peak = 0.21579 (92) mri peak = 0.15019 (94) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (943 voxels, overlap=1.002) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (943 voxels, peak = 91), gca=90.6 gca peak = 0.13705 (96) mri peak = 0.15278 (94) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (775 voxels, overlap=0.967) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (775 voxels, peak = 96), gca=95.5 gca peak = 0.28180 (56) mri peak = 0.11470 (70) Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (1174 voxels, overlap=0.022) Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (1174 voxels, peak = 69), gca=68.6 gca peak = 0.27854 (59) mri peak = 0.08901 (69) Left_Hippocampus (17): linear fit = 1.14 x + 0.0 (955 voxels, overlap=0.031) Left_Hippocampus (17): linear fit = 1.14 x + 0.0 (955 voxels, peak = 68), gca=67.6 gca peak = 0.09269 (102) mri peak = 0.17628 (101) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (58085 voxels, overlap=0.624) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (58085 voxels, peak = 101), gca=101.5 gca peak = 0.09448 (102) mri peak = 0.14377 (101) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (60233 voxels, overlap=0.682) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (60233 voxels, peak = 101), gca=101.5 gca peak = 0.09357 (56) mri peak = 0.03966 (71) Left_Cerebral_Cortex (3): linear fit = 1.18 x + 0.0 (46006 voxels, overlap=0.412) Left_Cerebral_Cortex (3): linear fit = 1.18 x + 0.0 (46006 voxels, peak = 66), gca=66.4 gca peak = 0.10853 (57) mri peak = 0.04626 (71) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (44238 voxels, overlap=0.234) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (44238 voxels, peak = 70), gca=69.8 gca peak = 0.22877 (65) mri peak = 0.14209 (78) Right_Caudate (50): linear fit = 1.16 x + 0.0 (875 voxels, overlap=0.017) Right_Caudate (50): linear fit = 1.16 x + 0.0 (875 voxels, peak = 76), gca=75.7 gca peak = 0.19901 (77) mri peak = 0.12872 (77) Left_Caudate (11): linear fit = 1.02 x + 0.0 (822 voxels, overlap=0.677) Left_Caudate (11): linear fit = 1.02 x + 0.0 (822 voxels, peak = 79), gca=78.9 gca peak = 0.13815 (57) mri peak = 0.06462 (71) Left_Cerebellum_Cortex (8): linear fit = 1.25 x + 0.0 (30024 voxels, overlap=0.028) Left_Cerebellum_Cortex (8): linear fit = 1.25 x + 0.0 (30024 voxels, peak = 72), gca=71.5 gca peak = 0.14395 (56) mri peak = 0.07387 (74) Right_Cerebellum_Cortex (47): linear fit = 1.26 x + 0.0 (30064 voxels, overlap=0.003) Right_Cerebellum_Cortex (47): linear fit = 1.26 x + 0.0 (30064 voxels, peak = 71), gca=70.8 gca peak = 0.15921 (87) mri peak = 0.14595 (88) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (6546 voxels, overlap=0.808) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (6546 voxels, peak = 89), gca=89.2 gca peak = 0.15745 (88) mri peak = 0.15974 (89) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (6081 voxels, overlap=0.695) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (6081 voxels, peak = 90), gca=90.2 gca peak = 0.33492 (58) mri peak = 0.10032 (70) Left_Amygdala (18): linear fit = 1.22 x + 0.0 (463 voxels, overlap=0.056) Left_Amygdala (18): linear fit = 1.22 x + 0.0 (463 voxels, peak = 70), gca=70.5 gca peak = 0.38792 (57) mri peak = 0.10467 (73) Right_Amygdala (54): linear fit = 1.25 x + 0.0 (535 voxels, overlap=0.056) Right_Amygdala (54): linear fit = 1.25 x + 0.0 (535 voxels, peak = 72), gca=71.5 gca peak = 0.10264 (89) mri peak = 0.07001 (86) Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (4844 voxels, overlap=0.999) Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (4844 voxels, peak = 87), gca=86.8 gca peak = 0.11924 (80) mri peak = 0.07813 (89) Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (4310 voxels, overlap=0.847) Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (4310 voxels, peak = 84), gca=83.6 gca peak = 0.08243 (73) mri peak = 0.08942 (84) Left_Putamen (12): linear fit = 1.07 x + 0.0 (2447 voxels, overlap=0.616) Left_Putamen (12): linear fit = 1.07 x + 0.0 (2447 voxels, peak = 78), gca=77.7 gca peak = 0.08499 (73) mri peak = 0.08799 (78) Right_Putamen (51): linear fit = 1.07 x + 0.0 (2531 voxels, overlap=0.546) Right_Putamen (51): linear fit = 1.07 x + 0.0 (2531 voxels, peak = 78), gca=77.7 gca peak = 0.08201 (81) mri peak = 0.10343 (89) Brain_Stem (16): linear fit = 1.09 x + 0.0 (12963 voxels, overlap=0.430) Brain_Stem (16): linear fit = 1.09 x + 0.0 (12963 voxels, peak = 88), gca=87.9 gca peak = 0.12033 (89) mri peak = 0.09580 (96) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (1483 voxels, overlap=0.794) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (1483 voxels, peak = 96), gca=95.7 gca peak = 0.13960 (88) mri peak = 0.08816 (96) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1605 voxels, overlap=0.858) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1605 voxels, peak = 95), gca=94.6 gca peak = 0.16463 (25) mri peak = 0.29350 (25) Third_Ventricle (14): linear fit = 0.90 x + 0.0 (84 voxels, overlap=0.652) Third_Ventricle (14): linear fit = 0.90 x + 0.0 (84 voxels, peak = 23), gca=22.6 gca peak = 0.17079 (16) mri peak = 0.19157 (24) Fourth_Ventricle (15): linear fit = 1.47 x + 0.0 (458 voxels, overlap=0.228) Fourth_Ventricle (15): linear fit = 1.47 x + 0.0 (458 voxels, peak = 23), gca=23.4 gca peak Unknown = 0.99973 ( 0) gca peak Left_Inf_Lat_Vent = 0.19138 (27) gca peak Left_Thalamus = 1.00000 (95) gca peak CSF = 0.18522 (37) gca peak Left_Accumbens_area = 0.81672 (61) gca peak Left_undetermined = 1.00000 (27) gca peak Left_vessel = 0.90109 (52) gca peak Left_choroid_plexus = 0.11021 (34) gca peak Right_Inf_Lat_Vent = 0.32288 (23) gca peak Right_Accumbens_area = 0.42985 (63) gca peak Right_vessel = 0.81415 (51) gca peak Right_choroid_plexus = 0.13411 (37) gca peak Fifth_Ventricle = 0.85881 (30) gca peak WM_hypointensities = 0.11222 (75) gca peak non_WM_hypointensities = 0.10810 (55) gca peak Optic_Chiasm = 0.54080 (77) not using caudate to estimate GM means estimating mean gm scale to be 1.21 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.26 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.13516 (22) mri peak = 0.29125 (20) Left_Lateral_Ventricle (4): linear fit = 0.93 x + 0.0 (1703 voxels, overlap=0.810) Left_Lateral_Ventricle (4): linear fit = 0.93 x + 0.0 (1703 voxels, peak = 20), gca=20.4 gca peak = 0.15134 (18) mri peak = 0.20000 (20) Right_Lateral_Ventricle (43): linear fit = 1.04 x + 0.0 (1380 voxels, overlap=0.630) Right_Lateral_Ventricle (43): linear fit = 1.04 x + 0.0 (1380 voxels, peak = 19), gca=18.8 gca peak = 0.20526 (91) mri peak = 0.15019 (94) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (943 voxels, overlap=1.002) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (943 voxels, peak = 92), gca=92.4 gca peak = 0.16507 (95) mri peak = 0.15278 (94) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (775 voxels, overlap=0.998) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (775 voxels, peak = 95), gca=94.5 gca peak = 0.30530 (68) mri peak = 0.11470 (70) Right_Hippocampus (53): linear fit = 1.01 x + 0.0 (1174 voxels, overlap=1.003) Right_Hippocampus (53): linear fit = 1.01 x + 0.0 (1174 voxels, peak = 69), gca=69.0 gca peak = 0.28764 (65) mri peak = 0.08901 (69) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (955 voxels, overlap=1.002) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (955 voxels, peak = 65), gca=65.0 gca peak = 0.09588 (101) mri peak = 0.17628 (101) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (58085 voxels, overlap=0.598) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (58085 voxels, peak = 100), gca=100.5 gca peak = 0.09849 (102) mri peak = 0.14377 (101) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (60233 voxels, overlap=0.659) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (60233 voxels, peak = 101), gca=101.5 gca peak = 0.08129 (67) mri peak = 0.03966 (71) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (46006 voxels, overlap=0.962) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (46006 voxels, peak = 67), gca=67.0 gca peak = 0.08839 (70) mri peak = 0.04626 (71) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (44238 voxels, overlap=0.956) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (44238 voxels, peak = 69), gca=69.0 gca peak = 0.20817 (75) mri peak = 0.14209 (78) Right_Caudate (50): linear fit = 0.98 x + 0.0 (875 voxels, overlap=0.998) Right_Caudate (50): linear fit = 0.98 x + 0.0 (875 voxels, peak = 73), gca=73.1 gca peak = 0.17822 (79) mri peak = 0.12872 (77) Left_Caudate (11): linear fit = 1.00 x + 0.0 (822 voxels, overlap=0.801) Left_Caudate (11): linear fit = 1.00 x + 0.0 (822 voxels, peak = 79), gca=79.0 gca peak = 0.10981 (71) mri peak = 0.06462 (71) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (30024 voxels, overlap=0.932) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (30024 voxels, peak = 71), gca=71.0 gca peak = 0.11720 (70) mri peak = 0.07387 (74) Right_Cerebellum_Cortex (47): linear fit = 1.01 x + 0.0 (30064 voxels, overlap=0.949) Right_Cerebellum_Cortex (47): linear fit = 1.01 x + 0.0 (30064 voxels, peak = 71), gca=71.0 gca peak = 0.15577 (89) mri peak = 0.14595 (88) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6546 voxels, overlap=0.902) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6546 voxels, peak = 89), gca=89.0 gca peak = 0.16039 (90) mri peak = 0.15974 (89) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6081 voxels, overlap=0.817) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6081 voxels, peak = 90), gca=90.0 gca peak = 0.31807 (70) mri peak = 0.10032 (70) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (463 voxels, overlap=1.009) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (463 voxels, peak = 70), gca=70.0 gca peak = 0.37496 (71) mri peak = 0.10467 (73) Right_Amygdala (54): linear fit = 1.03 x + 0.0 (535 voxels, overlap=1.022) Right_Amygdala (54): linear fit = 1.03 x + 0.0 (535 voxels, peak = 73), gca=73.5 gca peak = 0.10640 (87) mri peak = 0.07001 (86) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4844 voxels, overlap=0.972) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4844 voxels, peak = 87), gca=86.6 gca peak = 0.10663 (83) mri peak = 0.07813 (89) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4310 voxels, overlap=0.924) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4310 voxels, peak = 83), gca=82.6 gca peak = 0.09475 (78) mri peak = 0.08942 (84) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2447 voxels, overlap=0.833) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2447 voxels, peak = 78), gca=78.0 gca peak = 0.08266 (83) mri peak = 0.08799 (78) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2531 voxels, overlap=0.835) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2531 voxels, peak = 83), gca=83.0 gca peak = 0.06963 (88) mri peak = 0.10343 (89) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12963 voxels, overlap=0.736) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12963 voxels, peak = 88), gca=87.6 gca peak = 0.11595 (97) mri peak = 0.09580 (96) Right_VentralDC (60): linear fit = 0.99 x + 0.0 (1483 voxels, overlap=0.864) Right_VentralDC (60): linear fit = 0.99 x + 0.0 (1483 voxels, peak = 96), gca=95.5 gca peak = 0.13061 (95) mri peak = 0.08816 (96) Left_VentralDC (28): linear fit = 0.98 x + 0.0 (1605 voxels, overlap=0.874) Left_VentralDC (28): linear fit = 0.98 x + 0.0 (1605 voxels, peak = 93), gca=92.6 gca peak = 0.19008 (24) mri peak = 0.29350 (25) Third_Ventricle (14): linear fit = 1.03 x + 0.0 (84 voxels, overlap=0.736) Third_Ventricle (14): linear fit = 1.03 x + 0.0 (84 voxels, peak = 25), gca=24.8 gca peak = 0.18485 (23) mri peak = 0.19157 (24) Fourth_Ventricle (15): linear fit = 0.99 x + 0.0 (458 voxels, overlap=0.645) Fourth_Ventricle (15): linear fit = 0.99 x + 0.0 (458 voxels, peak = 23), gca=22.7 gca peak Unknown = 0.99973 ( 0) gca peak Left_Inf_Lat_Vent = 0.19593 (31) gca peak Left_Thalamus = 0.32757 (109) gca peak CSF = 0.20729 (46) gca peak Left_Accumbens_area = 0.69428 (63) gca peak Left_undetermined = 1.00000 (27) gca peak Left_vessel = 0.89575 (52) gca peak Left_choroid_plexus = 0.10177 (34) gca peak Right_Inf_Lat_Vent = 0.37950 (29) gca peak Right_Accumbens_area = 0.31907 (74) gca peak Right_vessel = 0.81415 (51) gca peak Right_choroid_plexus = 0.13660 (37) gca peak Fifth_Ventricle = 0.69651 (37) gca peak WM_hypointensities = 0.10261 (75) gca peak non_WM_hypointensities = 0.10657 (55) gca peak Optic_Chiasm = 0.54036 (77) not using caudate to estimate GM means estimating mean gm scale to be 1.01 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.00 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 50909 voxels changed in iteration 0 of unlikely voxel relabeling 247 voxels changed in iteration 1 of unlikely voxel relabeling 6 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 51687 gm and wm labels changed (%27 to gray, %73 to white out of all changed labels) 291 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 51608 changed. image ll: -1.966, PF=0.500 pass 2: 12415 changed. image ll: -1.965, PF=0.500 pass 3: 3891 changed. MRItoUCHAR: min=0, max=85 MRItoUCHAR: converting to UCHAR writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 31 minutes and 48 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/cc_up.lta subject7_V1 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/cc_up.lta reading aseg from /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/aseg.auto_noCCseg.mgz reading norm from /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/norm.mgz 60601 voxels in left wm, 101175 in right wm, xrange [118, 133] searching rotation angles z=[-8 6], y=[-10 4] searching scale 1 Z rot -8.3 searching scale 1 Z rot -8.0 searching scale 1 Z rot -7.8 searching scale 1 Z rot -7.5 searching scale 1 Z rot -7.3 searching scale 1 Z rot -7.0 searching scale 1 Z rot -6.8 searching scale 1 Z rot -6.5 searching scale 1 Z rot -6.3 searching scale 1 Z rot -6.0 searching scale 1 Z rot -5.8 searching scale 1 Z rot -5.5 searching scale 1 Z rot -5.3 searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.8 searching scale 1 Z rot -4.5 searching scale 1 Z rot -4.3 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.8 searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.3 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.8 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.3 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.8 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.3 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.8 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.3 searching scale 1 Z rot -0.0 searching scale 1 Z rot 0.2 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.7 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.2 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.7 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.2 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.7 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.2 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.7 searching scale 1 Z rot 4.0 searching scale 1 Z rot 4.2 searching scale 1 Z rot 4.5 searching scale 1 Z rot 4.7 searching scale 1 Z rot 5.0 searching scale 1 Z rot 5.2 searching scale 1 Z rot 5.5 searching scale 1 Z rot 5.7 searching scale 1 Z rot 6.0 global minimum found at slice 127.0, rotations (-2.55, -0.77) final transformation (x=127.0, yr=-2.547, zr=-0.768): 0.99892 0.01340 -0.04444 5.26461; -0.01338 0.99991 0.00060 49.63738; 0.04444 0.00000 0.99901 5.47113; 0.00000 0.00000 0.00000 1.00000; updating x range to be [125, 128] in xformed coordinates best xformed slice 127 cc center is found at 127 80 117 eigenvectors: 0.00032 -0.00234 1.00000; 0.14232 -0.98982 -0.00236; 0.98982 0.14232 0.00002; error in mid anterior detected - correcting... error in mid anterior detected - correcting... writing aseg with callosum to /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/aseg.auto.mgz... corpus callosum matter segmentation took 1.2 minutes #-------------------------------------- #@# Merge ASeg Sun May 10 23:16:25 CDT 2020 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Sun May 10 23:16:25 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri mri_normalize -aseg aseg.presurf.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.presurf.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 1076 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 83 (83), valley at 47 (47) csf peak at 22, setting threshold to 62 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 82 (82), valley at 46 (46) csf peak at 21, setting threshold to 61 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 2 minutes and 32 seconds. #-------------------------------------------- #@# Mask BFS Sun May 10 23:18:59 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1602871 voxels in mask (pct= 9.55) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Sun May 10 23:19:00 CDT 2020 mri_segment brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (104.0): 103.7 +- 6.3 [80.0 --> 125.0] GM (76.0) : 75.0 +- 10.4 [30.0 --> 96.0] setting bottom of white matter range to 85.4 setting top of gray matter range to 95.8 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 4766 sparsely connected voxels removed... thickening thin strands.... 20 segments, 3815 filled 16 bright non-wm voxels segmented. 3657 diagonally connected voxels added... white matter segmentation took 1.2 minutes writing output to wm.seg.mgz... mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.39 minutes reading wm segmentation from wm.seg.mgz... 138 voxels added to wm to prevent paths from MTL structures to cortex 3599 additional wm voxels added 0 additional wm voxels added SEG EDIT: 45389 voxels turned on, 59617 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+): 19 found - 19 modified | TOTAL: 19 pass 2 (xy+): 0 found - 19 modified | TOTAL: 19 pass 1 (xy-): 26 found - 26 modified | TOTAL: 45 pass 2 (xy-): 0 found - 26 modified | TOTAL: 45 pass 1 (yz+): 24 found - 24 modified | TOTAL: 69 pass 2 (yz+): 0 found - 24 modified | TOTAL: 69 pass 1 (yz-): 36 found - 36 modified | TOTAL: 105 pass 2 (yz-): 0 found - 36 modified | TOTAL: 105 pass 1 (xz+): 17 found - 17 modified | TOTAL: 122 pass 2 (xz+): 0 found - 17 modified | TOTAL: 122 pass 1 (xz-): 18 found - 18 modified | TOTAL: 140 pass 2 (xz-): 0 found - 18 modified | TOTAL: 140 Iteration Number : 1 pass 1 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 pass 1 (+++): 10 found - 10 modified | TOTAL: 14 pass 2 (+++): 0 found - 10 modified | TOTAL: 14 pass 1 (+++): 15 found - 15 modified | TOTAL: 29 pass 2 (+++): 0 found - 15 modified | TOTAL: 29 pass 1 (+++): 6 found - 6 modified | TOTAL: 35 pass 2 (+++): 0 found - 6 modified | TOTAL: 35 Iteration Number : 1 pass 1 (++): 65 found - 65 modified | TOTAL: 65 pass 2 (++): 0 found - 65 modified | TOTAL: 65 pass 1 (+-): 79 found - 79 modified | TOTAL: 144 pass 2 (+-): 1 found - 80 modified | TOTAL: 145 pass 3 (+-): 0 found - 80 modified | TOTAL: 145 pass 1 (--): 89 found - 89 modified | TOTAL: 234 pass 2 (--): 0 found - 89 modified | TOTAL: 234 pass 1 (-+): 95 found - 95 modified | TOTAL: 329 pass 2 (-+): 0 found - 95 modified | TOTAL: 329 Iteration Number : 2 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 2 found - 2 modified | TOTAL: 4 pass 2 (xy-): 0 found - 2 modified | TOTAL: 4 pass 1 (yz+): 5 found - 5 modified | TOTAL: 9 pass 2 (yz+): 0 found - 5 modified | TOTAL: 9 pass 1 (yz-): 2 found - 2 modified | TOTAL: 11 pass 2 (yz-): 0 found - 2 modified | TOTAL: 11 pass 1 (xz+): 2 found - 2 modified | TOTAL: 13 pass 2 (xz+): 0 found - 2 modified | TOTAL: 13 pass 1 (xz-): 6 found - 6 modified | TOTAL: 19 pass 2 (xz-): 0 found - 6 modified | TOTAL: 19 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 2 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 2 found - 2 modified | TOTAL: 3 pass 2 (+-): 0 found - 2 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 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 532 (out of 543557: 0.097874) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Sun May 10 23:20:42 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 1.01331 -0.03259 -0.03437 3.65623; 0.03502 1.04335 0.00689 13.34588; 0.03073 -0.00852 0.98423 -12.22646; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.01331 -0.03259 -0.03437 3.65623; 0.03502 1.04335 0.00689 13.34588; 0.03073 -0.00852 0.98423 -12.22646; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 912 (min = 350, max = 1400), aspect = 0.40 (min = 0.10, max = 0.75) no need to search using seed (124, 120, 145), TAL = (4.0, 17.0, 8.0) talairach voxel to voxel transform 0.98476 0.03104 0.03417 -3.59697; -0.03285 0.95736 -0.00785 -12.75272; -0.03103 0.00731 1.01489 12.42429; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (124, 120, 145) --> (4.0, 17.0, 8.0) done. writing output to filled.mgz... filling took 0.5 minutes talairach cc position changed to (4.00, 17.00, 8.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(22.00, 17.00, 8.00) SRC: (109.47, 97.51, 157.17) search lh wm seed point around talairach space (-14.00, 17.00, 8.00), SRC: (144.92, 96.33, 156.05) 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 Sun May 10 23:21:11 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 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 : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 0 (out of 264607: 0.000000) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.38 2014/03/22 00:41:04 greve Exp $ $Id: mrisurf.c,v 1.770 2015/08/26 16:48:39 fischl Exp $ slice 40: 1726 vertices, 1841 faces slice 50: 7087 vertices, 7315 faces slice 60: 14773 vertices, 15071 faces slice 70: 24369 vertices, 24735 faces slice 80: 35365 vertices, 35705 faces slice 90: 46457 vertices, 46827 faces slice 100: 57823 vertices, 58203 faces slice 110: 70520 vertices, 70924 faces slice 120: 82600 vertices, 83001 faces slice 130: 94766 vertices, 95151 faces slice 140: 105884 vertices, 106245 faces slice 150: 114300 vertices, 114604 faces slice 160: 121814 vertices, 122146 faces slice 170: 129713 vertices, 129981 faces slice 180: 135892 vertices, 136124 faces slice 190: 141084 vertices, 141251 faces slice 200: 143030 vertices, 143052 faces slice 210: 143030 vertices, 143052 faces slice 220: 143030 vertices, 143052 faces slice 230: 143030 vertices, 143052 faces slice 240: 143030 vertices, 143052 faces slice 250: 143030 vertices, 143052 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 143030 voxel in cpt #1: X=-22 [v=143030,e=429156,f=286104] located at (-25.944159, -16.784695, 37.694023) For the whole surface: X=-22 [v=143030,e=429156,f=286104] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Sun May 10 23:21:16 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 1 found - 1 modified | TOTAL: 2 pass 2 (yz-): 0 found - 1 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 1 found - 1 modified | TOTAL: 2 pass 2 (+-): 0 found - 1 modified | TOTAL: 2 pass 1 (--): 1 found - 1 modified | TOTAL: 3 pass 2 (--): 0 found - 1 modified | TOTAL: 3 pass 1 (-+): 0 found - 0 modified | TOTAL: 3 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 = 5 (out of 259968: 0.001923) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.38 2014/03/22 00:41:04 greve Exp $ $Id: mrisurf.c,v 1.770 2015/08/26 16:48:39 fischl Exp $ slice 50: 914 vertices, 1021 faces slice 60: 7803 vertices, 8092 faces slice 70: 16892 vertices, 17259 faces slice 80: 26862 vertices, 27190 faces slice 90: 37514 vertices, 37840 faces slice 100: 48104 vertices, 48460 faces slice 110: 60262 vertices, 60660 faces slice 120: 72638 vertices, 73085 faces slice 130: 85089 vertices, 85500 faces slice 140: 96496 vertices, 96871 faces slice 150: 106655 vertices, 107024 faces slice 160: 114952 vertices, 115212 faces slice 170: 122448 vertices, 122737 faces slice 180: 129732 vertices, 129981 faces slice 190: 135636 vertices, 135870 faces slice 200: 139116 vertices, 139166 faces slice 210: 139168 vertices, 139194 faces slice 220: 139168 vertices, 139194 faces slice 230: 139168 vertices, 139194 faces slice 240: 139168 vertices, 139194 faces slice 250: 139168 vertices, 139194 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 139168 voxel in cpt #1: X=-26 [v=139168,e=417582,f=278388] located at (28.236090, -10.283161, 39.742989) For the whole surface: X=-26 [v=139168,e=417582,f=278388] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Sun May 10 23:21:22 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix #-------------------------------------------- #@# Smooth1 rh Sun May 10 23:21:22 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix Waiting for PID 23172 of (23172 23175) to complete... Waiting for PID 23175 of (23172 23175) to complete... mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... PIDs (23172 23175) completed and logs appended. #-------------------------------------------- #@# Inflation1 lh Sun May 10 23:21:27 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix #-------------------------------------------- #@# Inflation1 rh Sun May 10 23:21:27 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Waiting for PID 23249 of (23249 23253) to complete... Waiting for PID 23253 of (23249 23253) to complete... mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 46.6 mm, total surface area = 75743 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.4 minutes step 000: RMS=0.151 (target=0.015) step 005: RMS=0.113 (target=0.015) step 010: RMS=0.083 (target=0.015) step 015: RMS=0.069 (target=0.015) step 020: RMS=0.059 (target=0.015) step 025: RMS=0.050 (target=0.015) step 030: RMS=0.045 (target=0.015) step 035: RMS=0.040 (target=0.015) step 040: RMS=0.037 (target=0.015) step 045: RMS=0.034 (target=0.015) step 050: RMS=0.031 (target=0.015) step 055: RMS=0.030 (target=0.015) step 060: RMS=0.029 (target=0.015) inflation complete. Not saving sulc mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 46.1 mm, total surface area = 73605 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.3 minutes step 000: RMS=0.152 (target=0.015) step 005: RMS=0.113 (target=0.015) step 010: RMS=0.085 (target=0.015) step 015: RMS=0.073 (target=0.015) step 020: RMS=0.062 (target=0.015) step 025: RMS=0.055 (target=0.015) step 030: RMS=0.049 (target=0.015) step 035: RMS=0.044 (target=0.015) step 040: RMS=0.042 (target=0.015) step 045: RMS=0.039 (target=0.015) step 050: RMS=0.038 (target=0.015) step 055: RMS=0.037 (target=0.015) step 060: RMS=0.037 (target=0.015) inflation complete. Not saving sulc PIDs (23249 23253) completed and logs appended. #-------------------------------------------- #@# QSphere lh Sun May 10 23:21:52 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix #-------------------------------------------- #@# QSphere rh Sun May 10 23:21:52 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix Waiting for PID 23361 of (23361 23364) to complete... Waiting for PID 23364 of (23361 23364) to complete... 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 1.59 2014/11/06 01:38:58 nicks Exp $ $Id: mrisurf.c,v 1.770 2015/08/26 16:48:39 fischl Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.96 +- 0.56 (0.00-->9.00) (max @ vno 57497 --> 58628) face area 0.02 +- 0.03 (-0.51-->0.71) == Number of threads available to mris_sphere for OpenMP = 8 == scaling brain by 0.298... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.223, avgs=0 005/300: dt: 0.9000, rms radial error=176.962, avgs=0 010/300: dt: 0.9000, rms radial error=176.402, avgs=0 015/300: dt: 0.9000, rms radial error=175.670, avgs=0 020/300: dt: 0.9000, rms radial error=174.838, avgs=0 025/300: dt: 0.9000, rms radial error=173.945, avgs=0 030/300: dt: 0.9000, rms radial error=173.020, avgs=0 035/300: dt: 0.9000, rms radial error=172.078, avgs=0 040/300: dt: 0.9000, rms radial error=171.129, avgs=0 045/300: dt: 0.9000, rms radial error=170.178, avgs=0 050/300: dt: 0.9000, rms radial error=169.229, avgs=0 055/300: dt: 0.9000, rms radial error=168.282, avgs=0 060/300: dt: 0.9000, rms radial error=167.340, avgs=0 065/300: dt: 0.9000, rms radial error=166.401, avgs=0 070/300: dt: 0.9000, rms radial error=165.468, avgs=0 075/300: dt: 0.9000, rms radial error=164.539, avgs=0 080/300: dt: 0.9000, rms radial error=163.616, avgs=0 085/300: dt: 0.9000, rms radial error=162.697, avgs=0 090/300: dt: 0.9000, rms radial error=161.784, avgs=0 095/300: dt: 0.9000, rms radial error=160.875, avgs=0 100/300: dt: 0.9000, rms radial error=159.972, avgs=0 105/300: dt: 0.9000, rms radial error=159.073, avgs=0 110/300: dt: 0.9000, rms radial error=158.180, avgs=0 115/300: dt: 0.9000, rms radial error=157.291, avgs=0 120/300: dt: 0.9000, rms radial error=156.407, avgs=0 125/300: dt: 0.9000, rms radial error=155.529, avgs=0 130/300: dt: 0.9000, rms radial error=154.655, avgs=0 135/300: dt: 0.9000, rms radial error=153.786, avgs=0 140/300: dt: 0.9000, rms radial error=152.922, avgs=0 145/300: dt: 0.9000, rms radial error=152.063, avgs=0 150/300: dt: 0.9000, rms radial error=151.209, avgs=0 155/300: dt: 0.9000, rms radial error=150.360, avgs=0 160/300: dt: 0.9000, rms radial error=149.515, avgs=0 165/300: dt: 0.9000, rms radial error=148.675, avgs=0 170/300: dt: 0.9000, rms radial error=147.839, avgs=0 175/300: dt: 0.9000, rms radial error=147.008, avgs=0 180/300: dt: 0.9000, rms radial error=146.181, avgs=0 185/300: dt: 0.9000, rms radial error=145.360, avgs=0 190/300: dt: 0.9000, rms radial error=144.542, avgs=0 195/300: dt: 0.9000, rms radial error=143.729, avgs=0 200/300: dt: 0.9000, rms radial error=142.921, avgs=0 205/300: dt: 0.9000, rms radial error=142.117, avgs=0 210/300: dt: 0.9000, rms radial error=141.317, avgs=0 215/300: dt: 0.9000, rms radial error=140.522, avgs=0 220/300: dt: 0.9000, rms radial error=139.731, avgs=0 225/300: dt: 0.9000, rms radial error=138.945, avgs=0 230/300: dt: 0.9000, rms radial error=138.163, avgs=0 235/300: dt: 0.9000, rms radial error=137.385, avgs=0 240/300: dt: 0.9000, rms radial error=136.611, avgs=0 245/300: dt: 0.9000, rms radial error=135.842, avgs=0 250/300: dt: 0.9000, rms radial error=135.077, avgs=0 255/300: dt: 0.9000, rms radial error=134.317, avgs=0 260/300: dt: 0.9000, rms radial error=133.560, avgs=0 265/300: dt: 0.9000, rms radial error=132.808, avgs=0 270/300: dt: 0.9000, rms radial error=132.060, avgs=0 275/300: dt: 0.9000, rms radial error=131.316, avgs=0 280/300: dt: 0.9000, rms radial error=130.576, avgs=0 285/300: dt: 0.9000, rms radial error=129.841, avgs=0 290/300: dt: 0.9000, rms radial error=129.109, avgs=0 295/300: dt: 0.9000, rms radial error=128.382, avgs=0 300/300: dt: 0.9000, rms radial error=127.659, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 16958.50 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00010 epoch 2 (K=40.0), pass 1, starting sse = 2907.69 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00003 epoch 3 (K=160.0), pass 1, starting sse = 302.17 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/10 = 0.00458 epoch 4 (K=640.0), pass 1, starting sse = 16.77 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.10/12 = 0.00816 final distance error %28.17 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.03 hours 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 1.59 2014/11/06 01:38:58 nicks Exp $ $Id: mrisurf.c,v 1.770 2015/08/26 16:48:39 fischl Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.98 +- 0.58 (0.00-->8.06) (max @ vno 46669 --> 47661) face area 0.03 +- 0.03 (-0.28-->0.77) == Number of threads available to mris_sphere for OpenMP = 8 == scaling brain by 0.323... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.683, avgs=0 005/300: dt: 0.9000, rms radial error=175.426, avgs=0 010/300: dt: 0.9000, rms radial error=174.873, avgs=0 015/300: dt: 0.9000, rms radial error=174.147, avgs=0 020/300: dt: 0.9000, rms radial error=173.320, avgs=0 025/300: dt: 0.9000, rms radial error=172.435, avgs=0 030/300: dt: 0.9000, rms radial error=171.518, avgs=0 035/300: dt: 0.9000, rms radial error=170.585, avgs=0 040/300: dt: 0.9000, rms radial error=169.643, avgs=0 045/300: dt: 0.9000, rms radial error=168.700, avgs=0 050/300: dt: 0.9000, rms radial error=167.760, avgs=0 055/300: dt: 0.9000, rms radial error=166.825, avgs=0 060/300: dt: 0.9000, rms radial error=165.894, avgs=0 065/300: dt: 0.9000, rms radial error=164.967, avgs=0 070/300: dt: 0.9000, rms radial error=164.045, avgs=0 075/300: dt: 0.9000, rms radial error=163.127, avgs=0 080/300: dt: 0.9000, rms radial error=162.214, avgs=0 085/300: dt: 0.9000, rms radial error=161.305, avgs=0 090/300: dt: 0.9000, rms radial error=160.402, avgs=0 095/300: dt: 0.9000, rms radial error=159.503, avgs=0 100/300: dt: 0.9000, rms radial error=158.609, avgs=0 105/300: dt: 0.9000, rms radial error=157.719, avgs=0 110/300: dt: 0.9000, rms radial error=156.835, avgs=0 115/300: dt: 0.9000, rms radial error=155.955, avgs=0 120/300: dt: 0.9000, rms radial error=155.079, avgs=0 125/300: dt: 0.9000, rms radial error=154.207, avgs=0 130/300: dt: 0.9000, rms radial error=153.342, avgs=0 135/300: dt: 0.9000, rms radial error=152.481, avgs=0 140/300: dt: 0.9000, rms radial error=151.625, avgs=0 145/300: dt: 0.9000, rms radial error=150.774, avgs=0 150/300: dt: 0.9000, rms radial error=149.927, avgs=0 155/300: dt: 0.9000, rms radial error=149.085, avgs=0 160/300: dt: 0.9000, rms radial error=148.249, avgs=0 165/300: dt: 0.9000, rms radial error=147.417, avgs=0 170/300: dt: 0.9000, rms radial error=146.589, avgs=0 175/300: dt: 0.9000, rms radial error=145.766, avgs=0 180/300: dt: 0.9000, rms radial error=144.948, avgs=0 185/300: dt: 0.9000, rms radial error=144.134, avgs=0 190/300: dt: 0.9000, rms radial error=143.325, avgs=0 195/300: dt: 0.9000, rms radial error=142.520, avgs=0 200/300: dt: 0.9000, rms radial error=141.720, avgs=0 205/300: dt: 0.9000, rms radial error=140.924, avgs=0 210/300: dt: 0.9000, rms radial error=140.132, avgs=0 215/300: dt: 0.9000, rms radial error=139.345, avgs=0 220/300: dt: 0.9000, rms radial error=138.562, avgs=0 225/300: dt: 0.9000, rms radial error=137.784, avgs=0 230/300: dt: 0.9000, rms radial error=137.010, avgs=0 235/300: dt: 0.9000, rms radial error=136.240, avgs=0 240/300: dt: 0.9000, rms radial error=135.475, avgs=0 245/300: dt: 0.9000, rms radial error=134.713, avgs=0 250/300: dt: 0.9000, rms radial error=133.956, avgs=0 255/300: dt: 0.9000, rms radial error=133.204, avgs=0 260/300: dt: 0.9000, rms radial error=132.455, avgs=0 265/300: dt: 0.9000, rms radial error=131.711, avgs=0 270/300: dt: 0.9000, rms radial error=130.971, avgs=0 275/300: dt: 0.9000, rms radial error=130.234, avgs=0 280/300: dt: 0.9000, rms radial error=129.502, avgs=0 285/300: dt: 0.9000, rms radial error=128.774, avgs=0 290/300: dt: 0.9000, rms radial error=128.050, avgs=0 295/300: dt: 0.9000, rms radial error=127.330, avgs=0 300/300: dt: 0.9000, rms radial error=126.615, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 16061.29 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00015 epoch 2 (K=40.0), pass 1, starting sse = 2608.87 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00034 epoch 3 (K=160.0), pass 1, starting sse = 254.14 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.08/11 = 0.00772 epoch 4 (K=640.0), pass 1, starting sse = 17.98 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/10 = 0.00614 final distance error %26.00 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.04 hours PIDs (23361 23364) completed and logs appended. #-------------------------------------------- #@# Fix Topology lh Sun May 10 23:24:03 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology rh Sun May 10 23:24:03 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 subject7_V1 lh mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 subject7_V1 rh Waiting for PID 23831 of (23831 23834) to complete... Waiting for PID 23834 of (23831 23834) to complete... mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 subject7_V1 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 1.770 2015/08/26 16:48:39 fischl Exp $ before topology correction, eno=-22 (nv=143030, nf=286104, ne=429156, g=12) 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... 1706 ambiguous faces found in tessellation segmenting defects... 19 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 19 defects to be corrected 0 vertices coincident reading input surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.2973 (-4.6486) -vertex loglikelihood: -6.0399 (-3.0200) -normal dot loglikelihood: -3.6213 (-3.6213) -quad curv loglikelihood: -6.5045 (-3.2523) Total Loglikelihood : -25.4631 CORRECTING DEFECT 0 (vertices=71, convex hull=122) After retessellation of defect 0, euler #=-16 (141995,425519,283508) : difference with theory (-16) = 0 CORRECTING DEFECT 1 (vertices=26, convex hull=53) After retessellation of defect 1, euler #=-15 (142006,425572,283551) : difference with theory (-15) = 0 CORRECTING DEFECT 2 (vertices=63, convex hull=88) After retessellation of defect 2, euler #=-14 (142030,425678,283634) : difference with theory (-14) = 0 CORRECTING DEFECT 3 (vertices=37, convex hull=67) After retessellation of defect 3, euler #=-13 (142046,425751,283692) : difference with theory (-13) = 0 CORRECTING DEFECT 4 (vertices=115, convex hull=160) After retessellation of defect 4, euler #=-12 (142055,425849,283782) : difference with theory (-12) = 0 CORRECTING DEFECT 5 (vertices=55, convex hull=89) After retessellation of defect 5, euler #=-11 (142082,425967,283874) : difference with theory (-11) = 0 CORRECTING DEFECT 6 (vertices=10, convex hull=27) After retessellation of defect 6, euler #=-10 (142085,425986,283891) : difference with theory (-10) = 0 CORRECTING DEFECT 7 (vertices=6, convex hull=27) After retessellation of defect 7, euler #=-9 (142087,425998,283902) : difference with theory (-9) = 0 CORRECTING DEFECT 8 (vertices=81, convex hull=83) After retessellation of defect 8, euler #=-8 (142121,426131,284002) : difference with theory (-8) = 0 CORRECTING DEFECT 9 (vertices=35, convex hull=75) After retessellation of defect 9, euler #=-7 (142132,426192,284053) : difference with theory (-7) = 0 CORRECTING DEFECT 10 (vertices=6, convex hull=20) After retessellation of defect 10, euler #=-6 (142133,426202,284063) : difference with theory (-6) = 0 CORRECTING DEFECT 11 (vertices=25, convex hull=26) After retessellation of defect 11, euler #=-5 (142135,426217,284077) : difference with theory (-5) = 0 CORRECTING DEFECT 12 (vertices=72, convex hull=74) After retessellation of defect 12, euler #=-4 (142146,426280,284130) : difference with theory (-4) = 0 CORRECTING DEFECT 13 (vertices=95, convex hull=146) After retessellation of defect 13, euler #=-3 (142194,426491,284294) : difference with theory (-3) = 0 CORRECTING DEFECT 14 (vertices=29, convex hull=34) After retessellation of defect 14, euler #=-2 (142199,426518,284317) : difference with theory (-2) = 0 CORRECTING DEFECT 15 (vertices=322, convex hull=92) After retessellation of defect 15, euler #=-1 (142208,426593,284384) : difference with theory (-1) = 0 CORRECTING DEFECT 16 (vertices=17, convex hull=22) After retessellation of defect 16, euler #=0 (142212,426611,284399) : difference with theory (0) = 0 CORRECTING DEFECT 17 (vertices=6, convex hull=19) After retessellation of defect 17, euler #=1 (142213,426618,284406) : difference with theory (1) = 0 CORRECTING DEFECT 18 (vertices=16, convex hull=40) After retessellation of defect 18, euler #=2 (142219,426651,284434) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.22 (0.13-->10.91) (max @ vno 56081 --> 59429) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.22 (0.13-->10.91) (max @ vno 56081 --> 59429) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 74 mutations (32.5%), 154 crossovers (67.5%), 107 vertices were eliminated building final representation... 811 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=142219, nf=284434, ne=426651, g=0) writing corrected surface to /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 8.9 minutes 0 defective edges removing intersecting faces 000: 169 intersecting 001: 7 intersecting mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 subject7_V1 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 1.770 2015/08/26 16:48:39 fischl Exp $ before topology correction, eno=-26 (nv=139168, nf=278388, ne=417582, g=14) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 8 iterations marking ambiguous vertices... 4993 ambiguous faces found in tessellation segmenting defects... 39 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 5 into 3 -merging segment 9 into 7 -merging segment 14 into 13 36 defects to be corrected 0 vertices coincident reading input surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.3560 (-4.6780) -vertex loglikelihood: -6.1373 (-3.0687) -normal dot loglikelihood: -3.6678 (-3.6678) -quad curv loglikelihood: -6.1309 (-3.0654) Total Loglikelihood : -25.2920 CORRECTING DEFECT 0 (vertices=365, convex hull=106) After retessellation of defect 0, euler #=-36 (136252,407957,271669) : difference with theory (-33) = 3 CORRECTING DEFECT 1 (vertices=118, convex hull=73) After retessellation of defect 1, euler #=-35 (136263,408018,271720) : difference with theory (-32) = 3 CORRECTING DEFECT 2 (vertices=63, convex hull=45) After retessellation of defect 2, euler #=-34 (136265,408043,271744) : difference with theory (-31) = 3 CORRECTING DEFECT 3 (vertices=481, convex hull=174) After retessellation of defect 3, euler #=-32 (136309,408259,271918) : difference with theory (-30) = 2 CORRECTING DEFECT 4 (vertices=65, convex hull=46) After retessellation of defect 4, euler #=-31 (136316,408299,271952) : difference with theory (-29) = 2 CORRECTING DEFECT 5 (vertices=28, convex hull=56) After retessellation of defect 5, euler #=-30 (136325,408346,271991) : difference with theory (-28) = 2 CORRECTING DEFECT 6 (vertices=244, convex hull=188) After retessellation of defect 6, euler #=-28 (136336,408468,272104) : difference with theory (-27) = 1 CORRECTING DEFECT 7 (vertices=6, convex hull=33) After retessellation of defect 7, euler #=-27 (136339,408486,272120) : difference with theory (-26) = 1 CORRECTING DEFECT 8 (vertices=11, convex hull=31) After retessellation of defect 8, euler #=-26 (136344,408510,272140) : difference with theory (-25) = 1 CORRECTING DEFECT 9 (vertices=29, convex hull=59) After retessellation of defect 9, euler #=-25 (136355,408566,272186) : difference with theory (-24) = 1 CORRECTING DEFECT 10 (vertices=7, convex hull=21) After retessellation of defect 10, euler #=-24 (136358,408578,272196) : difference with theory (-23) = 1 CORRECTING DEFECT 11 (vertices=257, convex hull=152) After retessellation of defect 11, euler #=-22 (136367,408677,272288) : difference with theory (-22) = 0 CORRECTING DEFECT 12 (vertices=100, convex hull=33) After retessellation of defect 12, euler #=-21 (136377,408717,272319) : difference with theory (-21) = 0 CORRECTING DEFECT 13 (vertices=6, convex hull=17) After retessellation of defect 13, euler #=-20 (136378,408726,272328) : difference with theory (-20) = 0 CORRECTING DEFECT 14 (vertices=5, convex hull=30) After retessellation of defect 14, euler #=-19 (136379,408738,272340) : difference with theory (-19) = 0 CORRECTING DEFECT 15 (vertices=122, convex hull=42) After retessellation of defect 15, euler #=-18 (136391,408789,272380) : difference with theory (-18) = 0 CORRECTING DEFECT 16 (vertices=27, convex hull=34) After retessellation of defect 16, euler #=-17 (136397,408818,272404) : difference with theory (-17) = 0 CORRECTING DEFECT 17 (vertices=90, convex hull=38) After retessellation of defect 17, euler #=-16 (136413,408880,272451) : difference with theory (-16) = 0 CORRECTING DEFECT 18 (vertices=10, convex hull=22) After retessellation of defect 18, euler #=-15 (136416,408896,272465) : difference with theory (-15) = 0 CORRECTING DEFECT 19 (vertices=202, convex hull=51) After retessellation of defect 19, euler #=-14 (136429,408954,272511) : difference with theory (-14) = 0 CORRECTING DEFECT 20 (vertices=8, convex hull=29) After retessellation of defect 20, euler #=-13 (136432,408970,272525) : difference with theory (-13) = 0 CORRECTING DEFECT 21 (vertices=41, convex hull=58) After retessellation of defect 21, euler #=-12 (136449,409044,272583) : difference with theory (-12) = 0 CORRECTING DEFECT 22 (vertices=229, convex hull=61) After retessellation of defect 22, euler #=-11 (136464,409112,272637) : difference with theory (-11) = 0 CORRECTING DEFECT 23 (vertices=25, convex hull=51) After retessellation of defect 23, euler #=-10 (136478,409172,272684) : difference with theory (-10) = 0 CORRECTING DEFECT 24 (vertices=36, convex hull=78) After retessellation of defect 24, euler #=-9 (136495,409249,272745) : difference with theory (-9) = 0 CORRECTING DEFECT 25 (vertices=10, convex hull=19) After retessellation of defect 25, euler #=-8 (136495,409252,272749) : difference with theory (-8) = 0 CORRECTING DEFECT 26 (vertices=16, convex hull=25) After retessellation of defect 26, euler #=-7 (136497,409266,272762) : difference with theory (-7) = 0 CORRECTING DEFECT 27 (vertices=35, convex hull=28) After retessellation of defect 27, euler #=-6 (136502,409289,272781) : difference with theory (-6) = 0 CORRECTING DEFECT 28 (vertices=25, convex hull=30) After retessellation of defect 28, euler #=-5 (136508,409319,272806) : difference with theory (-5) = 0 CORRECTING DEFECT 29 (vertices=35, convex hull=45) After retessellation of defect 29, euler #=-4 (136513,409353,272836) : difference with theory (-4) = 0 CORRECTING DEFECT 30 (vertices=39, convex hull=54) After retessellation of defect 30, euler #=-3 (136534,409439,272902) : difference with theory (-3) = 0 CORRECTING DEFECT 31 (vertices=24, convex hull=69) After retessellation of defect 31, euler #=-2 (136548,409507,272957) : difference with theory (-2) = 0 CORRECTING DEFECT 32 (vertices=36, convex hull=67) After retessellation of defect 32, euler #=-1 (136565,409583,273017) : difference with theory (-1) = 0 CORRECTING DEFECT 33 (vertices=31, convex hull=74) After retessellation of defect 33, euler #=0 (136578,409654,273076) : difference with theory (0) = 0 CORRECTING DEFECT 34 (vertices=63, convex hull=106) After retessellation of defect 34, euler #=1 (136598,409761,273164) : difference with theory (1) = 0 CORRECTING DEFECT 35 (vertices=35, convex hull=65) After retessellation of defect 35, euler #=2 (136618,409848,273232) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.23 (0.10-->10.06) (max @ vno 46517 --> 46605) 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 (0.10-->10.06) (max @ vno 46517 --> 46605) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 136 mutations (35.7%), 245 crossovers (64.3%), 156 vertices were eliminated building final representation... 2550 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=136618, nf=273232, ne=409848, g=0) writing corrected surface to /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 19.9 minutes 0 defective edges removing intersecting faces 000: 220 intersecting 001: 2 intersecting PIDs (23831 23834) completed and logs appended. mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 142219 - 426651 + 284434 = 2 --> 0 holes F =2V-4: 284434 = 284438-4 (0) 2E=3F: 853302 = 853302 (0) total defect index = 0 mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 136618 - 409848 + 273232 = 2 --> 0 holes F =2V-4: 273232 = 273236-4 (0) 2E=3F: 819696 = 819696 (0) total defect index = 0 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 28 intersecting 001: 5 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 21 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf lh Sun May 10 23:44:06 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -noaparc -whiteonly -mgz -T1 brain.finalsurfs subject7_V1 lh #-------------------------------------------- #@# Make White Surf rh Sun May 10 23:44:06 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -noaparc -whiteonly -mgz -T1 brain.finalsurfs subject7_V1 rh Waiting for PID 27759 of (27759 27762) to complete... Waiting for PID 27762 of (27759 27762) to complete... mris_make_surfaces -aseg ../mri/aseg.presurf -noaparc -whiteonly -mgz -T1 brain.finalsurfs subject7_V1 lh only generating white matter surface using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.158 2015/08/05 19:26:19 fischl Exp $ $Id: mrisurf.c,v 1.770 2015/08/26 16:48:39 fischl Exp $ reading volume /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/filled.mgz... reading volume /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/brain.finalsurfs.mgz... reading volume /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/wm.mgz... 13342 bright wm thresholded. 18 bright non-wm voxels segmented. reading original surface position from /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.orig... computing class statistics... border white: 260177 voxels (1.55%) border gray 290448 voxels (1.73%) WM (97.0): 98.0 +- 7.3 [70.0 --> 110.0] GM (86.0) : 84.0 +- 11.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 62.4 (was 70) setting MAX_BORDER_WHITE to 112.3 (was 105) setting MIN_BORDER_WHITE to 74.0 (was 85) setting MAX_CSF to 50.9 (was 40) setting MAX_GRAY to 97.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 68.2 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 39.3 (was 40) repositioning cortical surface to gray/white boundary reading volume /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/../mri/aseg.presurf.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.21 (0.03-->3.97) (max @ vno 56081 --> 59429) face area 0.28 +- 0.12 (0.00-->3.31) mean absolute distance = 0.80 +- 0.98 3914 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105+-4.3, GM=74+-8.7 mean inside = 97.3, mean outside = 81.3 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=84.2, 107 (107) missing vertices, mean dist 0.4 [0.7 (%30.5)->0.9 (%69.5))] %65 local maxima, %30 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=frame, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.26 (0.10-->5.56) (max @ vno 55019 --> 59405) face area 0.28 +- 0.14 (0.00-->4.48) mean absolute distance = 0.40 +- 0.64 3546 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5072030.5, rms=9.720 001: dt: 0.5000, sse=5531925.5, rms=7.089 (27.064%) 002: dt: 0.5000, sse=5811553.0, rms=5.410 (23.693%) 003: dt: 0.5000, sse=6081492.0, rms=4.311 (20.310%) 004: dt: 0.5000, sse=6290018.0, rms=3.610 (16.256%) 005: dt: 0.5000, sse=6392169.0, rms=3.221 (10.783%) 006: dt: 0.5000, sse=6499093.0, rms=2.991 (7.124%) 007: dt: 0.5000, sse=6530747.5, rms=2.887 (3.502%) 008: dt: 0.5000, sse=6557448.0, rms=2.804 (2.849%) rms = 2.78, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=6569639.5, rms=2.778 (0.927%) 010: dt: 0.2500, sse=3952739.8, rms=1.933 (30.414%) 011: dt: 0.2500, sse=3679184.8, rms=1.758 (9.071%) rms = 1.72, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=3565907.0, rms=1.722 (2.032%) rms = 1.69, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=3507768.0, rms=1.691 (1.822%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=87.1, 128 (52) missing vertices, mean dist -0.3 [0.5 (%71.7)->0.3 (%28.3))] %75 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=frame, 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 (0.06-->6.35) (max @ vno 55019 --> 59405) face area 0.35 +- 0.17 (0.00-->7.44) mean absolute distance = 0.30 +- 0.42 4506 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4115634.8, rms=4.570 014: dt: 0.5000, sse=4375948.5, rms=3.015 (34.026%) 015: dt: 0.5000, sse=4788590.5, rms=2.637 (12.537%) 016: dt: 0.5000, sse=5176549.0, rms=2.409 (8.641%) rms = 2.51, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=4274015.0, rms=1.846 (23.398%) 018: dt: 0.2500, sse=3951087.8, rms=1.519 (17.696%) 019: dt: 0.2500, sse=3833329.2, rms=1.402 (7.669%) rms = 1.37, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=3781081.8, rms=1.372 (2.157%) rms = 1.35, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=3742082.0, rms=1.346 (1.934%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 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 mean border=89.5, 106 (35) missing vertices, mean dist -0.2 [0.3 (%73.1)->0.2 (%26.9))] %85 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=frame, 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 (0.07-->6.43) (max @ vno 55019 --> 59405) face area 0.34 +- 0.16 (0.00-->7.53) mean absolute distance = 0.23 +- 0.33 3851 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3976264.8, rms=3.403 022: dt: 0.5000, sse=4216159.5, rms=2.192 (35.572%) rms = 2.20, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=4000689.8, rms=1.692 (22.809%) 024: dt: 0.2500, sse=3928733.8, rms=1.328 (21.536%) 025: dt: 0.2500, sse=3892549.0, rms=1.230 (7.385%) rms = 1.22, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=3860516.8, rms=1.224 (0.487%) rms = 1.20, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=3830778.0, rms=1.202 (1.764%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 4 vertex label from ripped group mean border=90.4, 110 (29) missing vertices, mean dist -0.1 [0.3 (%59.5)->0.2 (%40.5))] %89 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=frame, 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 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=3853114.2, rms=1.694 028: dt: 0.5000, sse=4776438.0, rms=1.377 (18.721%) rms = 1.79, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=4352121.5, rms=1.059 (23.074%) rms = 1.01, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=4174439.5, rms=1.011 (4.565%) rms = 0.97, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=4200902.0, rms=0.971 (3.975%) positioning took 0.4 minutes generating cortex label... 26 non-cortical segments detected only using segment with 6945 vertices erasing segment 1 (vno[0] = 66035) erasing segment 2 (vno[0] = 67287) erasing segment 3 (vno[0] = 74438) erasing segment 4 (vno[0] = 78207) erasing segment 5 (vno[0] = 80522) erasing segment 6 (vno[0] = 86861) erasing segment 7 (vno[0] = 89099) erasing segment 8 (vno[0] = 91418) erasing segment 9 (vno[0] = 93841) erasing segment 10 (vno[0] = 94960) erasing segment 11 (vno[0] = 95016) erasing segment 12 (vno[0] = 97933) erasing segment 13 (vno[0] = 97947) erasing segment 14 (vno[0] = 102452) erasing segment 15 (vno[0] = 102591) erasing segment 16 (vno[0] = 103648) erasing segment 17 (vno[0] = 103823) erasing segment 18 (vno[0] = 104764) erasing segment 19 (vno[0] = 104833) erasing segment 20 (vno[0] = 105665) erasing segment 21 (vno[0] = 106509) erasing segment 22 (vno[0] = 107330) erasing segment 23 (vno[0] = 108110) erasing segment 24 (vno[0] = 108926) erasing segment 25 (vno[0] = 113772) writing cortex label to /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/label/lh.cortex.label... writing curvature file /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.curv writing smoothed area to lh.area writing curvature file /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.area vertex spacing 0.88 +- 0.26 (0.03-->6.41) (max @ vno 55019 --> 59405) face area 0.33 +- 0.16 (0.00-->7.49) refinement took 3.8 minutes mris_make_surfaces -aseg ../mri/aseg.presurf -noaparc -whiteonly -mgz -T1 brain.finalsurfs subject7_V1 rh only generating white matter surface using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.158 2015/08/05 19:26:19 fischl Exp $ $Id: mrisurf.c,v 1.770 2015/08/26 16:48:39 fischl Exp $ reading volume /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/filled.mgz... reading volume /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/brain.finalsurfs.mgz... reading volume /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/wm.mgz... 12465 bright wm thresholded. 17 bright non-wm voxels segmented. reading original surface position from /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.orig... computing class statistics... border white: 260177 voxels (1.55%) border gray 290448 voxels (1.73%) WM (97.0): 97.9 +- 7.1 [70.0 --> 110.0] GM (87.0) : 84.6 +- 11.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 67.9 (was 70) setting MAX_BORDER_WHITE to 113.1 (was 105) setting MIN_BORDER_WHITE to 79.0 (was 85) setting MAX_CSF to 56.8 (was 40) setting MAX_GRAY to 98.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 73.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 45.7 (was 40) repositioning cortical surface to gray/white boundary reading volume /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/../mri/aseg.presurf.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.03-->4.06) (max @ vno 49861 --> 136331) face area 0.28 +- 0.12 (0.00-->3.94) mean absolute distance = 0.78 +- 1.03 3637 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=106+-4.3, GM=79+-8.7 mean inside = 97.4, mean outside = 81.3 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=86.9, 65 (65) missing vertices, mean dist 0.2 [0.8 (%37.4)->0.8 (%62.6))] %51 local maxima, %44 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=frame, 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 (0.10-->5.62) (max @ vno 46605 --> 46613) face area 0.28 +- 0.13 (0.00-->3.54) mean absolute distance = 0.38 +- 0.65 2763 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5043895.5, rms=10.042 001: dt: 0.5000, sse=5297682.5, rms=6.770 (32.583%) 002: dt: 0.5000, sse=5439519.0, rms=4.752 (29.802%) 003: dt: 0.5000, sse=5666821.5, rms=3.698 (22.191%) 004: dt: 0.5000, sse=5816623.0, rms=3.182 (13.945%) 005: dt: 0.5000, sse=5882946.0, rms=2.944 (7.486%) 006: dt: 0.5000, sse=5921815.0, rms=2.808 (4.612%) 007: dt: 0.5000, sse=5945400.0, rms=2.745 (2.254%) 008: dt: 0.5000, sse=5963905.5, rms=2.686 (2.131%) rms = 2.67, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=5944165.0, rms=2.670 (0.605%) 010: dt: 0.2500, sse=3669504.2, rms=1.830 (31.481%) 011: dt: 0.2500, sse=3423536.0, rms=1.665 (8.977%) rms = 1.64, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=3315615.0, rms=1.637 (1.693%) rms = 1.61, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=3259493.8, rms=1.606 (1.912%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=89.4, 48 (9) missing vertices, mean dist -0.2 [0.4 (%70.8)->0.2 (%29.2))] %66 local maxima, %29 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=frame, 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 0.89 +- 0.25 (0.06-->4.94) (max @ vno 47744 --> 46586) face area 0.34 +- 0.16 (0.00-->6.90) mean absolute distance = 0.28 +- 0.42 3087 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3689196.8, rms=3.905 014: dt: 0.5000, sse=3961525.0, rms=2.535 (35.085%) 015: dt: 0.5000, sse=4318941.0, rms=2.317 (8.624%) 016: dt: 0.5000, sse=4659337.5, rms=2.198 (5.099%) rms = 2.35, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=3917039.5, rms=1.687 (23.283%) 018: dt: 0.2500, sse=3669269.5, rms=1.452 (13.927%) 019: dt: 0.2500, sse=3578701.5, rms=1.389 (4.299%) rms = 1.38, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=3540897.2, rms=1.379 (0.719%) rms = 1.36, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=3504896.8, rms=1.356 (1.657%) 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 2 vertex label from ripped group removing 1 vertex label from ripped group mean border=91.6, 58 (4) missing vertices, mean dist -0.2 [0.3 (%72.9)->0.2 (%27.1))] %79 local maxima, %16 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=frame, 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 0.88 +- 0.25 (0.05-->5.71) (max @ vno 47744 --> 46586) face area 0.33 +- 0.16 (0.00-->7.75) mean absolute distance = 0.21 +- 0.33 2691 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3682326.0, rms=3.102 022: dt: 0.5000, sse=3910174.5, rms=2.039 (34.293%) rms = 2.06, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=3711770.5, rms=1.590 (22.007%) 024: dt: 0.2500, sse=3655400.5, rms=1.310 (17.618%) 025: dt: 0.2500, sse=3618484.5, rms=1.246 (4.886%) rms = 1.24, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=3592863.2, rms=1.245 (0.082%) rms = 1.23, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=3573968.5, rms=1.227 (1.425%) positioning took 0.4 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 3 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group mean border=92.4, 60 (4) missing vertices, mean dist -0.1 [0.2 (%57.8)->0.2 (%42.2))] %83 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=frame, 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 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=3587472.8, rms=1.600 028: dt: 0.5000, sse=4414161.0, rms=1.521 (4.932%) rms = 1.75, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=4060151.8, rms=1.156 (23.987%) 030: dt: 0.2500, sse=3917549.5, rms=1.095 (5.244%) rms = 1.10, time step reduction 2 of 3 to 0.125... rms = 1.07, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=3914546.0, rms=1.074 (1.934%) positioning took 0.3 minutes generating cortex label... 21 non-cortical segments detected only using segment with 6844 vertices erasing segment 0 (vno[0] = 29399) erasing segment 1 (vno[0] = 36186) erasing segment 2 (vno[0] = 38000) erasing segment 4 (vno[0] = 45564) erasing segment 5 (vno[0] = 51052) erasing segment 6 (vno[0] = 53228) erasing segment 7 (vno[0] = 54611) erasing segment 8 (vno[0] = 60765) erasing segment 9 (vno[0] = 65598) erasing segment 10 (vno[0] = 71786) erasing segment 11 (vno[0] = 73021) erasing segment 12 (vno[0] = 76876) erasing segment 13 (vno[0] = 77000) erasing segment 14 (vno[0] = 87347) erasing segment 15 (vno[0] = 94051) erasing segment 16 (vno[0] = 94067) erasing segment 17 (vno[0] = 94079) erasing segment 18 (vno[0] = 99849) erasing segment 19 (vno[0] = 111333) erasing segment 20 (vno[0] = 111452) writing cortex label to /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/label/rh.cortex.label... writing curvature file /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.curv writing smoothed area to rh.area writing curvature file /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.area vertex spacing 0.88 +- 0.26 (0.05-->5.93) (max @ vno 46586 --> 47744) face area 0.33 +- 0.16 (0.00-->7.90) refinement took 3.3 minutes PIDs (27759 27762) completed and logs appended. #-------------------------------------------- #@# Smooth2 lh Sun May 10 23:47:54 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm #-------------------------------------------- #@# Smooth2 rh Sun May 10 23:47:54 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm Waiting for PID 28657 of (28657 28660) to complete... Waiting for PID 28660 of (28657 28660) to complete... mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... PIDs (28657 28660) completed and logs appended. #-------------------------------------------- #@# Inflation2 lh Sun May 10 23:48:00 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated #-------------------------------------------- #@# Inflation2 rh Sun May 10 23:48:00 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated Waiting for PID 28743 of (28743 28746) to complete... Waiting for PID 28746 of (28743 28746) to complete... mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 46.8 mm, total surface area = 85325 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.172 (target=0.015) step 005: RMS=0.122 (target=0.015) step 010: RMS=0.089 (target=0.015) step 015: RMS=0.073 (target=0.015) step 020: RMS=0.062 (target=0.015) step 025: RMS=0.051 (target=0.015) step 030: RMS=0.042 (target=0.015) step 035: RMS=0.036 (target=0.015) step 040: RMS=0.032 (target=0.015) step 045: RMS=0.028 (target=0.015) step 050: RMS=0.025 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.022 (target=0.015) inflation complete. inflation took 0.4 minutes mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 46.1 mm, total surface area = 81425 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.170 (target=0.015) step 005: RMS=0.121 (target=0.015) step 010: RMS=0.089 (target=0.015) step 015: RMS=0.075 (target=0.015) step 020: RMS=0.062 (target=0.015) step 025: RMS=0.053 (target=0.015) step 030: RMS=0.044 (target=0.015) step 035: RMS=0.038 (target=0.015) step 040: RMS=0.034 (target=0.015) step 045: RMS=0.030 (target=0.015) step 050: RMS=0.027 (target=0.015) step 055: RMS=0.026 (target=0.015) step 060: RMS=0.024 (target=0.015) inflation complete. inflation took 0.4 minutes PIDs (28743 28746) completed and logs appended. #-------------------------------------------- #@# Curv .H and .K lh Sun May 10 23:48:24 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf mris_curvature -w lh.white mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated #-------------------------------------------- #@# Curv .H and .K rh Sun May 10 23:48:24 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf mris_curvature -w rh.white mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated Waiting for PID 28929 of (28929 28932 28935 28938) to complete... Waiting for PID 28932 of (28929 28932 28935 28938) to complete... Waiting for PID 28935 of (28929 28932 28935 28938) to complete... Waiting for PID 28938 of (28929 28932 28935 28938) to complete... mris_curvature -w lh.white total integrated curvature = -0.346*4pi (-4.353) --> 1 handles ICI = 148.0, FI = 1608.7, variation=25174.398 writing Gaussian curvature to ./lh.white.K...done. writing mean curvature to ./lh.white.H...done. mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 163 vertices thresholded to be in k1 ~ [-0.25 0.40], k2 ~ [-0.10 0.45] total integrated curvature = 0.533*4pi (6.696) --> 0 handles ICI = 1.5, FI = 9.1, variation=156.872 117 vertices thresholded to be in [-0.02 0.02] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 141 vertices thresholded to be in [-0.15 0.18] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.016, std = 0.022 done. mris_curvature -w rh.white total integrated curvature = -0.345*4pi (-4.339) --> 1 handles ICI = 139.1, FI = 1577.8, variation=24473.033 writing Gaussian curvature to ./rh.white.K...done. writing mean curvature to ./rh.white.H...done. mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 198 vertices thresholded to be in k1 ~ [-0.41 0.29], k2 ~ [-0.20 0.11] total integrated curvature = 0.219*4pi (2.753) --> 1 handles ICI = 1.5, FI = 10.6, variation=181.206 144 vertices thresholded to be in [-0.02 0.06] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 173 vertices thresholded to be in [-0.25 0.14] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.018, std = 0.028 done. PIDs (28929 28932 28935 28938) completed and logs appended. #----------------------------------------- #@# Curvature Stats lh Sun May 10 23:49:25 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm subject7_V1 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 [ subject7_V1/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 [ 249 ] Gb_filter = 0 WARN: S lookup min: -0.147998 WARN: S explicit min: 0.000000 vertex = 31 #----------------------------------------- #@# Curvature Stats rh Sun May 10 23:49:30 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm subject7_V1 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 [ subject7_V1/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: -0.083237 WARN: S explicit min: 0.000000 vertex = 107 #-------------------------------------------- #@# Sphere lh Sun May 10 23:49:33 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere #-------------------------------------------- #@# Sphere rh Sun May 10 23:49:33 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere Waiting for PID 29242 of (29242 29245) to complete... Waiting for PID 29245 of (29242 29245) to complete... mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.59 2014/11/06 01:38:58 nicks Exp $ $Id: mrisurf.c,v 1.770 2015/08/26 16:48:39 fischl Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... == Number of threads available to mris_sphere for OpenMP = 8 == scaling brain by 0.280... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=frame, 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 singular matrix in quadratic form singular matrix in quadratic form -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %20.02 pass 1: epoch 2 of 3 starting distance error %19.96 unfolding complete - removing small folds... starting distance error %19.90 removing remaining folds... final distance error %19.91 MRISunfold() return, current seed 1234 -01: dt=0.0000, 134 negative triangles 196: dt=0.9900, 134 negative triangles 197: dt=0.9900, 49 negative triangles 198: dt=0.9900, 42 negative triangles 199: dt=0.9900, 25 negative triangles 200: dt=0.9900, 29 negative triangles 201: dt=0.9900, 26 negative triangles 202: dt=0.9900, 22 negative triangles 203: dt=0.9900, 17 negative triangles 204: dt=0.9900, 14 negative triangles 205: dt=0.9900, 16 negative triangles 206: dt=0.9900, 14 negative triangles 207: dt=0.9900, 15 negative triangles 208: dt=0.9900, 16 negative triangles 209: dt=0.9900, 15 negative triangles 210: dt=0.9900, 12 negative triangles 211: dt=0.9900, 10 negative triangles 212: dt=0.9900, 10 negative triangles 213: dt=0.9900, 10 negative triangles 214: dt=0.9900, 12 negative triangles 215: dt=0.9900, 11 negative triangles 216: dt=0.9900, 8 negative triangles 217: dt=0.9900, 6 negative triangles 218: dt=0.9900, 8 negative triangles 219: dt=0.9900, 5 negative triangles 220: dt=0.9900, 8 negative triangles 221: dt=0.9900, 6 negative triangles 222: dt=0.9900, 4 negative triangles 223: dt=0.9900, 3 negative triangles 224: dt=0.9900, 6 negative triangles 225: dt=0.9900, 3 negative triangles 226: dt=0.9900, 2 negative triangles 227: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.32 hours mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.59 2014/11/06 01:38:58 nicks Exp $ $Id: mrisurf.c,v 1.770 2015/08/26 16:48:39 fischl Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... == Number of threads available to mris_sphere for OpenMP = 8 == scaling brain by 0.310... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=frame, 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 %19.29 pass 1: epoch 2 of 3 starting distance error %19.11 unfolding complete - removing small folds... starting distance error %18.67 removing remaining folds... final distance error %18.71 MRISunfold() return, current seed 1234 -01: dt=0.0000, 101 negative triangles 326: dt=0.9900, 101 negative triangles 327: dt=0.9900, 66 negative triangles 328: dt=0.9900, 44 negative triangles 329: dt=0.9900, 36 negative triangles 330: dt=0.9900, 27 negative triangles 331: dt=0.9900, 26 negative triangles 332: dt=0.9900, 19 negative triangles 333: dt=0.9900, 22 negative triangles 334: dt=0.9900, 15 negative triangles 335: dt=0.9900, 20 negative triangles 336: dt=0.9900, 13 negative triangles 337: dt=0.9900, 11 negative triangles 338: dt=0.9900, 13 negative triangles 339: dt=0.9900, 11 negative triangles 340: dt=0.9900, 9 negative triangles 341: dt=0.9900, 9 negative triangles 342: dt=0.9900, 6 negative triangles 343: dt=0.9900, 4 negative triangles 344: dt=0.9900, 5 negative triangles 345: dt=0.9900, 2 negative triangles 346: dt=0.9900, 2 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.32 hours PIDs (29242 29245) completed and logs appended. #-------------------------------------------- #@# Surf Reg lh Mon May 11 00:08:48 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts mris_register -curv ../surf/lh.sphere /opt/local/freesurfer-6.0/x86_64/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg #-------------------------------------------- #@# Surf Reg rh Mon May 11 00:08:48 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts mris_register -curv ../surf/rh.sphere /opt/local/freesurfer-6.0/x86_64/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg Waiting for PID 580 of (580 583) to complete... Waiting for PID 583 of (580 583) to complete... mris_register -curv ../surf/lh.sphere /opt/local/freesurfer-6.0/x86_64/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts cmdline mris_register -curv ../surf/lh.sphere /opt/local/freesurfer-6.0/x86_64/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.61 2013/01/15 17:19:03 greve Exp $ $Id: mrisurf.c,v 1.770 2015/08/26 16:48:39 fischl Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /opt/local/freesurfer-6.0/x86_64/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=frame, 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=frame, 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 = 0.612 curvature mean = 0.035, std = 0.939 curvature mean = 0.020, std = 0.859 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 16.00) sse = 341474.8, tmin=0.8899 d=32.00 min @ (0.00, 8.00, -8.00) sse = 284769.1, tmin=1.7977 d=16.00 min @ (0.00, -4.00, 0.00) sse = 271463.7, tmin=2.7250 d=8.00 min @ (0.00, 2.00, 2.00) sse = 269012.7, tmin=3.6135 d=4.00 min @ (0.00, -1.00, -1.00) sse = 267889.5, tmin=4.5291 d=2.00 min @ (0.50, 0.00, 0.50) sse = 267390.4, tmin=5.5043 d=1.00 min @ (-0.25, 0.00, 0.00) sse = 267381.3, tmin=6.9362 d=0.50 min @ (0.12, 0.12, 0.00) sse = 267341.1, tmin=8.4094 tol=1.0e+00, sigma=0.5, host=frame, 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 8.41 min curvature mean = 0.019, std = 0.952 curvature mean = 0.009, std = 0.941 curvature mean = 0.018, std = 0.964 curvature mean = 0.004, std = 0.974 curvature mean = 0.016, std = 0.966 curvature mean = 0.001, std = 0.990 2 Reading smoothwm curvature mean = -0.023, std = 0.282 curvature mean = 0.004, std = 0.067 curvature mean = 0.057, std = 0.347 curvature mean = 0.003, std = 0.080 curvature mean = 0.023, std = 0.549 curvature mean = 0.003, std = 0.086 curvature mean = 0.013, std = 0.691 curvature mean = 0.004, std = 0.089 curvature mean = 0.004, std = 0.798 MRISregister() return, current seed 0 -01: dt=0.0000, 45 negative triangles 114: dt=0.9900, 45 negative triangles expanding nbhd size to 1 115: dt=0.9900, 51 negative triangles 116: dt=0.9900, 36 negative triangles 117: dt=0.9900, 33 negative triangles 118: dt=0.9900, 30 negative triangles 119: dt=0.9900, 28 negative triangles 120: dt=0.9900, 25 negative triangles 121: dt=0.9900, 26 negative triangles 122: dt=0.9900, 17 negative triangles 123: dt=0.9900, 15 negative triangles 124: dt=0.9900, 11 negative triangles 125: dt=0.9900, 9 negative triangles 126: dt=0.9900, 9 negative triangles 127: dt=0.9900, 6 negative triangles 128: dt=0.9900, 6 negative triangles 129: dt=0.9900, 4 negative triangles 130: dt=0.9900, 4 negative triangles 131: dt=0.9900, 4 negative triangles 132: dt=0.9900, 3 negative triangles 133: dt=0.9900, 3 negative triangles 134: dt=0.9900, 3 negative triangles 135: dt=0.9900, 2 negative triangles 136: dt=0.9900, 2 negative triangles 137: dt=0.9900, 2 negative triangles 138: dt=0.9900, 2 negative triangles 139: dt=0.9900, 1 negative triangles 140: dt=0.9900, 1 negative triangles 141: dt=0.9900, 1 negative triangles 142: dt=0.9900, 2 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 0.62 hours mris_register -curv ../surf/rh.sphere /opt/local/freesurfer-6.0/x86_64/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment cwd /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts cmdline mris_register -curv ../surf/rh.sphere /opt/local/freesurfer-6.0/x86_64/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.61 2013/01/15 17:19:03 greve Exp $ $Id: mrisurf.c,v 1.770 2015/08/26 16:48:39 fischl Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /opt/local/freesurfer-6.0/x86_64/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=frame, 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=frame, 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 = 0.603 curvature mean = 0.038, std = 0.922 curvature mean = 0.027, std = 0.861 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 0.00, 16.00) sse = 343937.1, tmin=0.6494 d=32.00 min @ (-8.00, -8.00, 0.00) sse = 269000.6, tmin=1.3221 d=8.00 min @ (2.00, 2.00, 2.00) sse = 259476.0, tmin=2.6523 d=4.00 min @ (0.00, -1.00, -1.00) sse = 258449.4, tmin=3.3386 d=2.00 min @ (0.00, 0.50, 0.50) sse = 257759.8, tmin=4.0087 d=0.50 min @ (0.00, -0.12, -0.12) sse = 257725.1, tmin=5.3507 tol=1.0e+00, sigma=0.5, host=frame, 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 5.35 min curvature mean = 0.012, std = 0.945 curvature mean = 0.010, std = 0.942 curvature mean = 0.007, std = 0.955 curvature mean = 0.005, std = 0.975 curvature mean = 0.006, std = 0.956 curvature mean = 0.001, std = 0.989 2 Reading smoothwm curvature mean = -0.030, std = 0.285 curvature mean = 0.004, std = 0.070 curvature mean = 0.072, std = 0.351 curvature mean = 0.003, std = 0.085 curvature mean = 0.031, std = 0.548 curvature mean = 0.003, std = 0.091 curvature mean = 0.017, std = 0.691 curvature mean = 0.004, std = 0.093 curvature mean = 0.006, std = 0.802 MRISregister() return, current seed 0 -01: dt=0.0000, 64 negative triangles 116: dt=0.9900, 64 negative triangles expanding nbhd size to 1 117: dt=0.9900, 73 negative triangles 118: dt=0.9900, 51 negative triangles 119: dt=0.9900, 45 negative triangles 120: dt=0.9900, 36 negative triangles 121: dt=0.9900, 39 negative triangles 122: dt=0.9900, 33 negative triangles 123: dt=0.9900, 27 negative triangles 124: dt=0.9900, 19 negative triangles 125: dt=0.9900, 20 negative triangles 126: dt=0.9900, 19 negative triangles 127: dt=0.9900, 17 negative triangles 128: dt=0.9900, 16 negative triangles 129: dt=0.9900, 18 negative triangles 130: dt=0.9900, 16 negative triangles 131: dt=0.9900, 11 negative triangles 132: dt=0.9900, 10 negative triangles 133: dt=0.9900, 11 negative triangles 134: dt=0.9900, 7 negative triangles 135: dt=0.9900, 9 negative triangles 136: dt=0.9900, 7 negative triangles 137: dt=0.9900, 7 negative triangles 138: dt=0.9900, 5 negative triangles 139: dt=0.9900, 7 negative triangles 140: dt=0.9900, 3 negative triangles 141: dt=0.9900, 3 negative triangles 142: dt=0.9900, 3 negative triangles 143: dt=0.9900, 3 negative triangles 144: dt=0.9900, 3 negative triangles 145: dt=0.9900, 3 negative triangles 146: dt=0.9900, 3 negative triangles 147: dt=0.9900, 2 negative triangles 148: dt=0.9900, 3 negative triangles 149: dt=0.9900, 2 negative triangles 150: dt=0.9900, 3 negative triangles 151: dt=0.9900, 2 negative triangles 152: dt=0.9900, 3 negative triangles 153: dt=0.9900, 2 negative triangles 154: dt=0.9900, 2 negative triangles 155: dt=0.9900, 3 negative triangles 156: dt=0.9900, 1 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 0.64 hours PIDs (580 583) completed and logs appended. #-------------------------------------------- #@# Jacobian white lh Mon May 11 00:47:00 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white #-------------------------------------------- #@# Jacobian white rh Mon May 11 00:47:00 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white Waiting for PID 8215 of (8215 8218) to complete... Waiting for PID 8218 of (8215 8218) to complete... 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 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 PIDs (8215 8218) completed and logs appended. #-------------------------------------------- #@# AvgCurv lh Mon May 11 00:47:02 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts mrisp_paint -a 5 /opt/local/freesurfer-6.0/x86_64/average/lh.average.curvature.filled.buckner40.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv #-------------------------------------------- #@# AvgCurv rh Mon May 11 00:47:02 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts mrisp_paint -a 5 /opt/local/freesurfer-6.0/x86_64/average/rh.average.curvature.filled.buckner40.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv Waiting for PID 8279 of (8279 8282) to complete... Waiting for PID 8282 of (8279 8282) to complete... mrisp_paint -a 5 /opt/local/freesurfer-6.0/x86_64/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 /opt/local/freesurfer-6.0/x86_64/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... mrisp_paint -a 5 /opt/local/freesurfer-6.0/x86_64/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 /opt/local/freesurfer-6.0/x86_64/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... PIDs (8279 8282) completed and logs appended. #----------------------------------------- #@# Cortical Parc lh Mon May 11 00:47:04 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 subject7_V1 lh ../surf/lh.sphere.reg /opt/local/freesurfer-6.0/x86_64/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot #----------------------------------------- #@# Cortical Parc rh Mon May 11 00:47:04 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 subject7_V1 rh ../surf/rh.sphere.reg /opt/local/freesurfer-6.0/x86_64/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot Waiting for PID 8342 of (8342 8345) to complete... Waiting for PID 8345 of (8342 8345) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 subject7_V1 lh ../surf/lh.sphere.reg /opt/local/freesurfer-6.0/x86_64/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.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.770 2015/08/26 16:48:39 fischl Exp $ reading atlas from /opt/local/freesurfer-6.0/x86_64/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... 1071 labels changed using aseg relabeling using gibbs priors... 000: 3192 changed, 142219 examined... 001: 724 changed, 13591 examined... 002: 171 changed, 4015 examined... 003: 73 changed, 1045 examined... 004: 25 changed, 410 examined... 005: 12 changed, 157 examined... 006: 9 changed, 82 examined... 007: 4 changed, 44 examined... 008: 1 changed, 22 examined... 009: 0 changed, 6 examined... 179 labels changed using aseg 000: 105 total segments, 59 labels (229 vertices) changed 001: 41 total segments, 3 labels (15 vertices) changed 002: 38 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 55 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 2049 vertices marked for relabeling... 2049 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 36 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 subject7_V1 rh ../surf/rh.sphere.reg /opt/local/freesurfer-6.0/x86_64/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.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.770 2015/08/26 16:48:39 fischl Exp $ reading atlas from /opt/local/freesurfer-6.0/x86_64/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... 1005 labels changed using aseg relabeling using gibbs priors... 000: 2987 changed, 136618 examined... 001: 672 changed, 12629 examined... 002: 165 changed, 3710 examined... 003: 57 changed, 1006 examined... 004: 19 changed, 376 examined... 005: 12 changed, 116 examined... 006: 9 changed, 68 examined... 007: 3 changed, 51 examined... 008: 2 changed, 21 examined... 009: 1 changed, 8 examined... 010: 0 changed, 6 examined... 169 labels changed using aseg 000: 100 total segments, 62 labels (500 vertices) changed 001: 39 total segments, 1 labels (1 vertices) changed 002: 38 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 33 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1143 vertices marked for relabeling... 1143 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 32 seconds. PIDs (8342 8345) completed and logs appended. #-------------------------------------------- #@# Make Pial Surf lh Mon May 11 00:47:40 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts mris_make_surfaces -orig_white white -orig_pial white -aseg ../mri/aseg.presurf -nowhite -mgz -T1 brain.finalsurfs subject7_V1 lh #-------------------------------------------- #@# Make Pial Surf rh Mon May 11 00:47:40 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts mris_make_surfaces -orig_white white -orig_pial white -aseg ../mri/aseg.presurf -nowhite -mgz -T1 brain.finalsurfs subject7_V1 rh Waiting for PID 8632 of (8632 8635) to complete... Waiting for PID 8635 of (8632 8635) to complete... mris_make_surfaces -orig_white white -orig_pial white -aseg ../mri/aseg.presurf -nowhite -mgz -T1 brain.finalsurfs subject7_V1 lh reading previously compute gray/white surface using white starting white location... using white starting pial locations... using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.158 2015/08/05 19:26:19 fischl Exp $ $Id: mrisurf.c,v 1.770 2015/08/26 16:48:39 fischl Exp $ reading volume /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/filled.mgz... reading volume /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/brain.finalsurfs.mgz... reading volume /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/wm.mgz... 13342 bright wm thresholded. 18 bright non-wm voxels segmented. reading original surface position from /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.orig... computing class statistics... border white: 260177 voxels (1.55%) border gray 290448 voxels (1.73%) WM (97.0): 98.0 +- 7.3 [70.0 --> 110.0] GM (86.0) : 84.0 +- 11.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 62.4 (was 70) setting MAX_BORDER_WHITE to 112.3 (was 105) setting MIN_BORDER_WHITE to 74.0 (was 85) setting MAX_CSF to 50.9 (was 40) setting MAX_GRAY to 97.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 68.2 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 39.3 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105+-4.3, GM=74+-8.7 mean inside = 97.3, mean outside = 81.3 reading initial white vertex positions from white... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) reading volume /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/../mri/aseg.presurf.mgz... repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... reading white vertex positions from white... inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 2 vertex label from ripped group reading initial pial vertex positions from white... mean border=63.6, 112 (112) missing vertices, mean dist 1.8 [0.9 (%0.1)->2.6 (%99.9))] %23 local maxima, %44 large gradients and %30 min vals, 2301 gradients ignored tol=1.0e-04, sigma=2.0, host=frame, 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 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 30 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 averaging target values for 5 iterations... 000: dt: 0.0000, sse=25170130.0, rms=27.709 001: dt: 0.5000, sse=19127912.0, rms=23.433 (15.432%) 002: dt: 0.5000, sse=14628211.0, rms=19.779 (15.592%) 003: dt: 0.5000, sse=11389012.0, rms=16.919 (14.459%) 004: dt: 0.5000, sse=9382380.0, rms=14.871 (12.106%) 005: dt: 0.5000, sse=8194944.0, rms=13.225 (11.072%) 006: dt: 0.5000, sse=7477889.0, rms=11.782 (10.904%) 007: dt: 0.5000, sse=6935521.5, rms=10.436 (11.430%) 008: dt: 0.5000, sse=6622814.0, rms=9.190 (11.936%) 009: dt: 0.5000, sse=6372156.0, rms=8.016 (12.778%) 010: dt: 0.5000, sse=6234652.0, rms=6.958 (13.193%) 011: dt: 0.5000, sse=6145505.5, rms=6.004 (13.714%) 012: dt: 0.5000, sse=6149780.0, rms=5.240 (12.730%) 013: dt: 0.5000, sse=6170997.5, rms=4.680 (10.681%) 014: dt: 0.5000, sse=6248697.0, rms=4.334 (7.388%) 015: dt: 0.5000, sse=6285355.5, rms=4.090 (5.640%) 016: dt: 0.5000, sse=6335810.5, rms=3.953 (3.339%) 017: dt: 0.5000, sse=6350760.0, rms=3.849 (2.628%) 018: dt: 0.5000, sse=6366970.0, rms=3.792 (1.502%) 019: dt: 0.5000, sse=6368341.0, rms=3.737 (1.452%) rms = 3.70, time step reduction 1 of 3 to 0.250... 020: dt: 0.5000, sse=6393866.0, rms=3.704 (0.860%) 021: dt: 0.2500, sse=4393651.5, rms=2.904 (21.609%) 022: dt: 0.2500, sse=4220540.5, rms=2.685 (7.535%) rms = 2.65, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=4102275.5, rms=2.653 (1.205%) 024: dt: 0.1250, sse=3912798.0, rms=2.517 (5.112%) rms = 2.50, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=3882742.2, rms=2.500 (0.694%) positioning took 1.7 minutes mean border=61.5, 1140 (48) missing vertices, mean dist 0.1 [0.2 (%45.1)->0.5 (%54.9))] %42 local maxima, %30 large gradients and %23 min vals, 865 gradients ignored tol=1.0e-04, sigma=1.0, host=frame, 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=4377654.5, rms=4.423 026: dt: 0.5000, sse=4651549.5, rms=3.625 (18.045%) rms = 3.66, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=4311223.0, rms=3.028 (16.466%) 028: dt: 0.2500, sse=4355178.5, rms=2.729 (9.887%) 029: dt: 0.2500, sse=4295229.0, rms=2.591 (5.049%) 030: dt: 0.2500, sse=4314129.0, rms=2.537 (2.079%) rms = 2.49, time step reduction 2 of 3 to 0.125... 031: dt: 0.2500, sse=4314964.0, rms=2.491 (1.830%) 032: dt: 0.1250, sse=4165886.5, rms=2.351 (5.589%) rms = 2.32, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=4155057.8, rms=2.323 (1.231%) positioning took 0.6 minutes mean border=60.0, 1447 (43) missing vertices, mean dist 0.1 [0.2 (%40.1)->0.3 (%59.9))] %57 local maxima, %16 large gradients and %23 min vals, 878 gradients ignored tol=1.0e-04, sigma=0.5, host=frame, 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=4309334.0, rms=3.239 rms = 3.30, time step reduction 1 of 3 to 0.250... 034: dt: 0.2500, sse=4170153.2, rms=2.772 (14.435%) 035: dt: 0.2500, sse=4188337.5, rms=2.434 (12.170%) 036: dt: 0.2500, sse=4313313.5, rms=2.343 (3.740%) rms = 2.32, time step reduction 2 of 3 to 0.125... 037: dt: 0.2500, sse=4365003.5, rms=2.320 (1.013%) 038: dt: 0.1250, sse=4250372.5, rms=2.211 (4.705%) rms = 2.19, time step reduction 3 of 3 to 0.062... 039: dt: 0.1250, sse=4252745.5, rms=2.188 (1.000%) positioning took 0.5 minutes mean border=59.2, 2618 (42) missing vertices, mean dist 0.0 [0.2 (%46.1)->0.3 (%53.9))] %59 local maxima, %13 large gradients and %22 min vals, 777 gradients ignored tol=1.0e-04, sigma=0.2, host=frame, 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 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=4280705.5, rms=2.421 rms = 2.86, time step reduction 1 of 3 to 0.250... 040: dt: 0.2500, sse=4211578.0, rms=2.233 (7.780%) 041: dt: 0.2500, sse=4352237.5, rms=2.168 (2.906%) rms = 2.16, time step reduction 2 of 3 to 0.125... 042: dt: 0.2500, sse=4410011.5, rms=2.157 (0.487%) 043: dt: 0.1250, sse=4331275.0, rms=2.074 (3.852%) rms = 2.06, time step reduction 3 of 3 to 0.062... 044: dt: 0.1250, sse=4337712.5, rms=2.057 (0.836%) positioning took 0.4 minutes writing curvature file /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.area.pial vertex spacing 0.99 +- 0.43 (0.06-->6.28) (max @ vno 92639 --> 93830) face area 0.39 +- 0.30 (0.00-->7.31) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 142219 vertices processed 25000 of 142219 vertices processed 50000 of 142219 vertices processed 75000 of 142219 vertices processed 100000 of 142219 vertices processed 125000 of 142219 vertices processed 0 of 142219 vertices processed 25000 of 142219 vertices processed 50000 of 142219 vertices processed 75000 of 142219 vertices processed 100000 of 142219 vertices processed 125000 of 142219 vertices processed thickness calculation complete, 645:833 truncations. 38014 vertices at 0 distance 101935 vertices at 1 distance 81258 vertices at 2 distance 34250 vertices at 3 distance 11802 vertices at 4 distance 3820 vertices at 5 distance 1259 vertices at 6 distance 464 vertices at 7 distance 195 vertices at 8 distance 110 vertices at 9 distance 44 vertices at 10 distance 26 vertices at 11 distance 10 vertices at 12 distance 10 vertices at 13 distance 4 vertices at 14 distance 5 vertices at 15 distance 6 vertices at 16 distance 4 vertices at 17 distance 9 vertices at 18 distance 8 vertices at 19 distance 5 vertices at 20 distance writing curvature file /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.thickness positioning took 4.5 minutes mris_make_surfaces -orig_white white -orig_pial white -aseg ../mri/aseg.presurf -nowhite -mgz -T1 brain.finalsurfs subject7_V1 rh reading previously compute gray/white surface using white starting white location... using white starting pial locations... using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.158 2015/08/05 19:26:19 fischl Exp $ $Id: mrisurf.c,v 1.770 2015/08/26 16:48:39 fischl Exp $ reading volume /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/filled.mgz... reading volume /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/brain.finalsurfs.mgz... reading volume /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/wm.mgz... 12465 bright wm thresholded. 17 bright non-wm voxels segmented. reading original surface position from /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.orig... computing class statistics... border white: 260177 voxels (1.55%) border gray 290448 voxels (1.73%) WM (97.0): 97.9 +- 7.1 [70.0 --> 110.0] GM (87.0) : 84.6 +- 11.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 67.9 (was 70) setting MAX_BORDER_WHITE to 113.1 (was 105) setting MIN_BORDER_WHITE to 79.0 (was 85) setting MAX_CSF to 56.8 (was 40) setting MAX_GRAY to 98.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 73.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 45.7 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=106+-4.3, GM=79+-8.7 mean inside = 97.4, mean outside = 81.3 reading initial white vertex positions from white... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) reading volume /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/../mri/aseg.presurf.mgz... repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... reading white vertex positions from white... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 10 points - only 0.00% unknown removing 2 vertex label from ripped group reading initial pial vertex positions from white... mean border=68.0, 94 (94) missing vertices, mean dist 1.8 [1.1 (%0.1)->2.3 (%99.9))] %27 local maxima, %49 large gradients and %20 min vals, 1770 gradients ignored tol=1.0e-04, sigma=2.0, host=frame, 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 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 30 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 averaging target values for 5 iterations... 000: dt: 0.0000, sse=21113850.0, rms=25.595 001: dt: 0.5000, sse=15909376.0, rms=21.388 (16.437%) 002: dt: 0.5000, sse=12094237.0, rms=17.842 (16.578%) 003: dt: 0.5000, sse=9564955.0, rms=15.330 (14.078%) 004: dt: 0.5000, sse=8133872.5, rms=13.607 (11.243%) 005: dt: 0.5000, sse=7415998.5, rms=12.303 (9.577%) 006: dt: 0.5000, sse=6869489.0, rms=11.075 (9.983%) 007: dt: 0.5000, sse=6495304.0, rms=9.984 (9.854%) 008: dt: 0.5000, sse=6204188.5, rms=8.861 (11.246%) 009: dt: 0.5000, sse=6000655.0, rms=7.905 (10.786%) 010: dt: 0.5000, sse=5873616.0, rms=6.951 (12.075%) 011: dt: 0.5000, sse=5829445.5, rms=6.215 (10.586%) 012: dt: 0.5000, sse=5770850.0, rms=5.481 (11.812%) 013: dt: 0.5000, sse=5805524.5, rms=5.049 (7.877%) 014: dt: 0.5000, sse=5807024.0, rms=4.577 (9.345%) 015: dt: 0.5000, sse=5853267.5, rms=4.388 (4.138%) 016: dt: 0.5000, sse=5878464.5, rms=4.114 (6.229%) rms = 4.09, time step reduction 1 of 3 to 0.250... 017: dt: 0.5000, sse=5939499.0, rms=4.086 (0.681%) 018: dt: 0.2500, sse=4125809.2, rms=3.224 (21.099%) 019: dt: 0.2500, sse=3979484.5, rms=3.114 (3.432%) rms = 3.10, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=3889976.0, rms=3.097 (0.533%) 021: dt: 0.1250, sse=3667461.0, rms=2.720 (12.159%) 022: dt: 0.1250, sse=3643643.2, rms=2.605 (4.239%) rms = 2.58, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=3633144.2, rms=2.585 (0.786%) positioning took 1.7 minutes mean border=65.0, 798 (23) missing vertices, mean dist 0.2 [0.2 (%41.3)->0.6 (%58.7))] %46 local maxima, %34 large gradients and %16 min vals, 509 gradients ignored tol=1.0e-04, sigma=1.0, host=frame, 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=4353907.0, rms=5.323 024: dt: 0.5000, sse=4563232.5, rms=4.480 (15.843%) 025: dt: 0.5000, sse=5417742.5, rms=4.067 (9.216%) rms = 4.20, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=4545774.0, rms=3.236 (20.430%) 027: dt: 0.2500, sse=4275340.5, rms=3.085 (4.678%) rms = 3.13, time step reduction 2 of 3 to 0.125... 028: dt: 0.1250, sse=4181499.0, rms=2.917 (5.429%) 029: dt: 0.1250, sse=4051701.5, rms=2.689 (7.817%) 030: dt: 0.1250, sse=4019699.5, rms=2.578 (4.121%) rms = 2.54, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=4005383.0, rms=2.545 (1.310%) positioning took 0.7 minutes mean border=63.1, 896 (15) missing vertices, mean dist 0.2 [0.2 (%35.6)->0.4 (%64.4))] %60 local maxima, %19 large gradients and %16 min vals, 575 gradients ignored tol=1.0e-04, sigma=0.5, host=frame, 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=4258426.5, rms=3.915 rms = 4.10, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=4101916.8, rms=3.299 (15.717%) 033: dt: 0.2500, sse=4111655.5, rms=3.023 (8.381%) rms = 3.07, time step reduction 2 of 3 to 0.125... 034: dt: 0.1250, sse=4050497.0, rms=2.856 (5.519%) 035: dt: 0.1250, sse=4010359.8, rms=2.613 (8.517%) 036: dt: 0.1250, sse=4019589.2, rms=2.482 (5.005%) rms = 2.44, time step reduction 3 of 3 to 0.062... 037: dt: 0.1250, sse=4036768.8, rms=2.440 (1.703%) positioning took 0.5 minutes mean border=62.1, 1856 (14) missing vertices, mean dist 0.1 [0.2 (%41.9)->0.3 (%58.1))] %65 local maxima, %14 large gradients and %15 min vals, 447 gradients ignored tol=1.0e-04, sigma=0.2, host=frame, 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 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=4089457.2, rms=2.842 rms = 3.69, time step reduction 1 of 3 to 0.250... 038: dt: 0.2500, sse=4025161.0, rms=2.504 (11.899%) rms = 2.60, time step reduction 2 of 3 to 0.125... 039: dt: 0.1250, sse=4013678.0, rms=2.435 (2.739%) 040: dt: 0.1250, sse=4038065.5, rms=2.311 (5.091%) 041: dt: 0.1250, sse=4048281.8, rms=2.260 (2.237%) rms = 2.22, time step reduction 3 of 3 to 0.062... 042: dt: 0.1250, sse=4077868.5, rms=2.219 (1.822%) positioning took 0.5 minutes writing curvature file /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.area.pial vertex spacing 1.00 +- 0.42 (0.09-->7.24) (max @ vno 86510 --> 86509) face area 0.40 +- 0.30 (0.00-->10.78) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 136618 vertices processed 25000 of 136618 vertices processed 50000 of 136618 vertices processed 75000 of 136618 vertices processed 100000 of 136618 vertices processed 125000 of 136618 vertices processed 0 of 136618 vertices processed 25000 of 136618 vertices processed 50000 of 136618 vertices processed 75000 of 136618 vertices processed 100000 of 136618 vertices processed 125000 of 136618 vertices processed thickness calculation complete, 208:699 truncations. 47618 vertices at 0 distance 101972 vertices at 1 distance 72717 vertices at 2 distance 27897 vertices at 3 distance 8580 vertices at 4 distance 2574 vertices at 5 distance 726 vertices at 6 distance 242 vertices at 7 distance 73 vertices at 8 distance 32 vertices at 9 distance 25 vertices at 10 distance 24 vertices at 11 distance 22 vertices at 12 distance 11 vertices at 13 distance 7 vertices at 14 distance 10 vertices at 15 distance 10 vertices at 16 distance 7 vertices at 17 distance 6 vertices at 18 distance 2 vertices at 19 distance 9 vertices at 20 distance writing curvature file /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.thickness positioning took 4.7 minutes PIDs (8632 8635) completed and logs appended. #-------------------------------------------- #@# Refine Pial Surfs w/ T2/FLAIR Mon May 11 00:52:23 CDT 2020 bbregister --s subject7_V1 --mov /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/orig/T2raw.mgz --lta /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/T2raw.auto.lta --init-fsl --T2 tmp /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707 Log file is /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/T2raw.auto.dat.log Mon May 11 00:52:23 CDT 2020 setenv SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects cd /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts /opt/local/freesurfer-6.0/x86_64/bin/bbregister --s subject7_V1 --mov /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/orig/T2raw.mgz --lta /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/T2raw.auto.lta --init-fsl --T2 $Id: bbregister,v 1.67 2014/10/27 16:20:28 greve Exp $ Linux frames1.cmrr.umn.edu 3.10.0-1127.el7.x86_64 #1 SMP Tue Mar 31 23:36:51 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 mri_convert /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/orig/T2raw.mgz /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/template.nii mri_convert /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/orig/T2raw.mgz /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/template.nii $Id: mri_convert.c,v 1.222 2015/06/08 18:22:26 greve Exp $ reading from /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/orig/T2raw.mgz... TR=3200.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998529, -0.0509025, -0.0186871) j_ras = (-0.0472866, 0.986091, -0.159337) k_ras = (-0.0265378, 0.158218, 0.987047) writing to /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/template.nii... fslregister --s subject7_V1 --mov /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/template.nii --reg /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/reg.init.dat --niters 1 --maxangle 90 --tmp /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/fslregister --dof 6 --fsvol brainmask.mgz --nobetmov Log file is /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/reg.init.dat.fslregister.log Mon May 11 00:52:24 CDT 2020 --s subject7_V1 --mov /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/template.nii --reg /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/reg.init.dat --niters 1 --maxangle 90 --tmp /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/fslregister --dof 6 --fsvol brainmask.mgz --nobetmov $Id: fslregister,v 1.39 2014/07/07 18:59:07 greve Exp $ frames1.cmrr.umn.edu Linux frames1.cmrr.umn.edu 3.10.0-1127.el7.x86_64 #1 SMP Tue Mar 31 23:36:51 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts mri_convert /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/brainmask.mgz /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/fslregister/refvol.fslregister.nii mri_convert /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/brainmask.mgz /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/fslregister/refvol.fslregister.nii $Id: mri_convert.c,v 1.222 2015/06/08 18:22:26 greve Exp $ reading from /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/brainmask.mgz... TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 5.12227e-09, 1.86265e-09) j_ras = (0, 0, -1) k_ras = (-1.39698e-09, 1, -2.98023e-08) writing to /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/fslregister/refvol.fslregister.nii... -------------------------------------- /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts mri_convert /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/template.nii /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/fslregister/movvol.fslregister.nii --frame 0 mri_convert /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/template.nii /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.222 2015/06/08 18:22:26 greve Exp $ reading from /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/template.nii... TR=3200.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998529, -0.0509025, -0.0186871) j_ras = (-0.0472866, 0.986091, -0.159337) k_ras = (-0.0265378, 0.158218, 0.987047) keeping frame 0 writing to /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/fslregister/movvol.fslregister.nii... Mov determinant is -1 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts tkregister2_cmdl --mov /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/fslregister/movvol.fslregister.nii --reg /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/fslregister/reg0.9745.dat --regheader --fslregout /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/reg.init.dat.fsl.mat0 --s subject7_V1 --noedit tkregister_tcl /opt/local/freesurfer-6.0/x86_64/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/fslregister/movvol.fslregister.nii reg file /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/fslregister/reg0.9745.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.129 2014/02/26 21:31:58 greve Exp $ Diagnostic Level -1 INFO: loading target /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/orig.mgz Ttarg: -------------------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading movable /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/fslregister/movvol.fslregister.nii Tmov: -------------------- -1.00000 0.00000 0.00000 104.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 120.00000; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 0.99853 0.05090 0.01869 -0.00007; -0.02654 0.15822 0.98705 0.00002; 0.04729 -0.98609 0.15934 -0.00008; 0.00000 0.00000 0.00000 1.00000; --------------------------------------- ---- Input registration matrix -------- 0.99853 0.05090 0.01869 -0.00007; -0.02654 0.15822 0.98705 0.00002; 0.04729 -0.98609 0.15934 -0.00008; 0.00000 0.00000 0.00000 1.00000; Determinant 1 subject = subject7_V1 RegMat --------------------------- 0.99853 0.05090 0.01869 -0.00007; -0.02654 0.15822 0.98705 0.00002; 0.04729 -0.98609 0.15934 -0.00008; 0.00000 0.00000 0.00000 1.00000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -1, ref det = -1 Mon May 11 00:52:26 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts flirt.fsl -ref /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/fslregister/refvol.fslregister.nii -in /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/fslregister/fslmat0.trans.mat -schedule /opt/local/freesurfer-6.0/x86_64/bin/fsl.5.0.2.xyztrans.sch -init /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/reg.init.dat.fsl.mat0 Mon May 11 00:53:24 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts flirt.fsl -ref /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/fslregister/refvol.fslregister.nii -in /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/reg.init.dat.fsl.mat -init /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/fslregister/fslmat0.trans.mat -schedule /opt/local/freesurfer-6.0/x86_64/bin/flirt.newdefault.20080811.sch tkregister2_cmdl --s subject7_V1 --mov /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/template.nii --reg /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/reg.init.dat --fslreg /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/reg.init.dat.fsl.mat --noedit tkregister_tcl /opt/local/freesurfer-6.0/x86_64/tktools/tkregister2.tcl ---- FSL registration matrix -------- 0.99866 0.05050 0.01157 16.96523; 0.00249 0.17620 -0.98435 233.04861; -0.05175 0.98306 0.17584 -7.80887; 0.00000 0.00000 0.00000 1.00000; --------------------------------------- INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/template.nii reg file /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/reg.init.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.129 2014/02/26 21:31:58 greve Exp $ Diagnostic Level -1 INFO: loading target /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/orig.mgz Ttarg: -------------------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading movable /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/template.nii Tmov: -------------------- -1.00000 0.00000 0.00000 104.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 120.00000; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 0, float2int = 0 FSLOUTPUTTYPE NIFTI fsl2TkReg: mov det = -1, ref det = -1 ---- Input registration matrix (computed) -------- 0.99866 0.05175 0.00249 0.40414; -0.01157 0.17584 0.98435 0.57001; 0.05050 -0.98306 0.17620 -0.60532; 0.00000 0.00000 0.00000 1.00000; --------------------------------------- ---- Input registration matrix -------- 0.99866 0.05175 0.00249 0.40414; -0.01157 0.17584 0.98435 0.57001; 0.05050 -0.98306 0.17620 -0.60532; 0.00000 0.00000 0.00000 1.00000; Determinant 1 subject = subject7_V1 RegMat --------------------------- 0.99866 0.05175 0.00249 0.40414; -0.01157 0.17584 0.98435 0.57001; 0.05050 -0.98306 0.17620 -0.60532; 0.00000 0.00000 0.00000 1.00000; (standard_in) 1: illegal character: _ (standard_in) 1: illegal character: V (standard_in) 1: syntax error Started at Mon May 11 00:52:25 CDT 2020 Ended at Mon May 11 00:54:24 CDT 2020 fslregister Done To check results, run: tkregister2 --mov /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/template.nii --reg /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/reg.init.dat --surf orig mri_segreg --mov /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/template.nii --init-reg /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/reg.init.dat --out-reg /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.112 2014/02/25 19:06:37 greve Exp $ setenv SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects cd /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts mri_segreg --mov /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/template.nii --init-reg /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/reg.init.dat --out-reg /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Linux hostname frames1.cmrr.umn.edu machine x86_64 user isaaca movvol /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/template.nii regfile /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/reg.init.dat subject subject7_V1 dof 6 outregfile /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/bbr.pass1.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 100 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000100 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1589186082 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99866 0.05175 0.00249 0.40414; -0.01157 0.17584 0.98435 0.57001; 0.05050 -0.98306 0.17620 -0.60532; 0.00000 0.00000 0.00000 1.00000; Loading mov Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 0.985345 1 -25.0 -25.0 25.0 0.993617 2 -25.0 25.0 -25.0 1.008074 3 -25.0 25.0 25.0 0.952241 4 25.0 -25.0 -25.0 1.004091 5 25.0 -25.0 25.0 1.003643 6 25.0 25.0 -25.0 0.981048 7 25.0 25.0 25.0 1.024445 REL: 8 0.078373 7.952506 0.994063 rel = 0.0788406 Initial costs ---------------- Number of surface hits 2636 WM Intensity 696.1286 +/- 184.9051 Ctx Intensity 984.8106 +/- 183.8504 Pct Contrast 35.4282 +/- 20.3385 Cost 0.0784 RelCost 0.0788 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9425 0.9425 0.0 3 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 -4.0000 0.9214 0.9214 0.0 6 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.8642 0.8642 0.0 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.7841 0.7841 0.0 57 -4.0000 -4.0000 4.0000 -4.0000 0.0000 -4.0000 0.7570 0.7570 0.0 102 -4.0000 0.0000 -4.0000 4.0000 0.0000 -4.0000 0.7381 0.7381 0.0 120 -4.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.5564 0.5564 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0784 0.0784 0.0 Brute Force -------------------------- Min cost was 0.078373 Number of iterations 729 Search time 0.864000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000100 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.078373 8 0.016 0.000 0.000 0.000 0.000 0.000 0.0782584816 9 0.022 0.000 0.000 0.000 0.000 0.000 0.0782238014 10 0.032 0.000 0.000 0.000 0.000 0.000 0.0782201423 11 0.028 0.000 0.000 0.000 0.000 0.000 0.0782121363 20 0.028 -0.239 0.000 0.000 0.000 0.000 0.0724187302 21 0.028 -0.248 0.000 0.000 0.000 0.000 0.0722468657 23 0.028 -0.294 0.000 0.000 0.000 0.000 0.0706835179 24 0.028 -0.330 0.000 0.000 0.000 0.000 0.0703591538 25 0.028 -0.326 0.000 0.000 0.000 0.000 0.0702899204 26 0.028 -0.318 0.000 0.000 0.000 0.000 0.0702451975 27 0.028 -0.319 0.000 0.000 0.000 0.000 0.0702437110 37 0.028 -0.319 0.010 0.000 0.000 0.000 0.0702277618 46 0.028 -0.319 0.010 -0.267 0.000 0.000 0.0565332097 47 0.028 -0.319 0.010 -0.270 0.000 0.000 0.0564556291 49 0.028 -0.319 0.010 -0.291 0.000 0.000 0.0564316821 50 0.028 -0.319 0.010 -0.281 0.000 0.000 0.0563111708 60 0.028 -0.319 0.010 -0.281 -0.009 0.000 0.0560062480 61 0.028 -0.319 0.010 -0.281 -0.031 0.000 0.0555742937 63 0.028 -0.319 0.010 -0.281 -0.034 0.000 0.0555589402 64 0.028 -0.319 0.010 -0.281 -0.035 0.000 0.0555550349 66 0.028 -0.319 0.010 -0.281 -0.036 0.000 0.0555547019 79 0.028 -0.319 0.010 -0.281 -0.036 -0.009 0.0555196602 80 0.028 -0.319 0.010 -0.281 -0.036 -0.008 0.0555173275 81 0.028 -0.319 0.010 -0.281 -0.036 -0.007 0.0555165967 powell nthiter 1: fret = 0.055517 92 0.018 -0.319 0.010 -0.281 -0.036 -0.007 0.0554152274 93 0.017 -0.319 0.010 -0.281 -0.036 -0.007 0.0554137202 101 0.017 -0.300 0.010 -0.281 -0.036 -0.007 0.0553339789 102 0.017 -0.290 0.010 -0.281 -0.036 -0.007 0.0553213305 103 0.017 -0.289 0.010 -0.281 -0.036 -0.007 0.0553172012 106 0.017 -0.269 0.010 -0.281 -0.036 -0.007 0.0552994633 107 0.017 -0.275 0.010 -0.281 -0.036 -0.007 0.0552735351 110 0.017 -0.276 0.010 -0.281 -0.036 -0.007 0.0552729004 117 0.017 -0.276 0.112 -0.281 -0.036 -0.007 0.0538437713 118 0.017 -0.276 0.123 -0.281 -0.036 -0.007 0.0537665570 120 0.017 -0.276 0.147 -0.281 -0.036 -0.007 0.0537031255 129 0.017 -0.276 0.147 -0.319 -0.036 -0.007 0.0524908766 131 0.017 -0.276 0.147 -0.337 -0.036 -0.007 0.0523692076 132 0.017 -0.276 0.147 -0.336 -0.036 -0.007 0.0523680237 133 0.017 -0.276 0.147 -0.335 -0.036 -0.007 0.0523676280 145 0.017 -0.276 0.147 -0.335 -0.032 -0.007 0.0523606100 155 0.017 -0.276 0.147 -0.335 -0.032 -0.012 0.0522702390 156 0.017 -0.276 0.147 -0.335 -0.032 -0.032 0.0521208528 158 0.017 -0.276 0.147 -0.335 -0.032 -0.030 0.0521195521 160 0.017 -0.276 0.147 -0.335 -0.032 -0.031 0.0521192255 powell nthiter 2: fret = 0.052119 168 -0.004 -0.276 0.147 -0.335 -0.032 -0.031 0.0517484647 171 -0.008 -0.276 0.147 -0.335 -0.032 -0.031 0.0517425796 172 -0.007 -0.276 0.147 -0.335 -0.032 -0.031 0.0517414474 180 -0.007 -0.317 0.147 -0.335 -0.032 -0.031 0.0515441964 181 -0.007 -0.319 0.147 -0.335 -0.032 -0.031 0.0515438884 190 -0.007 -0.319 0.188 -0.335 -0.032 -0.031 0.0511050275 192 -0.007 -0.319 0.198 -0.335 -0.032 -0.031 0.0511029213 193 -0.007 -0.319 0.194 -0.335 -0.032 -0.031 0.0511026696 195 -0.007 -0.319 0.192 -0.335 -0.032 -0.031 0.0511022435 204 -0.007 -0.319 0.192 -0.351 -0.032 -0.031 0.0507942310 206 -0.007 -0.319 0.192 -0.373 -0.032 -0.031 0.0506310461 207 -0.007 -0.319 0.192 -0.374 -0.032 -0.031 0.0506297305 218 -0.007 -0.319 0.192 -0.374 -0.036 -0.031 0.0506145931 220 -0.007 -0.319 0.192 -0.374 -0.037 -0.031 0.0506134256 221 -0.007 -0.319 0.192 -0.374 -0.038 -0.031 0.0506131302 231 -0.007 -0.319 0.192 -0.374 -0.038 -0.044 0.0505979926 233 -0.007 -0.319 0.192 -0.374 -0.038 -0.039 0.0505888891 234 -0.007 -0.319 0.192 -0.374 -0.038 -0.040 0.0505888755 236 -0.030 -0.361 0.238 -0.413 -0.045 -0.048 0.0500829863 powell nthiter 3: fret = 0.050589 267 -0.017 -0.339 0.245 -0.374 -0.038 -0.040 0.0500723255 268 -0.017 -0.339 0.244 -0.374 -0.038 -0.040 0.0500716485 269 -0.017 -0.339 0.243 -0.374 -0.038 -0.040 0.0500714011 278 -0.017 -0.339 0.243 -0.385 -0.038 -0.040 0.0499828075 279 -0.017 -0.339 0.243 -0.402 -0.038 -0.040 0.0499570093 280 -0.017 -0.339 0.243 -0.397 -0.038 -0.040 0.0499345270 281 -0.017 -0.339 0.243 -0.395 -0.038 -0.040 0.0499344050 291 -0.017 -0.339 0.243 -0.395 -0.039 -0.040 0.0499289346 292 -0.017 -0.339 0.243 -0.395 -0.042 -0.040 0.0499200365 294 -0.017 -0.339 0.243 -0.395 -0.043 -0.040 0.0499194916 303 -0.017 -0.339 0.243 -0.395 -0.043 -0.048 0.0498655555 305 -0.017 -0.339 0.243 -0.395 -0.043 -0.052 0.0498620314 308 -0.026 -0.359 0.293 -0.417 -0.048 -0.064 0.0493217424 315 -0.027 -0.360 0.296 -0.418 -0.049 -0.065 0.0493042227 317 -0.028 -0.362 0.300 -0.420 -0.049 -0.066 0.0492947859 318 -0.028 -0.362 0.300 -0.420 -0.049 -0.066 0.0492947581 319 -0.028 -0.362 0.300 -0.420 -0.049 -0.066 0.0492945141 powell nthiter 4: fret = 0.049295 333 -0.029 -0.362 0.300 -0.420 -0.049 -0.066 0.0492933087 341 -0.029 -0.364 0.300 -0.420 -0.049 -0.066 0.0492233692 344 -0.029 -0.380 0.300 -0.420 -0.049 -0.066 0.0490928630 345 -0.029 -0.375 0.300 -0.420 -0.049 -0.066 0.0490743540 356 -0.029 -0.375 0.300 -0.420 -0.049 -0.073 0.0490495330 357 -0.029 -0.375 0.300 -0.420 -0.049 -0.072 0.0490490463 368 -0.029 -0.375 0.300 -0.412 -0.049 -0.072 0.0489932287 379 -0.029 -0.375 0.300 -0.412 -0.051 -0.072 0.0489806359 380 -0.029 -0.375 0.300 -0.412 -0.053 -0.072 0.0489741553 389 -0.026 -0.370 0.288 -0.407 -0.052 -0.069 0.0488915284 390 -0.026 -0.370 0.288 -0.407 -0.052 -0.069 0.0488915112 392 -0.026 -0.370 0.287 -0.407 -0.052 -0.069 0.0488912335 393 -0.026 -0.370 0.287 -0.407 -0.052 -0.069 0.0488912302 powell nthiter 5: fret = 0.048891 402 -0.038 -0.370 0.287 -0.407 -0.052 -0.069 0.0488809572 403 -0.036 -0.370 0.287 -0.407 -0.052 -0.069 0.0488604203 404 -0.032 -0.370 0.287 -0.407 -0.052 -0.069 0.0488478194 415 -0.032 -0.369 0.287 -0.407 -0.052 -0.069 0.0488466224 425 -0.032 -0.369 0.287 -0.407 -0.052 -0.079 0.0487846180 426 -0.032 -0.369 0.287 -0.407 -0.052 -0.078 0.0487834725 437 -0.032 -0.369 0.287 -0.406 -0.052 -0.078 0.0487833632 447 -0.032 -0.369 0.287 -0.406 -0.053 -0.078 0.0487785683 448 -0.032 -0.369 0.287 -0.406 -0.055 -0.078 0.0487739228 450 -0.032 -0.369 0.287 -0.406 -0.056 -0.078 0.0487737426 458 -0.031 -0.367 0.281 -0.403 -0.055 -0.076 0.0487563261 466 -0.036 -0.363 0.275 -0.399 -0.059 -0.083 0.0486770630 469 -0.044 -0.358 0.265 -0.393 -0.064 -0.095 0.0486478176 470 -0.042 -0.359 0.267 -0.395 -0.063 -0.092 0.0486466806 474 -0.043 -0.358 0.266 -0.394 -0.063 -0.094 0.0486461131 478 -0.043 -0.358 0.266 -0.394 -0.063 -0.094 0.0486460540 powell nthiter 6: fret = 0.048646 492 -0.045 -0.358 0.266 -0.394 -0.063 -0.094 0.0486365418 493 -0.046 -0.358 0.266 -0.394 -0.063 -0.094 0.0486358403 515 -0.046 -0.358 0.266 -0.394 -0.063 -0.094 0.0486357748 537 -0.046 -0.358 0.266 -0.394 -0.055 -0.094 0.0486120066 538 -0.046 -0.358 0.266 -0.394 -0.057 -0.094 0.0486082469 539 -0.046 -0.358 0.266 -0.394 -0.058 -0.094 0.0486079434 powell nthiter 7: fret = 0.048608 567 -0.047 -0.358 0.266 -0.394 -0.058 -0.094 0.0486064918 586 -0.047 -0.359 0.268 -0.395 -0.058 -0.094 0.0486055406 590 -0.047 -0.359 0.268 -0.395 -0.058 -0.094 0.0486054973 611 -0.047 -0.359 0.268 -0.395 -0.057 -0.094 0.0486051825 619 -0.048 -0.359 0.267 -0.394 -0.057 -0.095 0.0486044076 Powell done niters = 7 Computing relative cost 0 -25.0 -25.0 -25.0 0.984723 1 -25.0 -25.0 25.0 1.001460 2 -25.0 25.0 -25.0 1.003080 3 -25.0 25.0 25.0 0.957736 4 25.0 -25.0 -25.0 0.998534 5 25.0 -25.0 25.0 0.996959 6 25.0 25.0 -25.0 0.984732 7 25.0 25.0 25.0 1.015130 REL: 8 0.048604 7.942354 0.992794 rel = 0.0489572 Number of iterations 7 Min cost was 0.048604 Number of FunctionCalls 628 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.744000 sec Parameters at optimum (transmm) -0.04775 -0.35858 0.26691 Parameters at optimum (rotdeg) -0.39435 -0.05736 -0.09490 Final costs ---------------- Number of surface hits 2636 WM Intensity 694.5479 +/- 183.5647 Ctx Intensity 984.5883 +/- 180.6743 Pct Contrast 35.7294 +/- 19.6042 Cost 0.0486 RelCost 0.0788 Reg at min cost was 0.99859 0.05301 0.00396 0.35794; -0.01288 0.16898 0.98554 0.20658; 0.05158 -0.98419 0.16943 -0.34191; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/bbr.pass1.dat, type = 14 Original Reg 0.99866 0.05175 0.00249 0.40414; -0.01157 0.17584 0.98435 0.57001; 0.05050 -0.98306 0.17620 -0.60532; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.00007 -0.00127 -0.00146 0.04620; 0.00131 0.00686 -0.00118 0.36343; -0.00108 0.00113 0.00678 -0.26341; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.324929 Computing change in rh position Surface-RMS-Diff-mm 0.351982 0.186112 0.830807 mri_segreg done mri_segreg --mov /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/template.nii --init-reg /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/bbr.pass1.dat --out-reg /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/T2raw.auto.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/T2raw.auto.dat.mincost --dof 6 --nmax 36 --param /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/T2raw.auto.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.112 2014/02/25 19:06:37 greve Exp $ setenv SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects cd /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts mri_segreg --mov /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/template.nii --init-reg /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/bbr.pass1.dat --out-reg /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/T2raw.auto.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/T2raw.auto.dat.mincost --dof 6 --nmax 36 --param /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/T2raw.auto.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname frames1.cmrr.umn.edu machine x86_64 user isaaca movvol /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/template.nii regfile /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/tmp.bbregister.9707/bbr.pass1.dat subject subject7_V1 dof 6 outregfile /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/T2raw.auto.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1590059740 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99859 0.05301 0.00396 0.35794; -0.01288 0.16898 0.98554 0.20658; 0.05158 -0.98419 0.16943 -0.34191; 0.00000 0.00000 0.00000 1.00000; Loading mov Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 0.986609 1 -25.0 -25.0 25.0 0.991193 2 -25.0 25.0 -25.0 0.993034 3 -25.0 25.0 25.0 0.969385 4 25.0 -25.0 -25.0 1.002346 5 25.0 -25.0 25.0 1.007425 6 25.0 25.0 -25.0 1.003488 7 25.0 25.0 25.0 1.018686 REL: 8 0.051601 7.972168 0.996521 rel = 0.0517808 Initial costs ---------------- Number of surface hits 263081 WM Intensity 691.1232 +/- 175.5087 Ctx Intensity 980.5448 +/- 182.2693 Pct Contrast 35.6886 +/- 19.3044 Cost 0.0516 RelCost 0.0518 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0620 0.0620 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.0617 0.0617 0.0 7 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.0000 0.0614 0.0614 0.0 9 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 -0.1000 0.0557 0.0557 0.0 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.0521 0.0521 0.0 39 -0.1000 -0.1000 0.0000 0.0000 0.0000 -0.1000 0.0517 0.0517 0.0 102 -0.1000 0.0000 -0.1000 0.1000 0.0000 -0.1000 0.0497 0.0497 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0486 0.0486 0.0 Brute Force -------------------------- Min cost was 0.048604 Number of iterations 729 Search time 0.858000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000000 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.051601 7 0.014 0.000 0.000 0.000 0.000 0.000 0.0515895732 8 0.011 0.000 0.000 0.000 0.000 0.000 0.0515887776 17 0.011 -0.046 0.000 0.000 0.000 0.000 0.0514086719 18 0.011 -0.040 0.000 0.000 0.000 0.000 0.0514075016 19 0.011 -0.042 0.000 0.000 0.000 0.000 0.0514065775 29 0.011 -0.042 0.030 0.000 0.000 0.000 0.0513717991 31 0.011 -0.042 0.018 0.000 0.000 0.000 0.0513528176 41 0.011 -0.042 0.018 0.009 0.000 0.000 0.0513510886 43 0.011 -0.042 0.018 0.005 0.000 0.000 0.0513475248 52 0.011 -0.042 0.018 0.005 -0.019 0.000 0.0512570441 54 0.011 -0.042 0.018 0.005 -0.025 0.000 0.0512516251 63 0.011 -0.042 0.018 0.005 -0.025 -0.098 0.0502369762 64 0.011 -0.042 0.018 0.005 -0.025 -0.102 0.0502361903 powell nthiter 1: fret = 0.050236 74 -0.039 -0.042 0.018 0.005 -0.025 -0.102 0.0498429077 76 -0.046 -0.042 0.018 0.005 -0.025 -0.102 0.0498348780 78 -0.045 -0.042 0.018 0.005 -0.025 -0.102 0.0498347817 87 -0.045 -0.041 0.018 0.005 -0.025 -0.102 0.0498337164 88 -0.045 -0.038 0.018 0.005 -0.025 -0.102 0.0498314291 92 -0.045 -0.029 0.018 0.005 -0.025 -0.102 0.0498238376 93 -0.045 -0.025 0.018 0.005 -0.025 -0.102 0.0498237112 94 -0.045 -0.027 0.018 0.005 -0.025 -0.102 0.0498232793 103 -0.045 -0.027 -0.007 0.005 -0.025 -0.102 0.0498153858 104 -0.045 -0.027 0.004 0.005 -0.025 -0.102 0.0497977100 114 -0.045 -0.027 0.004 0.021 -0.025 -0.102 0.0497511401 123 -0.045 -0.027 0.004 0.021 -0.026 -0.102 0.0497494036 124 -0.045 -0.027 0.004 0.021 -0.034 -0.102 0.0497444448 126 -0.045 -0.027 0.004 0.021 -0.033 -0.102 0.0497436036 134 -0.045 -0.027 0.004 0.021 -0.033 -0.141 0.0496470042 135 -0.045 -0.027 0.004 0.021 -0.033 -0.133 0.0496386274 136 -0.045 -0.027 0.004 0.021 -0.033 -0.132 0.0496384798 144 -0.067 -0.021 -0.001 0.027 -0.036 -0.144 0.0495520567 145 -0.079 -0.017 -0.005 0.030 -0.037 -0.150 0.0495489811 146 -0.074 -0.019 -0.003 0.029 -0.037 -0.147 0.0495444525 148 -0.074 -0.019 -0.003 0.029 -0.037 -0.147 0.0495444256 powell nthiter 2: fret = 0.049544 158 -0.074 -0.019 -0.003 0.029 -0.037 -0.153 0.0495401601 159 -0.074 -0.019 -0.003 0.029 -0.037 -0.154 0.0495401595 168 -0.074 -0.020 -0.003 0.029 -0.037 -0.154 0.0495392611 169 -0.074 -0.021 -0.003 0.029 -0.037 -0.154 0.0495388595 178 -0.074 -0.021 -0.031 0.029 -0.037 -0.154 0.0494691712 180 -0.074 -0.021 -0.029 0.029 -0.037 -0.154 0.0494686061 201 -0.074 -0.021 -0.029 0.029 -0.035 -0.154 0.0494669045 210 -0.075 -0.021 -0.029 0.029 -0.035 -0.155 0.0494663851 211 -0.076 -0.021 -0.029 0.029 -0.035 -0.155 0.0494663656 212 -0.076 -0.021 -0.029 0.029 -0.035 -0.155 0.0494663147 powell nthiter 3: fret = 0.049466 224 -0.076 -0.021 -0.029 0.029 -0.035 -0.156 0.0494662399 233 -0.076 -0.022 -0.029 0.029 -0.035 -0.156 0.0494660628 261 -0.076 -0.022 -0.029 0.029 -0.034 -0.156 0.0494655995 269 -0.076 -0.022 -0.029 0.029 -0.034 -0.156 0.0494654912 270 -0.077 -0.021 -0.029 0.030 -0.034 -0.157 0.0494654481 powell nthiter 4: fret = 0.049465 324 -0.077 -0.021 -0.029 0.030 -0.033 -0.157 0.0494652175 332 -0.077 -0.021 -0.029 0.030 -0.033 -0.157 0.0494651378 337 -0.078 -0.021 -0.029 0.030 -0.033 -0.157 0.0494651147 powell nthiter 5: fret = 0.049465 347 -0.078 -0.021 -0.029 0.030 -0.033 -0.156 0.0494650986 357 -0.078 -0.022 -0.029 0.030 -0.033 -0.156 0.0494650342 367 -0.078 -0.022 -0.030 0.030 -0.033 -0.156 0.0494650047 387 -0.078 -0.022 -0.030 0.030 -0.032 -0.156 0.0494649472 397 -0.078 -0.022 -0.031 0.030 -0.032 -0.156 0.0494649435 398 -0.078 -0.022 -0.031 0.030 -0.032 -0.156 0.0494649202 399 -0.078 -0.022 -0.031 0.030 -0.032 -0.156 0.0494649073 400 -0.078 -0.022 -0.031 0.030 -0.032 -0.156 0.0494649062 powell nthiter 6: fret = 0.049465 437 -0.078 -0.022 -0.031 0.031 -0.032 -0.156 0.0494648282 455 -0.078 -0.022 -0.030 0.031 -0.032 -0.156 0.0494648236 456 -0.078 -0.022 -0.030 0.031 -0.032 -0.156 0.0494648190 powell nthiter 7: fret = 0.049465 484 -0.078 -0.022 -0.031 0.031 -0.032 -0.156 0.0494646903 514 -0.077 -0.022 -0.031 0.031 -0.032 -0.156 0.0494646852 powell nthiter 8: fret = 0.049465 Powell done niters = 8 Computing relative cost 0 -25.0 -25.0 -25.0 0.986013 1 -25.0 -25.0 25.0 0.991653 2 -25.0 25.0 -25.0 0.994266 3 -25.0 25.0 25.0 0.968572 4 25.0 -25.0 -25.0 1.001654 5 25.0 -25.0 25.0 1.008274 6 25.0 25.0 -25.0 1.003723 7 25.0 25.0 25.0 1.018818 REL: 8 0.049465 7.972975 0.996622 rel = 0.0496324 Number of iterations 8 Min cost was 0.049465 Number of FunctionCalls 574 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 37.993000 sec Parameters at optimum (transmm) -0.07741 -0.02237 -0.03139 Parameters at optimum (rotdeg) 0.03076 -0.03170 -0.15587 Final costs ---------------- Number of surface hits 263081 WM Intensity 690.8259 +/- 175.0733 Ctx Intensity 980.1048 +/- 181.4349 Pct Contrast 35.6922 +/- 19.2217 Cost 0.0495 RelCost 0.0518 Reg at min cost was 0.99852 0.05402 0.00654 0.28128; -0.01562 0.16936 0.98543 0.18342; 0.05212 -0.98407 0.16996 -0.37299; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/T2raw.auto.dat, type = 14 Original Reg 0.99859 0.05301 0.00396 0.35794; -0.01288 0.16898 0.98554 0.20658; 0.05158 -0.98419 0.16943 -0.34191; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.00007 -0.00101 -0.00259 0.07666; 0.00274 -0.00038 0.00011 0.02316; -0.00055 -0.00012 -0.00053 0.03108; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.093266 Computing change in rh position Surface-RMS-Diff-mm 0.112844 0.042809 0.221975 mri_segreg done MinCost: 0.049465 690.825855 980.104834 35.692162 tkregister2_cmdl --mov /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/orig/T2raw.mgz --reg /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/T2raw.auto.dat --noedit --ltaout /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/T2raw.auto.lta tkregister_tcl /opt/local/freesurfer-6.0/x86_64/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/orig/T2raw.mgz reg file /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/T2raw.auto.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.129 2014/02/26 21:31:58 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- 0.99852 0.05402 0.00654 0.28128; -0.01562 0.16936 0.98543 0.18342; 0.05212 -0.98407 0.16996 -0.37299; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: loading target /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/orig.mgz Ttarg: -------------------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading movable /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/orig/T2raw.mgz Tmov: -------------------- -1.00000 0.00000 0.00000 104.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 120.00000; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 0.99852 0.05402 0.00654 0.28128; -0.01562 0.16936 0.98543 0.18342; 0.05212 -0.98407 0.16996 -0.37299; 0.00000 0.00000 0.00000 1.00000; Determinant 1 subject = subject7_V1 RegMat --------------------------- 0.99852 0.05402 0.00654 0.28128; -0.01562 0.16936 0.98543 0.18342; 0.05212 -0.98407 0.16996 -0.37299; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at Mon May 11 00:52:23 CDT 2020 Ended at Mon May 11 00:55:20 CDT 2020 BBR-Run-Time-Sec 177 bbregister Done To check results, run: tkregister2 --mov /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/orig/T2raw.mgz --reg /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/T2raw.auto.dat --surf cp /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/T2raw.auto.lta /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/T2raw.lta mri_convert -odt short -at /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/T2raw.lta -rl /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/orig.mgz /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/orig/T2raw.mgz /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/T2.prenorm.mgz mri_convert -odt short -at /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/T2raw.lta -rl /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/orig.mgz /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/orig/T2raw.mgz /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/T2.prenorm.mgz $Id: mri_convert.c,v 1.222 2015/06/08 18:22:26 greve Exp $ reading from /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/orig/T2raw.mgz... TR=3200.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998529, -0.0509025, -0.0186871) j_ras = (-0.0472866, 0.986091, -0.159337) k_ras = (-0.0265378, 0.158218, 0.987047) INFO: Reading transformation from file /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/T2raw.lta... Reading transform with LTAreadEx() reading template info from volume /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/orig.mgz... INFO: Applying transformation from file /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/transforms/T2raw.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 0.99993 -0.00304 0.01155 -0.22571; 0.00291 0.99993 0.01138 -0.42466; -0.01158 -0.01135 0.99987 0.05074; 0.00000 0.00000 0.00000 1.00000; --------------------------------- Applying LTAtransformInterp (resample_type 1) changing data type from float to short (noscale = 0)... MRIchangeType: Building histogram writing to /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/T2.prenorm.mgz... mri_normalize -sigma 0.5 -nonmax_suppress 0 -min_dist 1 -aseg /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/aseg.presurf.mgz -surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.white identity.nofile -surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.white identity.nofile /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/T2.prenorm.mgz /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/T2.mgz using Gaussian smoothing of bias field, sigma=0.500 disabling nonmaximum suppression retaining points that are at least 1.000mm from the boundary using segmentation for initial intensity normalization reading from /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/T2.prenorm.mgz... computing distance transform computing distance transform 50454 non wm control points removed 3280 control points within 2.0mm of the surface removed as intensity outliers building Voronoi diagram... performing soap bubble smoothing, sigma = 0... smoothing bias field with sigma=0.500 writing normalized volume to /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/T2.mgz /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts cp -v /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.pial /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.woT2.pial ???/home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.pial??? -> ???/home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.woT2.pial??? mris_make_surfaces -orig_white white -orig_pial woT2.pial -aseg ../mri/aseg.presurf -nowhite -mgz -T1 brain.finalsurfs -T2 ../mri/T2 -nsigma_above 2 -nsigma_below 5 subject7_V1 lh /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts cp -v /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.pial /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.woT2.pial ???/home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.pial??? -> ???/home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.woT2.pial??? mris_make_surfaces -orig_white white -orig_pial woT2.pial -aseg ../mri/aseg.presurf -nowhite -mgz -T1 brain.finalsurfs -T2 ../mri/T2 -nsigma_above 2 -nsigma_below 5 subject7_V1 rh Waiting for PID 10688 of (10688 10691) to complete... Waiting for PID 10691 of (10688 10691) to complete... mris_make_surfaces -orig_white white -orig_pial woT2.pial -aseg ../mri/aseg.presurf -nowhite -mgz -T1 brain.finalsurfs -T2 ../mri/T2 -nsigma_above 2 -nsigma_below 5 subject7_V1 lh reading previously compute gray/white surface refining pial surfaces placement using T2 volume ../mri/T2 using T2 threshold of 2.00 sigmas above the mean (default=2) using T2 threshold of 5.00 sigmas below the mean (default=2) using white starting white location... using woT2.pial starting pial locations... using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.158 2015/08/05 19:26:19 fischl Exp $ $Id: mrisurf.c,v 1.770 2015/08/26 16:48:39 fischl Exp $ reading volume /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/filled.mgz... reading volume /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/brain.finalsurfs.mgz... reading volume /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/wm.mgz... 13342 bright wm thresholded. 18 bright non-wm voxels segmented. reading original surface position from /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.orig... computing class statistics... border white: 260177 voxels (1.55%) border gray 290448 voxels (1.73%) WM (97.0): 98.0 +- 7.3 [70.0 --> 110.0] GM (86.0) : 84.0 +- 11.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 62.4 (was 70) setting MAX_BORDER_WHITE to 112.3 (was 105) setting MIN_BORDER_WHITE to 74.0 (was 85) setting MAX_CSF to 50.9 (was 40) setting MAX_GRAY to 97.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 68.2 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 39.3 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105+-4.3, GM=74+-8.7 mean inside = 97.3, mean outside = 81.3 reading initial white vertex positions from white... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) reading volume /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/../mri/aseg.presurf.mgz... repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... reading white vertex positions from white... inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 2 vertex label from ripped group reading initial pial vertex positions from woT2.pial... repositioning pial surface locations using ../mri/T2.mgz compressed histogram detected, changing bin size to 0.005426 locating cortical regions not in the range [-82.85 111.59], gm=56.03+-27.78, and vertices in regions > 42.1 10422 surface locations found to contain inconsistent values (3696 in, 6726 out) tol=1.0e-04, sigma=2.0, host=frame, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.100, l_nspring=0.050, l_location=1.000, l_curv=0.100 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 30 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 averaging target values for 5 iterations... 000: dt: 0.0000, sse=425632.6, rms=0.166 001: dt: 0.5000, sse=403159.9, rms=0.162 (2.483%) 002: dt: 0.5000, sse=388663.8, rms=0.155 (4.306%) 003: dt: 0.5000, sse=379531.3, rms=0.150 (3.478%) 004: dt: 0.5000, sse=372489.5, rms=0.145 (3.322%) 005: dt: 0.5000, sse=367555.2, rms=0.140 (3.000%) 006: dt: 0.5000, sse=363896.8, rms=0.136 (2.722%) 007: dt: 0.5000, sse=360426.3, rms=0.133 (2.563%) 008: dt: 0.5000, sse=358231.0, rms=0.130 (2.291%) 009: dt: 0.5000, sse=355848.3, rms=0.127 (2.100%) 010: dt: 0.5000, sse=353696.7, rms=0.125 (1.917%) 011: dt: 0.5000, sse=352080.1, rms=0.123 (1.644%) 012: dt: 0.5000, sse=350382.8, rms=0.121 (1.461%) 013: dt: 0.5000, sse=348887.6, rms=0.119 (1.265%) 014: dt: 0.5000, sse=347436.6, rms=0.118 (1.247%) 015: dt: 0.5000, sse=346478.1, rms=0.117 (1.067%) 016: dt: 0.5000, sse=345230.8, rms=0.116 (0.825%) 017: dt: 0.5000, sse=344259.0, rms=0.115 (0.749%) 018: dt: 0.5000, sse=343342.8, rms=0.114 (0.654%) 019: dt: 0.5000, sse=342294.3, rms=0.113 (0.656%) 020: dt: 0.5000, sse=341371.1, rms=0.113 (0.496%) 021: dt: 0.5000, sse=340520.2, rms=0.112 (0.408%) 022: dt: 0.5000, sse=339947.3, rms=0.112 (0.327%) 023: dt: 0.5000, sse=339235.3, rms=0.112 (0.218%) 024: dt: 0.5000, sse=338512.1, rms=0.111 (0.202%) 025: dt: 0.5000, sse=337559.5, rms=0.111 (0.198%) 026: dt: 0.5000, sse=336878.1, rms=0.111 (0.124%) 027: dt: 0.5000, sse=336410.2, rms=0.111 (0.058%) 028: dt: 0.5000, sse=335932.8, rms=0.111 (0.063%) 029: dt: 0.5000, sse=335207.8, rms=0.111 (0.010%) 030: dt: 0.5000, sse=334787.4, rms=0.111 (-0.084%) positioning took 2.1 minutes repositioning pial surface locations using ../mri/T2.mgz compressed histogram detected, changing bin size to 0.005426 locating cortical regions not in the range [-83.49 113.83], gm=57.45+-28.19, and vertices in regions > 43.4 9811 surface locations found to contain inconsistent values (1111 in, 8700 out) tol=1.0e-04, sigma=1.0, host=frame, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.100, l_nspring=0.050, l_location=1.000, l_curv=0.100 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=332900.0, rms=0.096 031: dt: 0.5000, sse=322753.7, rms=0.096 (-0.066%) 032: dt: 0.5000, sse=320266.8, rms=0.093 (2.825%) 033: dt: 0.5000, sse=318743.8, rms=0.092 (1.604%) 034: dt: 0.5000, sse=317799.7, rms=0.091 (1.538%) 035: dt: 0.5000, sse=317557.9, rms=0.089 (1.238%) 036: dt: 0.5000, sse=317231.9, rms=0.088 (1.193%) 037: dt: 0.5000, sse=317160.8, rms=0.087 (1.095%) 038: dt: 0.5000, sse=317537.9, rms=0.087 (0.905%) 039: dt: 0.5000, sse=317460.7, rms=0.086 (0.843%) 040: dt: 0.5000, sse=317749.2, rms=0.085 (0.788%) 041: dt: 0.5000, sse=317774.5, rms=0.085 (0.605%) 042: dt: 0.5000, sse=317793.4, rms=0.084 (0.612%) 043: dt: 0.5000, sse=318123.8, rms=0.084 (0.520%) 044: dt: 0.5000, sse=318142.9, rms=0.083 (0.419%) 045: dt: 0.5000, sse=318121.2, rms=0.083 (0.486%) 046: dt: 0.5000, sse=318503.5, rms=0.083 (0.475%) 047: dt: 0.5000, sse=318046.7, rms=0.082 (0.350%) 048: dt: 0.5000, sse=318268.5, rms=0.082 (0.252%) 049: dt: 0.5000, sse=318250.0, rms=0.082 (0.370%) 050: dt: 0.5000, sse=318157.1, rms=0.082 (0.206%) 051: dt: 0.5000, sse=317927.7, rms=0.081 (0.319%) 052: dt: 0.5000, sse=317940.2, rms=0.081 (0.287%) 053: dt: 0.5000, sse=317785.5, rms=0.081 (0.293%) 054: dt: 0.5000, sse=318041.1, rms=0.081 (-0.028%) 055: dt: 0.5000, sse=318163.7, rms=0.081 (0.128%) 056: dt: 0.5000, sse=317974.8, rms=0.081 (0.308%) 057: dt: 0.5000, sse=317895.4, rms=0.080 (0.179%) 058: dt: 0.5000, sse=317784.7, rms=0.080 (0.093%) 059: dt: 0.5000, sse=317966.0, rms=0.080 (0.107%) 060: dt: 0.5000, sse=317924.7, rms=0.080 (0.061%) positioning took 2.0 minutes repositioning pial surface locations using ../mri/T2.mgz compressed histogram detected, changing bin size to 0.005426 locating cortical regions not in the range [-83.30 113.99], gm=57.62+-28.18, and vertices in regions > 43.5 9644 surface locations found to contain inconsistent values (808 in, 8836 out) tol=1.0e-04, sigma=0.5, host=frame, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.100, l_nspring=0.050, l_location=1.000, l_curv=0.100 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=317575.3, rms=0.079 061: dt: 0.5000, sse=309334.5, rms=0.079 (-0.910%) 062: dt: 0.5000, sse=308072.6, rms=0.078 (2.074%) 063: dt: 0.5000, sse=306747.7, rms=0.077 (1.224%) 064: dt: 0.5000, sse=306688.3, rms=0.076 (0.996%) 065: dt: 0.5000, sse=306802.4, rms=0.075 (0.948%) 066: dt: 0.5000, sse=306826.1, rms=0.074 (1.031%) 067: dt: 0.5000, sse=307091.5, rms=0.074 (0.742%) 068: dt: 0.5000, sse=307516.7, rms=0.073 (0.747%) 069: dt: 0.5000, sse=307894.0, rms=0.073 (0.832%) 070: dt: 0.5000, sse=308116.2, rms=0.072 (0.601%) 071: dt: 0.5000, sse=308575.4, rms=0.072 (0.715%) 072: dt: 0.5000, sse=308617.5, rms=0.071 (0.580%) 073: dt: 0.5000, sse=308825.7, rms=0.071 (0.261%) 074: dt: 0.5000, sse=309014.7, rms=0.071 (0.651%) 075: dt: 0.5000, sse=309172.5, rms=0.070 (0.402%) 076: dt: 0.5000, sse=309328.6, rms=0.070 (0.202%) 077: dt: 0.5000, sse=309234.7, rms=0.070 (0.442%) 078: dt: 0.5000, sse=309344.0, rms=0.070 (0.427%) 079: dt: 0.5000, sse=309577.8, rms=0.069 (0.315%) 080: dt: 0.5000, sse=309776.9, rms=0.069 (0.201%) 081: dt: 0.5000, sse=310099.2, rms=0.069 (0.294%) 082: dt: 0.5000, sse=310015.7, rms=0.069 (0.318%) 083: dt: 0.5000, sse=310057.5, rms=0.069 (0.077%) 084: dt: 0.5000, sse=310252.8, rms=0.069 (0.262%) 085: dt: 0.5000, sse=310261.6, rms=0.069 (-0.362%) 086: dt: 0.5000, sse=310293.6, rms=0.069 (0.325%) 087: dt: 0.5000, sse=310302.4, rms=0.069 (0.215%) 088: dt: 0.5000, sse=310396.5, rms=0.068 (0.244%) 089: dt: 0.5000, sse=310304.4, rms=0.068 (0.144%) 090: dt: 0.5000, sse=310410.6, rms=0.069 (-0.406%) positioning took 2.0 minutes repositioning pial surface locations using ../mri/T2.mgz compressed histogram detected, changing bin size to 0.005426 locating cortical regions not in the range [-83.56 113.87], gm=57.46+-28.20, and vertices in regions > 43.4 9563 surface locations found to contain inconsistent values (759 in, 8804 out) tol=1.0e-04, sigma=0.2, host=frame, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.100, l_nspring=0.050, l_location=1.000, l_curv=0.100 mom=0.00, dt=0.50 writing pial surface to /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=310198.4, rms=0.069 091: dt: 0.5000, sse=302697.1, rms=0.070 (-0.718%) 092: dt: 0.5000, sse=302428.0, rms=0.069 (1.430%) 093: dt: 0.5000, sse=301689.9, rms=0.068 (0.974%) 094: dt: 0.5000, sse=301725.9, rms=0.067 (1.035%) 095: dt: 0.5000, sse=301876.3, rms=0.067 (0.802%) 096: dt: 0.5000, sse=302330.8, rms=0.066 (0.676%) 097: dt: 0.5000, sse=302674.5, rms=0.066 (0.729%) 098: dt: 0.5000, sse=303045.2, rms=0.065 (0.916%) 099: dt: 0.5000, sse=303387.7, rms=0.065 (0.245%) 100: dt: 0.5000, sse=303631.3, rms=0.065 (0.537%) 101: dt: 0.5000, sse=303903.3, rms=0.064 (0.741%) 102: dt: 0.5000, sse=304504.5, rms=0.064 (0.692%) 103: dt: 0.5000, sse=304972.8, rms=0.064 (0.034%) 104: dt: 0.5000, sse=305194.8, rms=0.063 (0.676%) 105: dt: 0.5000, sse=305494.9, rms=0.063 (0.634%) 106: dt: 0.5000, sse=305590.8, rms=0.063 (0.495%) 107: dt: 0.5000, sse=306014.5, rms=0.063 (0.032%) 108: dt: 0.5000, sse=306201.1, rms=0.062 (0.530%) 109: dt: 0.5000, sse=306371.5, rms=0.062 (0.236%) 110: dt: 0.5000, sse=306424.5, rms=0.062 (0.415%) 111: dt: 0.5000, sse=306756.8, rms=0.062 (-0.280%) 112: dt: 0.5000, sse=306833.8, rms=0.062 (0.514%) 113: dt: 0.5000, sse=307028.6, rms=0.062 (0.403%) 114: dt: 0.5000, sse=307100.7, rms=0.061 (0.434%) 115: dt: 0.5000, sse=307222.4, rms=0.061 (0.282%) 116: dt: 0.5000, sse=307559.7, rms=0.061 (-0.365%) 117: dt: 0.5000, sse=307527.9, rms=0.061 (0.319%) 118: dt: 0.5000, sse=307498.7, rms=0.061 (0.212%) 119: dt: 0.5000, sse=307559.9, rms=0.061 (0.357%) 120: dt: 0.5000, sse=307585.3, rms=0.061 (0.369%) positioning took 1.9 minutes writing curvature file /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.area.pial vertex spacing 0.98 +- 0.43 (0.06-->6.85) (max @ vno 86144 --> 86145) face area 0.38 +- 0.30 (0.00-->7.35) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 142219 vertices processed 25000 of 142219 vertices processed 50000 of 142219 vertices processed 75000 of 142219 vertices processed 100000 of 142219 vertices processed 125000 of 142219 vertices processed 0 of 142219 vertices processed 25000 of 142219 vertices processed 50000 of 142219 vertices processed 75000 of 142219 vertices processed 100000 of 142219 vertices processed 125000 of 142219 vertices processed thickness calculation complete, 743:757 truncations. 38015 vertices at 0 distance 101470 vertices at 1 distance 82197 vertices at 2 distance 34161 vertices at 3 distance 11634 vertices at 4 distance 3724 vertices at 5 distance 1272 vertices at 6 distance 396 vertices at 7 distance 158 vertices at 8 distance 104 vertices at 9 distance 31 vertices at 10 distance 13 vertices at 11 distance 7 vertices at 12 distance 11 vertices at 13 distance 7 vertices at 14 distance 4 vertices at 15 distance 5 vertices at 16 distance 7 vertices at 17 distance 6 vertices at 18 distance 10 vertices at 19 distance 6 vertices at 20 distance writing curvature file /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.thickness positioning took 15.0 minutes mris_make_surfaces -orig_white white -orig_pial woT2.pial -aseg ../mri/aseg.presurf -nowhite -mgz -T1 brain.finalsurfs -T2 ../mri/T2 -nsigma_above 2 -nsigma_below 5 subject7_V1 rh reading previously compute gray/white surface refining pial surfaces placement using T2 volume ../mri/T2 using T2 threshold of 2.00 sigmas above the mean (default=2) using T2 threshold of 5.00 sigmas below the mean (default=2) using white starting white location... using woT2.pial starting pial locations... using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.158 2015/08/05 19:26:19 fischl Exp $ $Id: mrisurf.c,v 1.770 2015/08/26 16:48:39 fischl Exp $ reading volume /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/filled.mgz... reading volume /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/brain.finalsurfs.mgz... reading volume /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/wm.mgz... 12465 bright wm thresholded. 17 bright non-wm voxels segmented. reading original surface position from /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.orig... computing class statistics... border white: 260177 voxels (1.55%) border gray 290448 voxels (1.73%) WM (97.0): 97.9 +- 7.1 [70.0 --> 110.0] GM (87.0) : 84.6 +- 11.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 67.9 (was 70) setting MAX_BORDER_WHITE to 113.1 (was 105) setting MIN_BORDER_WHITE to 79.0 (was 85) setting MAX_CSF to 56.8 (was 40) setting MAX_GRAY to 98.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 73.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 45.7 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=106+-4.3, GM=79+-8.7 mean inside = 97.4, mean outside = 81.3 reading initial white vertex positions from white... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) reading volume /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/../mri/aseg.presurf.mgz... repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... reading white vertex positions from white... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 10 points - only 0.00% unknown removing 2 vertex label from ripped group reading initial pial vertex positions from woT2.pial... repositioning pial surface locations using ../mri/T2.mgz compressed histogram detected, changing bin size to 0.005493 locating cortical regions not in the range [-92.61 136.55], gm=71.07+-32.74, and vertices in regions > 54.7 6264 surface locations found to contain inconsistent values (788 in, 5476 out) tol=1.0e-04, sigma=2.0, host=frame, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.100, l_nspring=0.050, l_location=1.000, l_curv=0.100 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 30 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 averaging target values for 5 iterations... 000: dt: 0.0000, sse=396428.7, rms=0.124 001: dt: 0.5000, sse=378562.1, rms=0.121 (2.296%) 002: dt: 0.5000, sse=366943.4, rms=0.115 (4.875%) 003: dt: 0.5000, sse=359382.1, rms=0.110 (3.835%) 004: dt: 0.5000, sse=353598.9, rms=0.106 (3.919%) 005: dt: 0.5000, sse=349489.0, rms=0.103 (3.418%) 006: dt: 0.5000, sse=346194.6, rms=0.099 (3.259%) 007: dt: 0.5000, sse=343720.1, rms=0.096 (2.814%) 008: dt: 0.5000, sse=341527.3, rms=0.094 (2.592%) 009: dt: 0.5000, sse=339735.0, rms=0.092 (2.223%) 010: dt: 0.5000, sse=338101.4, rms=0.090 (1.844%) 011: dt: 0.5000, sse=336949.1, rms=0.089 (1.470%) 012: dt: 0.5000, sse=335756.7, rms=0.088 (1.242%) 013: dt: 0.5000, sse=334562.7, rms=0.087 (0.936%) 014: dt: 0.5000, sse=333633.7, rms=0.086 (0.716%) 015: dt: 0.5000, sse=332618.9, rms=0.086 (0.458%) 016: dt: 0.5000, sse=332003.7, rms=0.086 (0.292%) 017: dt: 0.5000, sse=331188.6, rms=0.085 (0.126%) 018: dt: 0.5000, sse=330431.7, rms=0.085 (0.093%) 019: dt: 0.5000, sse=329706.1, rms=0.085 (-0.103%) 020: dt: 0.5000, sse=328904.0, rms=0.086 (-0.206%) 021: dt: 0.5000, sse=328418.2, rms=0.086 (-0.258%) 022: dt: 0.5000, sse=327741.6, rms=0.086 (-0.282%) 023: dt: 0.5000, sse=327163.6, rms=0.086 (-0.288%) 024: dt: 0.5000, sse=326568.0, rms=0.087 (-0.340%) 025: dt: 0.5000, sse=326030.8, rms=0.087 (-0.361%) 026: dt: 0.5000, sse=325530.2, rms=0.087 (-0.451%) 027: dt: 0.5000, sse=325257.6, rms=0.088 (-0.458%) 028: dt: 0.5000, sse=324794.3, rms=0.088 (-0.383%) 029: dt: 0.5000, sse=324214.5, rms=0.088 (-0.399%) 030: dt: 0.5000, sse=323658.8, rms=0.089 (-0.406%) positioning took 2.2 minutes repositioning pial surface locations using ../mri/T2.mgz compressed histogram detected, changing bin size to 0.005561 locating cortical regions not in the range [-94.15 136.55], gm=70.64+-32.96, and vertices in regions > 54.2 5885 surface locations found to contain inconsistent values (503 in, 5382 out) tol=1.0e-04, sigma=1.0, host=frame, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.100, l_nspring=0.050, l_location=1.000, l_curv=0.100 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=322295.0, rms=0.068 031: dt: 0.5000, sse=314346.3, rms=0.068 (-0.473%) 032: dt: 0.5000, sse=311628.1, rms=0.066 (3.079%) 033: dt: 0.5000, sse=309715.4, rms=0.065 (1.572%) 034: dt: 0.5000, sse=308856.6, rms=0.064 (1.565%) 035: dt: 0.5000, sse=308314.4, rms=0.063 (1.398%) 036: dt: 0.5000, sse=308131.7, rms=0.062 (1.273%) 037: dt: 0.5000, sse=307922.6, rms=0.061 (1.139%) 038: dt: 0.5000, sse=307892.4, rms=0.061 (0.910%) 039: dt: 0.5000, sse=307934.1, rms=0.060 (0.902%) 040: dt: 0.5000, sse=308062.8, rms=0.060 (0.785%) 041: dt: 0.5000, sse=308094.6, rms=0.060 (0.553%) 042: dt: 0.5000, sse=308230.1, rms=0.059 (0.597%) 043: dt: 0.5000, sse=308259.2, rms=0.059 (0.446%) 044: dt: 0.5000, sse=308306.6, rms=0.059 (0.297%) 045: dt: 0.5000, sse=308172.0, rms=0.059 (0.384%) 046: dt: 0.5000, sse=308257.5, rms=0.058 (0.274%) 047: dt: 0.5000, sse=308139.7, rms=0.058 (0.197%) 048: dt: 0.5000, sse=308315.3, rms=0.058 (0.204%) 049: dt: 0.5000, sse=308210.1, rms=0.058 (0.162%) 050: dt: 0.5000, sse=308070.8, rms=0.058 (0.060%) 051: dt: 0.5000, sse=308187.4, rms=0.058 (-0.088%) 052: dt: 0.5000, sse=308164.9, rms=0.058 (0.039%) 053: dt: 0.5000, sse=308109.6, rms=0.058 (0.053%) 054: dt: 0.5000, sse=308067.7, rms=0.058 (0.064%) 055: dt: 0.5000, sse=307960.7, rms=0.058 (-0.026%) 056: dt: 0.5000, sse=308049.0, rms=0.058 (-0.015%) 057: dt: 0.5000, sse=307951.8, rms=0.058 (-0.008%) 058: dt: 0.5000, sse=307785.8, rms=0.058 (-0.002%) 059: dt: 0.5000, sse=307733.3, rms=0.058 (-0.088%) 060: dt: 0.5000, sse=307761.6, rms=0.058 (-0.018%) positioning took 2.0 minutes repositioning pial surface locations using ../mri/T2.mgz compressed histogram detected, changing bin size to 0.005561 locating cortical regions not in the range [-94.70 136.84], gm=70.69+-33.08, and vertices in regions > 54.1 5875 surface locations found to contain inconsistent values (400 in, 5475 out) tol=1.0e-04, sigma=0.5, host=frame, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.100, l_nspring=0.050, l_location=1.000, l_curv=0.100 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=307376.8, rms=0.054 061: dt: 0.5000, sse=300770.6, rms=0.055 (-1.441%) 062: dt: 0.5000, sse=299426.2, rms=0.053 (2.271%) 063: dt: 0.5000, sse=298299.3, rms=0.053 (1.026%) 064: dt: 0.5000, sse=297904.7, rms=0.052 (1.060%) 065: dt: 0.5000, sse=297853.6, rms=0.052 (1.039%) 066: dt: 0.5000, sse=297886.7, rms=0.051 (0.945%) 067: dt: 0.5000, sse=297907.3, rms=0.051 (0.914%) 068: dt: 0.5000, sse=298027.1, rms=0.050 (0.864%) 069: dt: 0.5000, sse=298234.6, rms=0.050 (0.751%) 070: dt: 0.5000, sse=298355.2, rms=0.049 (0.807%) 071: dt: 0.5000, sse=298583.7, rms=0.049 (0.467%) 072: dt: 0.5000, sse=298711.2, rms=0.049 (0.619%) 073: dt: 0.5000, sse=298881.5, rms=0.049 (0.537%) 074: dt: 0.5000, sse=298976.6, rms=0.048 (0.457%) 075: dt: 0.5000, sse=299067.9, rms=0.048 (0.422%) 076: dt: 0.5000, sse=299235.7, rms=0.048 (0.405%) 077: dt: 0.5000, sse=299372.3, rms=0.048 (0.314%) 078: dt: 0.5000, sse=299444.1, rms=0.048 (0.325%) 079: dt: 0.5000, sse=299552.6, rms=0.048 (0.172%) 080: dt: 0.5000, sse=299622.9, rms=0.048 (0.308%) 081: dt: 0.5000, sse=299701.2, rms=0.047 (0.119%) 082: dt: 0.5000, sse=299781.6, rms=0.047 (0.222%) 083: dt: 0.5000, sse=299869.1, rms=0.047 (0.221%) 084: dt: 0.5000, sse=299957.8, rms=0.047 (0.158%) 085: dt: 0.5000, sse=299946.8, rms=0.047 (0.176%) 086: dt: 0.5000, sse=300084.1, rms=0.047 (0.138%) 087: dt: 0.5000, sse=300007.8, rms=0.047 (0.084%) 088: dt: 0.5000, sse=300009.7, rms=0.047 (0.045%) 089: dt: 0.5000, sse=300033.4, rms=0.047 (0.069%) 090: dt: 0.5000, sse=300150.9, rms=0.047 (0.045%) positioning took 2.0 minutes repositioning pial surface locations using ../mri/T2.mgz compressed histogram detected, changing bin size to 0.005561 locating cortical regions not in the range [-79.81 130.65], gm=70.52+-30.07, and vertices in regions > 55.5 5233 surface locations found to contain inconsistent values (1716 in, 3517 out) tol=1.0e-04, sigma=0.2, host=frame, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.100, l_nspring=0.050, l_location=1.000, l_curv=0.100 mom=0.00, dt=0.50 writing pial surface to /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=299989.1, rms=0.054 091: dt: 0.5000, sse=294249.9, rms=0.054 (0.182%) 092: dt: 0.5000, sse=293097.2, rms=0.052 (2.601%) 093: dt: 0.5000, sse=292425.7, rms=0.052 (1.704%) 094: dt: 0.5000, sse=292155.8, rms=0.051 (1.655%) 095: dt: 0.5000, sse=292094.6, rms=0.050 (1.618%) 096: dt: 0.5000, sse=292160.1, rms=0.049 (1.562%) 097: dt: 0.5000, sse=292418.5, rms=0.048 (1.406%) 098: dt: 0.5000, sse=292591.7, rms=0.048 (1.433%) 099: dt: 0.5000, sse=292800.1, rms=0.047 (1.334%) 100: dt: 0.5000, sse=292937.2, rms=0.047 (1.259%) 101: dt: 0.5000, sse=293185.1, rms=0.046 (1.122%) 102: dt: 0.5000, sse=293479.4, rms=0.045 (1.127%) 103: dt: 0.5000, sse=293703.7, rms=0.045 (0.945%) 104: dt: 0.5000, sse=294005.4, rms=0.045 (0.944%) 105: dt: 0.5000, sse=294123.5, rms=0.044 (0.740%) 106: dt: 0.5000, sse=294398.6, rms=0.044 (0.759%) 107: dt: 0.5000, sse=294522.4, rms=0.044 (0.700%) 108: dt: 0.5000, sse=294873.6, rms=0.043 (0.635%) 109: dt: 0.5000, sse=294978.9, rms=0.043 (0.603%) 110: dt: 0.5000, sse=295114.2, rms=0.043 (0.451%) 111: dt: 0.5000, sse=295322.5, rms=0.043 (0.592%) 112: dt: 0.5000, sse=295444.8, rms=0.042 (0.436%) 113: dt: 0.5000, sse=295684.5, rms=0.042 (0.306%) 114: dt: 0.5000, sse=295831.5, rms=0.042 (0.400%) 115: dt: 0.5000, sse=295908.1, rms=0.042 (0.405%) 116: dt: 0.5000, sse=295962.1, rms=0.042 (0.290%) 117: dt: 0.5000, sse=295997.3, rms=0.042 (0.313%) 118: dt: 0.5000, sse=296274.9, rms=0.042 (0.155%) 119: dt: 0.5000, sse=296344.4, rms=0.042 (0.270%) 120: dt: 0.5000, sse=296367.5, rms=0.041 (0.301%) positioning took 1.8 minutes writing curvature file /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.area.pial vertex spacing 0.99 +- 0.43 (0.05-->7.08) (max @ vno 86510 --> 86509) face area 0.39 +- 0.30 (0.00-->10.77) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 136618 vertices processed 25000 of 136618 vertices processed 50000 of 136618 vertices processed 75000 of 136618 vertices processed 100000 of 136618 vertices processed 125000 of 136618 vertices processed 0 of 136618 vertices processed 25000 of 136618 vertices processed 50000 of 136618 vertices processed 75000 of 136618 vertices processed 100000 of 136618 vertices processed 125000 of 136618 vertices processed thickness calculation complete, 342:792 truncations. 47225 vertices at 0 distance 101110 vertices at 1 distance 73732 vertices at 2 distance 28072 vertices at 3 distance 8736 vertices at 4 distance 2557 vertices at 5 distance 697 vertices at 6 distance 210 vertices at 7 distance 64 vertices at 8 distance 26 vertices at 9 distance 25 vertices at 10 distance 17 vertices at 11 distance 17 vertices at 12 distance 14 vertices at 13 distance 8 vertices at 14 distance 12 vertices at 15 distance 10 vertices at 16 distance 16 vertices at 17 distance 8 vertices at 18 distance 4 vertices at 19 distance 4 vertices at 20 distance writing curvature file /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.thickness positioning took 17.2 minutes PIDs (10688 10691) completed and logs appended. #-------------------------------------------- #@# Surf Volume lh Mon May 11 01:13:22 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume subject7_V1 lh /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.volume masking with /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/label/lh.cortex.label Total face volume 254114 Total vertex volume 250037 (mask=0) #@# subject7_V1 lh 250037 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Mon May 11 01:13:26 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume subject7_V1 rh /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.volume masking with /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/label/rh.cortex.label Total face volume 241169 Total vertex volume 237015 (mask=0) #@# subject7_V1 rh 237015 vertexvol Done #-------------------------------------------- #@# Cortical ribbon mask Mon May 11 01:13:30 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri mris_volmask --aseg_name aseg.presurf --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon subject7_V1 SUBJECTS_DIR is /home/server1/data/freesurfer_workingdir/subjects 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 = 10 writing volume /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/ribbon.mgz writing ribbon files #----------------------------------------- #@# Parcellation Stats lh Mon May 11 01:19:59 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab subject7_V1 lh white mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab subject7_V1 lh pial #----------------------------------------- #@# Parcellation Stats rh Mon May 11 01:19:59 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab subject7_V1 rh white mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab subject7_V1 rh pial Waiting for PID 20941 of (20941 20944 20947 20950) to complete... Waiting for PID 20944 of (20941 20944 20947 20950) to complete... Waiting for PID 20947 of (20941 20944 20947 20950) to complete... Waiting for PID 20950 of (20941 20944 20947 20950) to complete... mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab subject7_V1 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/wm.mgz... reading input surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.white... reading input pial surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.pial... reading input white surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 254114 Total vertex volume 250037 (mask=0) 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 atlas_icv (eTIV) = 1576049 mm^3 (det: 1.236069 ) lhCtxGM: 249367.335 249428.000 diff= -60.7 pctdiff=-0.024 rhCtxGM: 237349.818 237706.000 diff= -356.2 pctdiff=-0.150 lhCtxWM: 230995.026 230911.500 diff= 83.5 pctdiff= 0.036 rhCtxWM: 216994.301 217423.500 diff= -429.2 pctdiff=-0.198 SubCortGMVol 60253.000 SupraTentVol 1010772.480 (1009395.000) diff=1377.480 pctdiff=0.136 SupraTentVolNotVent 997183.480 (995806.000) diff=1377.480 pctdiff=0.138 BrainSegVol 1187900.000 (1183807.000) diff=4093.000 pctdiff=0.345 BrainSegVolNotVent 1167134.000 (1165804.480) diff=1329.520 pctdiff=0.114 BrainSegVolNotVent 1167134.000 CerebellumVol 170761.000 VentChorVol 13589.000 3rd4th5thCSF 7177.000 CSFVol 3095.000, OptChiasmVol 556.000 MaskVol 1609937.000 1506 1014 2566 2.634 0.357 0.079 0.010 7 0.6 bankssts 1074 690 2105 2.717 0.741 0.116 0.018 12 0.8 caudalanteriorcingulate 3438 2247 6689 2.678 0.555 0.112 0.021 31 3.0 caudalmiddlefrontal 2685 1627 3193 1.896 0.523 0.139 0.032 37 3.5 cuneus 449 290 1204 3.481 0.680 0.102 0.026 3 0.4 entorhinal 5276 3486 11099 2.886 0.629 0.130 0.027 70 5.9 fusiform 7329 4824 13401 2.517 0.558 0.121 0.024 87 6.8 inferiorparietal 5898 3932 13299 2.924 0.674 0.124 0.031 82 7.0 inferiortemporal 1860 1209 3125 2.518 0.819 0.128 0.031 26 2.1 isthmuscingulate 8716 5308 12083 2.139 0.590 0.126 0.027 99 9.4 lateraloccipital 4279 2846 8399 2.629 0.759 0.127 0.038 66 6.2 lateralorbitofrontal 5200 3410 7065 2.086 0.688 0.137 0.033 63 7.1 lingual 3052 2018 5021 2.278 0.914 0.119 0.035 43 4.6 medialorbitofrontal 5035 3445 13107 3.166 0.631 0.120 0.024 58 4.7 middletemporal 989 637 2065 2.845 0.560 0.097 0.018 8 0.6 parahippocampal 1930 1261 3120 2.354 0.566 0.118 0.022 17 1.7 paracentral 2421 1652 5103 2.767 0.442 0.112 0.019 24 1.9 parsopercularis 905 594 2195 2.859 0.589 0.144 0.035 15 1.2 parsorbitalis 1953 1265 3885 2.661 0.620 0.125 0.025 24 1.7 parstriangularis 2481 1630 2164 1.495 0.512 0.109 0.019 22 1.8 pericalcarine 6545 4055 8818 2.012 0.731 0.097 0.019 52 5.1 postcentral 1755 1175 3021 2.538 0.703 0.134 0.028 29 1.9 posteriorcingulate 6600 4106 11682 2.638 0.567 0.103 0.020 50 5.3 precentral 5898 3930 10005 2.412 0.584 0.125 0.025 72 5.9 precuneus 1276 906 3014 2.865 1.062 0.138 0.036 21 1.7 rostralanteriorcingulate 8452 5693 16506 2.494 0.667 0.136 0.030 129 10.9 rostralmiddlefrontal 10768 7263 24221 2.996 0.615 0.127 0.028 130 12.1 superiorfrontal 9518 6038 13862 2.115 0.496 0.114 0.024 95 9.3 superiorparietal 5999 3903 14041 3.148 0.634 0.105 0.019 48 4.5 superiortemporal 6372 4216 12428 2.655 0.598 0.115 0.023 72 5.8 supramarginal 307 214 1039 3.179 0.869 0.156 0.037 6 0.5 frontalpole 616 410 2126 3.864 0.907 0.128 0.035 10 0.8 temporalpole 676 405 1146 2.721 0.399 0.114 0.022 6 0.6 transversetemporal 3154 2082 7243 3.313 0.764 0.108 0.028 27 3.3 insula mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab subject7_V1 lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/wm.mgz... reading input surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.pial... reading input pial surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.pial... reading input white surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 254114 Total vertex volume 250037 (mask=0) 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 atlas_icv (eTIV) = 1576049 mm^3 (det: 1.236069 ) lhCtxGM: 249367.335 249428.000 diff= -60.7 pctdiff=-0.024 rhCtxGM: 237349.818 237706.000 diff= -356.2 pctdiff=-0.150 lhCtxWM: 230995.026 230911.500 diff= 83.5 pctdiff= 0.036 rhCtxWM: 216994.301 217423.500 diff= -429.2 pctdiff=-0.198 SubCortGMVol 60253.000 SupraTentVol 1010772.480 (1009395.000) diff=1377.480 pctdiff=0.136 SupraTentVolNotVent 997183.480 (995806.000) diff=1377.480 pctdiff=0.138 BrainSegVol 1187900.000 (1183807.000) diff=4093.000 pctdiff=0.345 BrainSegVolNotVent 1167134.000 (1165804.480) diff=1329.520 pctdiff=0.114 BrainSegVolNotVent 1167134.000 CerebellumVol 170761.000 VentChorVol 13589.000 3rd4th5thCSF 7177.000 CSFVol 3095.000, OptChiasmVol 556.000 MaskVol 1609937.000 1506 981 2566 2.634 0.357 0.077 0.013 8 0.9 bankssts 1074 786 2105 2.717 0.741 0.124 0.037 71 1.0 caudalanteriorcingulate 3438 2565 6689 2.678 0.555 0.110 0.020 29 3.1 caudalmiddlefrontal 2685 1833 3193 1.896 0.523 0.111 0.021 21 2.4 cuneus 449 442 1204 3.481 0.680 0.115 0.021 2 0.4 entorhinal 5276 4017 11099 2.886 0.629 0.112 0.023 50 5.3 fusiform 7329 5614 13401 2.517 0.558 0.118 0.022 64 7.3 inferiorparietal 5898 4890 13299 2.924 0.674 0.116 0.023 46 6.0 inferiortemporal 1860 1297 3125 2.518 0.819 0.112 0.027 25 1.7 isthmuscingulate 8716 6040 12083 2.139 0.590 0.103 0.020 73 7.7 lateraloccipital 4279 3266 8399 2.629 0.759 0.120 0.027 47 5.0 lateralorbitofrontal 5200 3533 7065 2.086 0.688 0.104 0.021 43 4.6 lingual 3052 2334 5021 2.278 0.914 0.123 0.035 46 4.0 medialorbitofrontal 5035 4560 13107 3.166 0.631 0.122 0.023 39 5.2 middletemporal 989 832 2065 2.845 0.560 0.108 0.019 5 0.9 parahippocampal 1930 1385 3120 2.354 0.566 0.106 0.018 18 1.3 paracentral 2421 1984 5103 2.767 0.442 0.117 0.019 20 2.1 parsopercularis 905 890 2195 2.859 0.589 0.157 0.029 10 1.3 parsorbitalis 1953 1555 3885 2.661 0.620 0.127 0.024 19 1.9 parstriangularis 2481 1348 2164 1.495 0.512 0.083 0.014 22 1.4 pericalcarine 6545 4721 8818 2.012 0.731 0.099 0.017 39 5.1 postcentral 1755 1221 3021 2.538 0.703 0.102 0.018 17 1.2 posteriorcingulate 6600 4638 11682 2.638 0.567 0.096 0.020 56 5.3 precentral 5898 4254 10005 2.412 0.584 0.117 0.024 61 5.6 precuneus 1276 1176 3014 2.865 1.062 0.159 0.048 39 1.6 rostralanteriorcingulate 8452 7012 16506 2.494 0.667 0.137 0.028 101 10.2 rostralmiddlefrontal 10768 8582 24221 2.996 0.615 0.121 0.024 112 11.4 superiorfrontal 9518 6954 13862 2.115 0.496 0.115 0.021 86 8.8 superiorparietal 5999 4665 14041 3.148 0.634 0.107 0.019 47 5.5 superiortemporal 6372 4921 12428 2.655 0.598 0.113 0.022 61 6.2 supramarginal 307 419 1039 3.179 0.869 0.202 0.041 2 0.6 frontalpole 616 681 2126 3.864 0.907 0.150 0.026 5 0.8 temporalpole 676 476 1146 2.721 0.399 0.094 0.015 3 0.4 transversetemporal 3154 1899 7243 3.313 0.764 0.099 0.021 34 2.7 insula mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab subject7_V1 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/wm.mgz... reading input surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.white... reading input pial surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.pial... reading input white surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 241169 Total vertex volume 237015 (mask=0) 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 atlas_icv (eTIV) = 1576049 mm^3 (det: 1.236069 ) lhCtxGM: 249367.335 249428.000 diff= -60.7 pctdiff=-0.024 rhCtxGM: 237349.818 237706.000 diff= -356.2 pctdiff=-0.150 lhCtxWM: 230995.026 230911.500 diff= 83.5 pctdiff= 0.036 rhCtxWM: 216994.301 217423.500 diff= -429.2 pctdiff=-0.198 SubCortGMVol 60253.000 SupraTentVol 1010772.480 (1009395.000) diff=1377.480 pctdiff=0.136 SupraTentVolNotVent 997183.480 (995806.000) diff=1377.480 pctdiff=0.138 BrainSegVol 1187900.000 (1183807.000) diff=4093.000 pctdiff=0.345 BrainSegVolNotVent 1167134.000 (1165804.480) diff=1329.520 pctdiff=0.114 BrainSegVolNotVent 1167134.000 CerebellumVol 170761.000 VentChorVol 13589.000 3rd4th5thCSF 7177.000 CSFVol 3095.000, OptChiasmVol 556.000 MaskVol 1609937.000 1707 1191 3261 2.813 0.446 0.110 0.017 16 1.3 bankssts 1177 766 2137 2.440 0.907 0.125 0.021 19 0.9 caudalanteriorcingulate 3236 2176 5642 2.361 0.638 0.111 0.023 31 3.0 caudalmiddlefrontal 1616 1035 1841 1.662 0.426 0.133 0.032 26 2.1 cuneus 357 223 1210 3.787 0.539 0.094 0.024 2 0.3 entorhinal 4962 3231 10298 2.857 0.578 0.121 0.024 62 4.4 fusiform 8047 5193 15656 2.647 0.570 0.109 0.021 79 6.5 inferiorparietal 6235 3952 14160 2.990 0.686 0.115 0.027 76 6.7 inferiortemporal 1542 983 2656 2.428 0.731 0.127 0.030 24 1.6 isthmuscingulate 6629 4062 9498 2.180 0.733 0.123 0.032 82 9.3 lateraloccipital 4198 2690 7307 2.344 0.697 0.131 0.040 69 6.8 lateralorbitofrontal 4041 2443 5651 2.175 0.581 0.126 0.029 50 4.6 lingual 2920 1877 4469 2.047 0.713 0.119 0.025 46 3.3 medialorbitofrontal 6038 3927 15342 3.208 0.722 0.119 0.026 80 5.9 middletemporal 894 569 1879 2.885 0.554 0.100 0.021 7 0.7 parahippocampal 2190 1372 3320 2.234 0.498 0.108 0.018 18 1.6 paracentral 2476 1673 5142 2.569 0.560 0.112 0.020 24 2.1 parsopercularis 1059 705 2544 2.638 0.650 0.135 0.030 17 1.2 parsorbitalis 1835 1254 3377 2.323 0.708 0.131 0.026 24 2.0 parstriangularis 1586 994 1467 1.539 0.413 0.098 0.021 12 1.4 pericalcarine 6013 3698 8471 1.999 0.709 0.096 0.018 47 4.3 postcentral 1616 1109 3043 2.459 0.681 0.133 0.029 24 1.7 posteriorcingulate 6382 4019 10335 2.364 0.596 0.095 0.016 42 4.1 precentral 6504 4309 10928 2.344 0.615 0.119 0.026 77 6.6 precuneus 982 641 2052 2.600 0.847 0.130 0.028 15 1.0 rostralanteriorcingulate 8088 5423 14535 2.207 0.727 0.133 0.031 133 10.5 rostralmiddlefrontal 10716 7167 21982 2.610 0.706 0.123 0.027 130 11.3 superiorfrontal 8120 5057 11616 2.077 0.516 0.112 0.022 83 7.5 superiorparietal 5743 3689 12833 3.099 0.636 0.100 0.018 49 3.9 superiortemporal 6677 4296 12574 2.570 0.622 0.120 0.024 81 5.9 supramarginal 298 194 884 2.862 0.562 0.170 0.050 8 0.6 frontalpole 587 383 2190 3.854 0.624 0.137 0.051 8 1.4 temporalpole 663 367 1227 2.766 0.304 0.099 0.020 8 0.5 transversetemporal 3535 2357 7489 3.079 0.773 0.105 0.025 31 3.3 insula mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab subject7_V1 rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/wm.mgz... reading input surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.pial... reading input pial surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.pial... reading input white surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 241169 Total vertex volume 237015 (mask=0) 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 atlas_icv (eTIV) = 1576049 mm^3 (det: 1.236069 ) lhCtxGM: 249367.335 249428.000 diff= -60.7 pctdiff=-0.024 rhCtxGM: 237349.818 237706.000 diff= -356.2 pctdiff=-0.150 lhCtxWM: 230995.026 230911.500 diff= 83.5 pctdiff= 0.036 rhCtxWM: 216994.301 217423.500 diff= -429.2 pctdiff=-0.198 SubCortGMVol 60253.000 SupraTentVol 1010772.480 (1009395.000) diff=1377.480 pctdiff=0.136 SupraTentVolNotVent 997183.480 (995806.000) diff=1377.480 pctdiff=0.138 BrainSegVol 1187900.000 (1183807.000) diff=4093.000 pctdiff=0.345 BrainSegVolNotVent 1167134.000 (1165804.480) diff=1329.520 pctdiff=0.114 BrainSegVolNotVent 1167134.000 CerebellumVol 170761.000 VentChorVol 13589.000 3rd4th5thCSF 7177.000 CSFVol 3095.000, OptChiasmVol 556.000 MaskVol 1609937.000 1707 1114 3261 2.813 0.446 0.093 0.017 11 1.2 bankssts 1177 841 2137 2.440 0.907 0.104 0.017 97 0.6 caudalanteriorcingulate 3236 2463 5642 2.361 0.638 0.113 0.020 37 2.9 caudalmiddlefrontal 1616 1257 1841 1.662 0.426 0.116 0.019 14 1.3 cuneus 357 424 1210 3.787 0.539 0.122 0.019 1 0.3 entorhinal 4962 3735 10298 2.857 0.578 0.107 0.020 38 4.4 fusiform 8047 6258 15656 2.647 0.570 0.113 0.021 62 7.5 inferiorparietal 6235 5259 14160 2.990 0.686 0.122 0.023 51 6.9 inferiortemporal 1542 1133 2656 2.428 0.731 0.113 0.026 22 1.4 isthmuscingulate 6629 4785 9498 2.180 0.733 0.097 0.021 39 6.1 lateraloccipital 4198 3361 7307 2.344 0.697 0.136 0.029 47 5.2 lateralorbitofrontal 4041 2704 5651 2.175 0.581 0.101 0.021 34 3.6 lingual 2920 2421 4469 2.047 0.713 0.131 0.024 36 3.2 medialorbitofrontal 6038 5342 15342 3.208 0.722 0.119 0.023 62 6.0 middletemporal 894 722 1879 2.885 0.554 0.101 0.020 4 0.7 parahippocampal 2190 1563 3320 2.234 0.498 0.110 0.017 21 1.5 paracentral 2476 2211 5142 2.569 0.560 0.123 0.019 19 2.3 parsopercularis 1059 1141 2544 2.638 0.650 0.159 0.027 9 1.4 parsorbitalis 1835 1594 3377 2.323 0.708 0.144 0.025 20 2.1 parstriangularis 1586 949 1467 1.539 0.413 0.079 0.019 17 1.1 pericalcarine 6013 4567 8471 1.999 0.709 0.105 0.017 36 4.5 postcentral 1616 1311 3043 2.459 0.681 0.118 0.023 13 1.5 posteriorcingulate 6382 4503 10335 2.364 0.596 0.095 0.015 45 4.2 precentral 6504 4821 10928 2.344 0.615 0.117 0.024 105 6.4 precuneus 982 871 2052 2.600 0.847 0.133 0.025 11 1.1 rostralanteriorcingulate 8088 7227 14535 2.207 0.727 0.147 0.028 75 10.2 rostralmiddlefrontal 10716 8984 21982 2.610 0.706 0.131 0.025 100 11.3 superiorfrontal 8120 5989 11616 2.077 0.516 0.116 0.020 103 7.4 superiorparietal 5743 4431 12833 3.099 0.636 0.104 0.018 44 4.6 superiortemporal 6677 5046 12574 2.570 0.622 0.119 0.023 64 6.4 supramarginal 298 398 884 2.862 0.562 0.213 0.040 3 0.5 frontalpole 587 724 2190 3.854 0.624 0.168 0.031 5 0.9 temporalpole 663 490 1227 2.766 0.304 0.090 0.013 3 0.3 transversetemporal 3535 2263 7489 3.079 0.773 0.105 0.021 35 2.9 insula PIDs (20941 20944 20947 20950) completed and logs appended. #----------------------------------------- #@# Cortical Parc 2 lh Mon May 11 01:20:33 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 subject7_V1 lh ../surf/lh.sphere.reg /opt/local/freesurfer-6.0/x86_64/average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot #----------------------------------------- #@# Cortical Parc 2 rh Mon May 11 01:20:33 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 subject7_V1 rh ../surf/rh.sphere.reg /opt/local/freesurfer-6.0/x86_64/average/rh.destrieux.simple.2009-07-29.gcs ../label/rh.aparc.a2009s.annot Waiting for PID 21234 of (21234 21237) to complete... Waiting for PID 21237 of (21234 21237) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 subject7_V1 lh ../surf/lh.sphere.reg /opt/local/freesurfer-6.0/x86_64/average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.770 2015/08/26 16:48:39 fischl Exp $ reading atlas from /opt/local/freesurfer-6.0/x86_64/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... 7 labels changed using aseg relabeling using gibbs priors... 000: 9416 changed, 142219 examined... 001: 2372 changed, 35839 examined... 002: 735 changed, 11989 examined... 003: 363 changed, 4052 examined... 004: 196 changed, 2085 examined... 005: 95 changed, 1073 examined... 006: 60 changed, 557 examined... 007: 41 changed, 335 examined... 008: 19 changed, 229 examined... 009: 12 changed, 101 examined... 010: 8 changed, 66 examined... 011: 1 changed, 43 examined... 012: 0 changed, 7 examined... 3 labels changed using aseg 000: 283 total segments, 199 labels (1654 vertices) changed 001: 95 total segments, 12 labels (48 vertices) changed 002: 83 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 149 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1320 vertices marked for relabeling... 1320 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 38 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 subject7_V1 rh ../surf/rh.sphere.reg /opt/local/freesurfer-6.0/x86_64/average/rh.destrieux.simple.2009-07-29.gcs ../label/rh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.770 2015/08/26 16:48:39 fischl Exp $ reading atlas from /opt/local/freesurfer-6.0/x86_64/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... 5 labels changed using aseg relabeling using gibbs priors... 000: 9723 changed, 136618 examined... 001: 2340 changed, 37166 examined... 002: 744 changed, 11987 examined... 003: 329 changed, 4054 examined... 004: 156 changed, 1862 examined... 005: 83 changed, 881 examined... 006: 50 changed, 453 examined... 007: 22 changed, 270 examined... 008: 9 changed, 110 examined... 009: 4 changed, 49 examined... 010: 2 changed, 27 examined... 011: 2 changed, 14 examined... 012: 0 changed, 14 examined... 0 labels changed using aseg 000: 282 total segments, 204 labels (2270 vertices) changed 001: 99 total segments, 21 labels (69 vertices) changed 002: 78 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 151 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 707 vertices marked for relabeling... 707 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 41 seconds. PIDs (21234 21237) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 2 lh Mon May 11 01:21:13 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab subject7_V1 lh white #----------------------------------------- #@# Parcellation Stats 2 rh Mon May 11 01:21:13 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab subject7_V1 rh white Waiting for PID 21381 of (21381 21384) to complete... Waiting for PID 21384 of (21381 21384) to complete... mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab subject7_V1 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/wm.mgz... reading input surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.white... reading input pial surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.pial... reading input white surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 254114 Total vertex volume 250037 (mask=0) 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 atlas_icv (eTIV) = 1576049 mm^3 (det: 1.236069 ) lhCtxGM: 249367.335 249428.000 diff= -60.7 pctdiff=-0.024 rhCtxGM: 237349.818 237706.000 diff= -356.2 pctdiff=-0.150 lhCtxWM: 230995.026 230911.500 diff= 83.5 pctdiff= 0.036 rhCtxWM: 216994.301 217423.500 diff= -429.2 pctdiff=-0.198 SubCortGMVol 60253.000 SupraTentVol 1010772.480 (1009395.000) diff=1377.480 pctdiff=0.136 SupraTentVolNotVent 997183.480 (995806.000) diff=1377.480 pctdiff=0.138 BrainSegVol 1187900.000 (1183807.000) diff=4093.000 pctdiff=0.345 BrainSegVolNotVent 1167134.000 (1165804.480) diff=1329.520 pctdiff=0.114 BrainSegVolNotVent 1167134.000 CerebellumVol 170761.000 VentChorVol 13589.000 3rd4th5thCSF 7177.000 CSFVol 3095.000, OptChiasmVol 556.000 MaskVol 1609937.000 1087 759 2324 2.441 0.890 0.144 0.035 18 1.5 G_and_S_frontomargin 2209 1378 3680 2.331 0.535 0.122 0.024 26 2.0 G_and_S_occipital_inf 1402 833 1924 2.039 0.473 0.124 0.026 15 1.6 G_and_S_paracentral 1356 877 2752 2.805 0.628 0.125 0.027 16 1.4 G_and_S_subcentral 865 578 1993 2.803 0.679 0.149 0.041 20 1.6 G_and_S_transv_frontopol 2205 1547 4848 2.854 0.722 0.128 0.028 27 2.6 G_and_S_cingul-Ant 1560 1046 3314 2.949 0.484 0.109 0.022 11 1.4 G_and_S_cingul-Mid-Ant 1302 872 2281 2.699 0.543 0.130 0.034 18 1.5 G_and_S_cingul-Mid-Post 621 408 1658 3.185 0.490 0.143 0.039 10 0.9 G_cingul-Post-dorsal 478 282 525 1.990 0.886 0.131 0.035 7 0.6 G_cingul-Post-ventral 2607 1574 2954 1.785 0.559 0.139 0.033 36 3.4 G_cuneus 1566 1039 3956 2.955 0.371 0.124 0.021 22 1.5 G_front_inf-Opercular 424 262 979 2.872 0.424 0.148 0.042 9 0.6 G_front_inf-Orbital 1026 647 2565 2.941 0.522 0.127 0.027 14 1.1 G_front_inf-Triangul 4698 3101 11676 2.856 0.616 0.140 0.032 80 6.3 G_front_middle 7337 4953 18461 3.140 0.588 0.137 0.031 105 9.0 G_front_sup 505 324 1267 3.438 0.539 0.138 0.037 8 0.7 G_Ins_lg_and_S_cent_ins 661 438 2677 4.222 0.680 0.116 0.033 8 0.7 G_insular_short 2310 1375 4727 2.663 0.588 0.129 0.030 33 2.5 G_occipital_middle 1891 1136 2299 1.901 0.516 0.127 0.031 23 2.4 G_occipital_sup 2257 1458 5280 2.977 0.505 0.136 0.029 37 2.6 G_oc-temp_lat-fusifor 3697 2343 5085 2.036 0.717 0.145 0.038 53 5.6 G_oc-temp_med-Lingual 985 606 2391 3.242 0.686 0.103 0.030 9 1.2 G_oc-temp_med-Parahip 2780 1810 6805 2.800 0.784 0.144 0.049 61 5.2 G_orbital 3190 2044 7399 2.766 0.624 0.128 0.029 50 3.4 G_pariet_inf-Angular 3031 2001 7009 2.856 0.509 0.121 0.021 37 2.6 G_pariet_inf-Supramar 3453 2124 6244 2.329 0.528 0.128 0.030 50 4.0 G_parietal_sup 2405 1346 3376 2.050 0.683 0.099 0.022 22 2.1 G_postcentral 2488 1464 5532 2.900 0.550 0.099 0.019 20 1.8 G_precentral 2725 1814 5851 2.586 0.548 0.140 0.030 47 3.2 G_precuneus 1046 707 2583 2.719 0.711 0.140 0.038 23 1.6 G_rectus 817 501 913 1.848 1.289 0.139 0.073 14 2.7 G_subcallosal 503 288 917 2.716 0.361 0.117 0.022 5 0.4 G_temp_sup-G_T_transv 2451 1550 7338 3.277 0.606 0.124 0.025 30 2.4 G_temp_sup-Lateral 694 457 1832 3.865 0.864 0.080 0.015 2 0.4 G_temp_sup-Plan_polar 1097 753 2581 2.950 0.510 0.114 0.021 11 0.9 G_temp_sup-Plan_tempo 3399 2282 8983 2.989 0.671 0.136 0.039 64 5.1 G_temporal_inf 3014 2093 9272 3.383 0.580 0.136 0.029 44 3.4 G_temporal_middle 414 279 614 2.244 0.529 0.120 0.019 4 0.3 Lat_Fis-ant-Horizont 294 206 421 2.420 0.524 0.116 0.017 2 0.2 Lat_Fis-ant-Vertical 1193 813 1647 2.571 0.433 0.113 0.022 7 1.1 Lat_Fis-post 2234 1312 2407 1.770 0.499 0.126 0.029 24 2.7 Pole_occipital 1638 1118 5934 3.683 0.785 0.141 0.037 29 2.4 Pole_temporal 3286 2220 3365 1.750 0.659 0.108 0.017 26 2.4 S_calcarine 2816 1865 2862 1.783 0.628 0.091 0.017 14 1.9 S_central 1125 758 1684 2.362 0.532 0.095 0.012 6 0.6 S_cingul-Marginalis 596 394 1022 2.869 0.464 0.087 0.016 2 0.3 S_circular_insula_ant 1369 906 2209 3.036 0.633 0.069 0.009 4 0.4 S_circular_insula_inf 1819 1222 2801 2.708 0.430 0.103 0.018 9 1.4 S_circular_insula_sup 949 651 1926 3.020 0.652 0.125 0.023 9 1.0 S_collat_transv_ant 491 328 586 2.197 0.375 0.122 0.020 5 0.4 S_collat_transv_post 2195 1477 3144 2.277 0.465 0.113 0.021 20 1.8 S_front_inf 1405 953 2096 2.321 0.466 0.118 0.022 11 1.3 S_front_middle 2739 1834 3995 2.339 0.508 0.103 0.019 17 2.2 S_front_sup 728 473 942 2.374 0.340 0.088 0.011 3 0.4 S_interm_prim-Jensen 3702 2479 4610 2.040 0.401 0.097 0.016 21 2.4 S_intrapariet_and_P_trans 1089 722 1087 1.834 0.346 0.139 0.029 12 1.4 S_oc_middle_and_Lunatus 1646 1087 2031 2.025 0.342 0.124 0.023 17 1.5 S_oc_sup_and_transversal 986 654 1275 2.352 0.369 0.107 0.017 7 0.7 S_occipital_ant 1503 998 2217 2.649 0.413 0.107 0.022 12 1.3 S_oc-temp_lat 2123 1432 3460 2.722 0.379 0.113 0.022 15 2.0 S_oc-temp_med_and_Lingual 449 290 698 2.414 0.686 0.116 0.022 6 0.3 S_orbital_lateral 940 660 1358 2.286 0.555 0.096 0.013 5 0.5 S_orbital_med-olfact 1326 914 2324 2.472 0.750 0.128 0.032 17 1.6 S_orbital-H_Shaped 2220 1432 2853 2.226 0.554 0.121 0.024 22 2.2 S_parieto_occipital 1428 915 1325 2.061 0.857 0.123 0.021 23 0.8 S_pericallosal 3560 2330 4399 2.067 0.521 0.099 0.023 31 3.3 S_postcentral 1587 1060 2531 2.713 0.412 0.099 0.017 8 1.1 S_precentral-inf-part 1168 768 1534 2.339 0.467 0.098 0.017 7 0.8 S_precentral-sup-part 596 395 895 2.434 0.824 0.099 0.017 6 0.3 S_suborbital 1316 875 1927 2.329 0.484 0.114 0.021 11 1.2 S_subparietal 1628 1069 2221 2.482 0.409 0.092 0.014 8 1.0 S_temporal_inf 5439 3632 8957 2.668 0.456 0.097 0.015 34 3.4 S_temporal_sup 273 189 429 3.115 0.412 0.135 0.023 3 0.3 S_temporal_transverse mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab subject7_V1 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/wm.mgz... reading input surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.white... reading input pial surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.pial... reading input white surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 241169 Total vertex volume 237015 (mask=0) 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 atlas_icv (eTIV) = 1576049 mm^3 (det: 1.236069 ) lhCtxGM: 249367.335 249428.000 diff= -60.7 pctdiff=-0.024 rhCtxGM: 237349.818 237706.000 diff= -356.2 pctdiff=-0.150 lhCtxWM: 230995.026 230911.500 diff= 83.5 pctdiff= 0.036 rhCtxWM: 216994.301 217423.500 diff= -429.2 pctdiff=-0.198 SubCortGMVol 60253.000 SupraTentVol 1010772.480 (1009395.000) diff=1377.480 pctdiff=0.136 SupraTentVolNotVent 997183.480 (995806.000) diff=1377.480 pctdiff=0.138 BrainSegVol 1187900.000 (1183807.000) diff=4093.000 pctdiff=0.345 BrainSegVolNotVent 1167134.000 (1165804.480) diff=1329.520 pctdiff=0.114 BrainSegVolNotVent 1167134.000 CerebellumVol 170761.000 VentChorVol 13589.000 3rd4th5thCSF 7177.000 CSFVol 3095.000, OptChiasmVol 556.000 MaskVol 1609937.000 962 642 1591 2.068 0.643 0.140 0.034 19 1.4 G_and_S_frontomargin 1525 862 2672 2.529 0.679 0.111 0.028 16 1.9 G_and_S_occipital_inf 1404 777 2060 2.242 0.486 0.099 0.019 10 1.1 G_and_S_paracentral 1520 997 3164 2.690 0.591 0.122 0.024 19 1.3 G_and_S_subcentral 1001 652 2460 2.669 0.656 0.166 0.049 28 2.2 G_and_S_transv_frontopol 2585 1766 4632 2.326 0.779 0.107 0.021 25 2.1 G_and_S_cingul-Ant 1461 977 2845 2.632 0.669 0.119 0.020 15 1.1 G_and_S_cingul-Mid-Ant 1469 989 2566 2.438 0.491 0.119 0.025 15 1.3 G_and_S_cingul-Mid-Post 646 420 1667 3.086 0.491 0.159 0.043 14 0.9 G_cingul-Post-dorsal 247 132 442 2.463 0.694 0.134 0.040 5 0.3 G_cingul-Post-ventral 1422 901 1617 1.613 0.405 0.130 0.031 21 1.8 G_cuneus 1566 1037 3849 2.854 0.511 0.118 0.023 19 1.3 G_front_inf-Opercular 319 203 868 2.793 0.571 0.150 0.033 6 0.4 G_front_inf-Orbital 864 592 2267 2.858 0.536 0.151 0.036 16 1.3 G_front_inf-Triangul 4439 2922 10613 2.698 0.606 0.142 0.035 85 6.7 G_front_middle 7589 4958 17236 2.711 0.716 0.137 0.031 124 9.6 G_front_sup 541 369 1417 3.333 0.782 0.100 0.023 5 0.4 G_Ins_lg_and_S_cent_ins 623 393 2172 3.783 0.673 0.141 0.043 12 1.1 G_insular_short 2124 1238 4603 2.725 0.770 0.122 0.032 34 2.5 G_occipital_middle 1646 857 1988 1.921 0.583 0.103 0.026 24 2.0 G_occipital_sup 1881 1185 4490 2.992 0.469 0.122 0.025 31 1.7 G_oc-temp_lat-fusifor 2218 1256 3326 2.187 0.686 0.124 0.032 32 2.5 G_oc-temp_med-Lingual 1090 688 2832 3.308 0.672 0.105 0.027 9 0.9 G_oc-temp_med-Parahip 3128 1977 6867 2.577 0.737 0.134 0.046 64 5.8 G_orbital 3469 2091 8240 2.895 0.617 0.122 0.027 51 3.4 G_pariet_inf-Angular 3517 2222 7634 2.715 0.598 0.125 0.026 51 3.4 G_pariet_inf-Supramar 2651 1606 4756 2.323 0.520 0.123 0.030 39 3.0 G_parietal_sup 2194 1178 3346 2.151 0.601 0.097 0.019 21 1.7 G_postcentral 2293 1371 4681 2.537 0.527 0.097 0.017 19 1.5 G_precentral 3006 1962 5895 2.444 0.591 0.126 0.028 46 3.2 G_precuneus 888 554 1763 2.300 0.591 0.133 0.043 19 1.8 G_rectus 215 135 390 3.190 0.425 0.112 0.022 2 0.2 G_subcallosal 544 307 1091 2.778 0.276 0.098 0.021 7 0.4 G_temp_sup-G_T_transv 2122 1282 6004 3.510 0.551 0.122 0.027 31 2.1 G_temp_sup-Lateral 662 438 1701 3.503 0.547 0.080 0.015 3 0.4 G_temp_sup-Plan_polar 748 499 1403 2.633 0.484 0.080 0.012 3 0.3 G_temp_sup-Plan_tempo 3599 2240 9772 3.211 0.711 0.127 0.035 59 5.0 G_temporal_inf 3520 2224 10610 3.474 0.629 0.127 0.032 60 4.1 G_temporal_middle 480 323 615 2.033 0.376 0.094 0.011 2 0.2 Lat_Fis-ant-Horizont 90 67 134 1.989 0.481 0.096 0.018 0 0.1 Lat_Fis-ant-Vertical 1562 1046 2310 2.570 0.520 0.103 0.017 9 1.1 Lat_Fis-post 3302 2081 4131 1.873 0.680 0.140 0.037 43 5.7 Pole_occipital 1770 1143 6246 3.637 0.828 0.138 0.041 27 2.9 Pole_temporal 2185 1417 2621 2.008 0.783 0.112 0.026 21 2.4 S_calcarine 2563 1721 2415 1.635 0.501 0.085 0.014 10 1.4 S_central 1228 840 1626 1.992 0.419 0.093 0.011 6 0.6 S_cingul-Marginalis 575 388 957 2.920 0.427 0.105 0.022 3 0.5 S_circular_insula_ant 1319 873 2066 2.941 0.554 0.071 0.009 4 0.5 S_circular_insula_inf 1477 1006 2147 2.468 0.605 0.097 0.016 6 1.0 S_circular_insula_sup 819 555 1512 2.711 0.505 0.108 0.021 7 0.6 S_collat_transv_ant 592 401 719 2.449 0.375 0.140 0.030 5 0.8 S_collat_transv_post 2093 1403 2484 1.889 0.451 0.111 0.020 15 1.7 S_front_inf 2023 1382 2291 1.677 0.481 0.114 0.021 19 1.8 S_front_middle 2291 1592 3491 2.258 0.567 0.097 0.017 14 1.5 S_front_sup 460 296 564 2.038 0.430 0.104 0.014 3 0.3 S_interm_prim-Jensen 3155 2091 3984 2.024 0.470 0.109 0.018 24 2.4 S_intrapariet_and_P_trans 476 327 508 1.840 0.616 0.107 0.019 3 0.4 S_oc_middle_and_Lunatus 1353 933 1773 2.114 0.345 0.095 0.011 8 0.7 S_oc_sup_and_transversal 1122 763 1727 2.435 0.470 0.119 0.023 9 1.1 S_occipital_ant 1539 1015 2239 2.635 0.303 0.099 0.017 9 0.9 S_oc-temp_lat 2015 1338 3272 2.544 0.377 0.108 0.017 17 1.3 S_oc-temp_med_and_Lingual 301 214 459 1.874 0.709 0.150 0.032 4 0.4 S_orbital_lateral 901 621 934 1.651 0.552 0.099 0.013 5 0.5 S_orbital_med-olfact 1458 961 2117 2.145 0.557 0.130 0.034 18 1.8 S_orbital-H_Shaped 2052 1336 2653 2.215 0.558 0.105 0.020 16 1.6 S_parieto_occipital 1448 921 1271 1.811 0.670 0.124 0.021 22 1.0 S_pericallosal 2644 1769 2967 1.921 0.379 0.105 0.019 17 2.0 S_postcentral 1685 1131 2321 2.187 0.549 0.087 0.018 10 1.0 S_precentral-inf-part 1006 692 1321 2.219 0.681 0.102 0.014 6 0.6 S_precentral-sup-part 492 321 598 1.829 0.757 0.136 0.021 6 0.4 S_suborbital 1764 1186 2680 2.189 0.521 0.123 0.025 19 1.8 S_subparietal 1979 1298 2726 2.519 0.373 0.106 0.015 12 1.3 S_temporal_inf 6440 4464 11075 2.653 0.467 0.096 0.015 38 3.9 S_temporal_sup 312 210 529 2.753 0.265 0.131 0.022 4 0.3 S_temporal_transverse PIDs (21381 21384) completed and logs appended. #----------------------------------------- #@# Cortical Parc 3 lh Mon May 11 01:21:41 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 subject7_V1 lh ../surf/lh.sphere.reg /opt/local/freesurfer-6.0/x86_64/average/lh.DKTatlas40.gcs ../label/lh.aparc.DKTatlas40.annot #----------------------------------------- #@# Cortical Parc 3 rh Mon May 11 01:21:42 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 subject7_V1 rh ../surf/rh.sphere.reg /opt/local/freesurfer-6.0/x86_64/average/rh.DKTatlas40.gcs ../label/rh.aparc.DKTatlas40.annot Waiting for PID 21528 of (21528 21531) to complete... Waiting for PID 21531 of (21528 21531) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 subject7_V1 lh ../surf/lh.sphere.reg /opt/local/freesurfer-6.0/x86_64/average/lh.DKTatlas40.gcs ../label/lh.aparc.DKTatlas40.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.770 2015/08/26 16:48:39 fischl Exp $ reading atlas from /opt/local/freesurfer-6.0/x86_64/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... 897 labels changed using aseg relabeling using gibbs priors... 000: 2921 changed, 142219 examined... 001: 719 changed, 12389 examined... 002: 198 changed, 3907 examined... 003: 62 changed, 1171 examined... 004: 24 changed, 403 examined... 005: 10 changed, 140 examined... 006: 8 changed, 62 examined... 007: 3 changed, 52 examined... 008: 4 changed, 21 examined... 009: 4 changed, 20 examined... 010: 3 changed, 24 examined... 011: 1 changed, 17 examined... 012: 1 changed, 7 examined... 013: 1 changed, 7 examined... 014: 1 changed, 7 examined... 015: 1 changed, 7 examined... 016: 1 changed, 7 examined... 017: 1 changed, 7 examined... 018: 1 changed, 7 examined... 019: 2 changed, 7 examined... 020: 0 changed, 10 examined... 111 labels changed using aseg 000: 80 total segments, 47 labels (324 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... 1074 vertices marked for relabeling... 1074 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas40.annot... classification took 0 minutes and 35 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 subject7_V1 rh ../surf/rh.sphere.reg /opt/local/freesurfer-6.0/x86_64/average/rh.DKTatlas40.gcs ../label/rh.aparc.DKTatlas40.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.770 2015/08/26 16:48:39 fischl Exp $ reading atlas from /opt/local/freesurfer-6.0/x86_64/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... 868 labels changed using aseg relabeling using gibbs priors... 000: 2675 changed, 136618 examined... 001: 591 changed, 11355 examined... 002: 157 changed, 3301 examined... 003: 59 changed, 917 examined... 004: 26 changed, 346 examined... 005: 10 changed, 153 examined... 006: 9 changed, 67 examined... 007: 4 changed, 55 examined... 008: 2 changed, 27 examined... 009: 2 changed, 14 examined... 010: 2 changed, 8 examined... 011: 2 changed, 11 examined... 012: 2 changed, 11 examined... 013: 3 changed, 11 examined... 014: 5 changed, 19 examined... 015: 2 changed, 25 examined... 016: 0 changed, 14 examined... 143 labels changed using aseg 000: 57 total segments, 24 labels (135 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, 39 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 495 vertices marked for relabeling... 495 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas40.annot... classification took 0 minutes and 32 seconds. PIDs (21528 21531) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 3 lh Mon May 11 01:22:17 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts mris_anatomical_stats -th3 -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 subject7_V1 lh white #----------------------------------------- #@# Parcellation Stats 3 rh Mon May 11 01:22:17 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts mris_anatomical_stats -th3 -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 subject7_V1 rh white Waiting for PID 21661 of (21661 21664) to complete... Waiting for PID 21664 of (21661 21664) to complete... mris_anatomical_stats -th3 -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 subject7_V1 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot. reading volume /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/wm.mgz... reading input surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.white... reading input pial surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.pial... reading input white surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 254114 Total vertex volume 250037 (mask=0) 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 atlas_icv (eTIV) = 1576049 mm^3 (det: 1.236069 ) lhCtxGM: 249367.335 249428.000 diff= -60.7 pctdiff=-0.024 rhCtxGM: 237349.818 237706.000 diff= -356.2 pctdiff=-0.150 lhCtxWM: 230995.026 230911.500 diff= 83.5 pctdiff= 0.036 rhCtxWM: 216994.301 217423.500 diff= -429.2 pctdiff=-0.198 SubCortGMVol 60253.000 SupraTentVol 1010772.480 (1009395.000) diff=1377.480 pctdiff=0.136 SupraTentVolNotVent 997183.480 (995806.000) diff=1377.480 pctdiff=0.138 BrainSegVol 1187900.000 (1183807.000) diff=4093.000 pctdiff=0.345 BrainSegVolNotVent 1167134.000 (1165804.480) diff=1329.520 pctdiff=0.114 BrainSegVolNotVent 1167134.000 CerebellumVol 170761.000 VentChorVol 13589.000 3rd4th5thCSF 7177.000 CSFVol 3095.000, OptChiasmVol 556.000 MaskVol 1609937.000 1861 1217 3757 2.796 0.628 0.114 0.019 18 1.5 caudalanteriorcingulate 3458 2254 6718 2.686 0.556 0.112 0.020 32 2.9 caudalmiddlefrontal 3695 2261 4419 1.934 0.495 0.130 0.030 45 4.5 cuneus 371 238 1067 3.590 0.647 0.103 0.024 2 0.4 entorhinal 4873 3213 9476 2.803 0.537 0.127 0.026 61 5.2 fusiform 7010 4618 12817 2.514 0.569 0.123 0.025 85 6.5 inferiorparietal 5815 3895 13872 2.993 0.734 0.127 0.032 84 7.3 inferiortemporal 1844 1193 3108 2.516 0.819 0.129 0.032 26 2.1 isthmuscingulate 9043 5449 12599 2.146 0.592 0.124 0.027 103 9.7 lateraloccipital 4751 3138 9731 2.619 0.814 0.132 0.041 81 7.5 lateralorbitofrontal 5226 3429 7147 2.093 0.695 0.136 0.032 63 7.0 lingual 2331 1573 4339 2.364 0.890 0.117 0.030 34 2.9 medialorbitofrontal 6579 4458 15871 3.054 0.629 0.113 0.022 69 5.8 middletemporal 955 614 1996 2.846 0.550 0.097 0.018 7 0.5 parahippocampal 2287 1488 3659 2.389 0.603 0.117 0.023 20 2.0 paracentral 2219 1493 4595 2.775 0.438 0.112 0.019 22 1.8 parsopercularis 1143 751 2151 2.609 0.520 0.121 0.024 13 1.1 parsorbitalis 2331 1535 4588 2.614 0.627 0.122 0.024 27 2.1 parstriangularis 2493 1636 2170 1.500 0.513 0.110 0.019 22 1.8 pericalcarine 7244 4533 9827 2.040 0.724 0.101 0.020 59 6.0 postcentral 1870 1259 3177 2.547 0.689 0.133 0.029 30 2.0 posteriorcingulate 6540 4065 11516 2.638 0.565 0.103 0.020 49 5.3 precentral 5637 3768 9820 2.436 0.582 0.128 0.026 72 5.8 precuneus 1814 1231 3647 2.703 1.149 0.138 0.041 30 3.0 rostralanteriorcingulate 5855 3922 11649 2.530 0.649 0.132 0.028 83 6.9 rostralmiddlefrontal 11812 8015 26545 2.921 0.663 0.132 0.030 159 14.8 superiorfrontal 7731 4945 11374 2.102 0.502 0.113 0.024 83 7.6 superiorparietal 8077 5276 18982 3.126 0.691 0.108 0.021 73 7.1 superiortemporal 6074 4039 11553 2.639 0.582 0.113 0.021 60 5.0 supramarginal 675 403 1140 2.723 0.397 0.114 0.022 6 0.6 transversetemporal 2798 1878 6731 3.365 0.757 0.103 0.023 22 2.3 insula mris_anatomical_stats -th3 -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 subject7_V1 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot. reading volume /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/wm.mgz... reading input surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.white... reading input pial surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.pial... reading input white surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 241169 Total vertex volume 237015 (mask=0) 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 atlas_icv (eTIV) = 1576049 mm^3 (det: 1.236069 ) lhCtxGM: 249367.335 249428.000 diff= -60.7 pctdiff=-0.024 rhCtxGM: 237349.818 237706.000 diff= -356.2 pctdiff=-0.150 lhCtxWM: 230995.026 230911.500 diff= 83.5 pctdiff= 0.036 rhCtxWM: 216994.301 217423.500 diff= -429.2 pctdiff=-0.198 SubCortGMVol 60253.000 SupraTentVol 1010772.480 (1009395.000) diff=1377.480 pctdiff=0.136 SupraTentVolNotVent 997183.480 (995806.000) diff=1377.480 pctdiff=0.138 BrainSegVol 1187900.000 (1183807.000) diff=4093.000 pctdiff=0.345 BrainSegVolNotVent 1167134.000 (1165804.480) diff=1329.520 pctdiff=0.114 BrainSegVolNotVent 1167134.000 CerebellumVol 170761.000 VentChorVol 13589.000 3rd4th5thCSF 7177.000 CSFVol 3095.000, OptChiasmVol 556.000 MaskVol 1609937.000 1246 807 2292 2.469 0.873 0.125 0.021 20 1.0 caudalanteriorcingulate 3269 2195 5659 2.368 0.632 0.113 0.023 31 3.1 caudalmiddlefrontal 2128 1350 2423 1.742 0.467 0.127 0.031 30 2.7 cuneus 403 252 1299 3.733 0.593 0.100 0.023 2 0.3 entorhinal 4325 2812 8466 2.776 0.480 0.118 0.022 53 3.6 fusiform 7508 4825 14591 2.631 0.575 0.112 0.022 77 6.3 inferiorparietal 6770 4310 15761 3.032 0.710 0.118 0.028 83 7.4 inferiortemporal 1555 993 2696 2.433 0.727 0.127 0.030 24 1.6 isthmuscingulate 6718 4128 9714 2.180 0.732 0.123 0.031 83 9.3 lateraloccipital 4727 3019 8143 2.305 0.720 0.132 0.041 84 7.9 lateralorbitofrontal 4087 2467 5737 2.176 0.582 0.126 0.029 51 4.7 lingual 2334 1499 3756 2.130 0.751 0.122 0.029 38 2.9 medialorbitofrontal 7311 4811 17720 3.135 0.702 0.116 0.024 90 6.7 middletemporal 889 567 1876 2.889 0.552 0.099 0.021 7 0.7 parahippocampal 2300 1447 3489 2.227 0.494 0.108 0.018 18 1.7 paracentral 2480 1669 5104 2.582 0.583 0.111 0.020 23 2.0 parsopercularis 1144 769 2617 2.584 0.655 0.122 0.024 14 1.0 parsorbitalis 1906 1309 3573 2.323 0.721 0.133 0.027 25 2.2 parstriangularis 1549 972 1431 1.537 0.409 0.098 0.021 12 1.4 pericalcarine 6752 4187 9560 2.024 0.686 0.099 0.019 54 5.0 postcentral 1674 1148 3095 2.443 0.681 0.133 0.029 24 1.7 posteriorcingulate 6107 3827 9909 2.360 0.571 0.094 0.016 40 3.8 precentral 6817 4472 11240 2.311 0.621 0.119 0.026 81 6.9 precuneus 1122 735 2177 2.490 0.877 0.131 0.027 16 1.1 rostralanteriorcingulate 5285 3516 9757 2.264 0.729 0.133 0.031 82 6.8 rostralmiddlefrontal 13823 9270 27634 2.510 0.741 0.126 0.028 187 15.5 superiorfrontal 6875 4290 10041 2.095 0.519 0.112 0.022 71 6.3 superiorparietal 7582 4906 17604 3.132 0.659 0.106 0.022 72 6.4 superiortemporal 6139 3967 11544 2.567 0.608 0.117 0.023 71 5.1 supramarginal 664 366 1228 2.771 0.304 0.099 0.020 8 0.5 transversetemporal 3180 2138 6880 3.120 0.745 0.104 0.023 26 2.8 insula PIDs (21661 21664) completed and logs appended. #----------------------------------------- #@# WM/GM Contrast lh Mon May 11 01:22:45 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts pctsurfcon --s subject7_V1 --lh-only #----------------------------------------- #@# WM/GM Contrast rh Mon May 11 01:22:45 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts pctsurfcon --s subject7_V1 --rh-only Waiting for PID 21810 of (21810 21814) to complete... Waiting for PID 21814 of (21810 21814) to complete... pctsurfcon --s subject7_V1 --lh-only Log file is /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts/pctsurfcon.log Mon May 11 01:22:45 CDT 2020 setenv SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects cd /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts /opt/local/freesurfer-6.0/x86_64/bin/pctsurfcon $Id: pctsurfcon,v 1.14 2014/10/27 16:10:47 greve Exp $ Linux frames1.cmrr.umn.edu 3.10.0-1127.el7.x86_64 #1 SMP Tue Mar 31 23:36:51 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 mri_vol2surf --mov /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/tmp.pctsurfcon.21810/lh.wm.mgh --regheader subject7_V1 --cortex srcvol = /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/orig.mgz as target reference. -------- original matrix ----------- 0.99853 0.05090 0.01869 -0.00005; -0.02654 0.15822 0.98705 0.00000; 0.04729 -0.98609 0.15934 -0.00005; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/label/lh.cortex.label Reading surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 = 78261 Masking with /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/label/lh.cortex.label Writing to /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/tmp.pctsurfcon.21810/lh.wm.mgh Dim: 142219 1 1 mri_vol2surf --mov /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/tmp.pctsurfcon.21810/lh.gm.mgh --projfrac 0.3 --regheader subject7_V1 --cortex srcvol = /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/orig.mgz as target reference. -------- original matrix ----------- 0.99853 0.05090 0.01869 -0.00005; -0.02654 0.15822 0.98705 0.00000; 0.04729 -0.98609 0.15934 -0.00005; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/label/lh.cortex.label Reading surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.white Done reading source surface Reading thickness /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 = 91575 Masking with /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/label/lh.cortex.label Writing to /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/tmp.pctsurfcon.21810/lh.gm.mgh Dim: 142219 1 1 mri_concat /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/tmp.pctsurfcon.21810/lh.wm.mgh /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/tmp.pctsurfcon.21810/lh.gm.mgh --paired-diff-norm --mul 100 --o /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.w-g.pct.mgh mri_segstats --in /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.w-g.pct.mgh --annot subject7_V1 lh aparc --sum /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/stats/lh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.117 2015/07/02 15:52:06 fischl Exp $ cwd cmdline mri_segstats --in /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.w-g.pct.mgh --annot subject7_V1 lh aparc --sum /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/stats/lh.w-g.pct.stats --snr sysname Linux hostname frames1.cmrr.umn.edu machine x86_64 user isaaca UseRobust 0 Constructing seg from annotation Reading annotation /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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) Seg base 1000 Loading /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.w-g.pct.mgh Vertex Area is 0.653071 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up pctsurfcon --s subject7_V1 --rh-only Log file is /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts/pctsurfcon.log Mon May 11 01:22:45 CDT 2020 setenv SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects cd /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts /opt/local/freesurfer-6.0/x86_64/bin/pctsurfcon $Id: pctsurfcon,v 1.14 2014/10/27 16:10:47 greve Exp $ Linux frames1.cmrr.umn.edu 3.10.0-1127.el7.x86_64 #1 SMP Tue Mar 31 23:36:51 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 mri_vol2surf --mov /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/tmp.pctsurfcon.21814/rh.wm.mgh --regheader subject7_V1 --cortex srcvol = /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/orig.mgz as target reference. -------- original matrix ----------- 0.99853 0.05090 0.01869 -0.00005; -0.02654 0.15822 0.98705 0.00000; 0.04729 -0.98609 0.15934 -0.00005; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/label/rh.cortex.label Reading surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 = 73846 Masking with /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/label/rh.cortex.label Writing to /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/tmp.pctsurfcon.21814/rh.wm.mgh Dim: 136618 1 1 mri_vol2surf --mov /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/tmp.pctsurfcon.21814/rh.gm.mgh --projfrac 0.3 --regheader subject7_V1 --cortex srcvol = /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/orig.mgz as target reference. -------- original matrix ----------- 0.99853 0.05090 0.01869 -0.00005; -0.02654 0.15822 0.98705 0.00000; 0.04729 -0.98609 0.15934 -0.00005; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/label/rh.cortex.label Reading surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.white Done reading source surface Reading thickness /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 = 88721 Masking with /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/label/rh.cortex.label Writing to /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/tmp.pctsurfcon.21814/rh.gm.mgh Dim: 136618 1 1 mri_concat /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/tmp.pctsurfcon.21814/rh.wm.mgh /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/tmp.pctsurfcon.21814/rh.gm.mgh --paired-diff-norm --mul 100 --o /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.w-g.pct.mgh mri_segstats --in /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.w-g.pct.mgh --annot subject7_V1 rh aparc --sum /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/stats/rh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.117 2015/07/02 15:52:06 fischl Exp $ cwd cmdline mri_segstats --in /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.w-g.pct.mgh --annot subject7_V1 rh aparc --sum /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/stats/rh.w-g.pct.stats --snr sysname Linux hostname frames1.cmrr.umn.edu machine x86_64 user isaaca UseRobust 0 Constructing seg from annotation Reading annotation /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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) Seg base 2000 Loading /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.w-g.pct.mgh Vertex Area is 0.646628 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up PIDs (21810 21814) completed and logs appended. #----------------------------------------- #@# Relabel Hypointensities Mon May 11 01:22:52 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 249 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 126 voxels changed to hypointensity... 626 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg Mon May 11 01:23:10 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1 mri_aparc2aseg --s subject7_V1 --volmask --aseg aseg.presurf.hypos SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects subject subject7_V1 outvol /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.white Reading lh pial surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.pial Loading lh annotations from /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.white Reading rh pial surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.pial Loading rh annotations from /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- 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 = 486191 Used brute-force search on 0 voxels Writing output aseg to /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/aparc+aseg.mgz mri_aparc2aseg --s subject7_V1 --volmask --aseg aseg.presurf.hypos --a2009s SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects subject subject7_V1 outvol /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.white Reading lh pial surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.pial Loading lh annotations from /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.white Reading rh pial surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.pial Loading rh annotations from /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- 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 = 486191 Used brute-force search on 0 voxels Writing output aseg to /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# APas-to-ASeg Mon May 11 01:25:28 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri apas2aseg --i aparc+aseg.mgz --o aseg.mgz Mon May 11 01:25:28 CDT 2020 setenv SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects cd /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri /opt/local/freesurfer-6.0/x86_64/bin/apas2aseg --i aparc+aseg.mgz --o aseg.mgz freesurfer-Linux-centos6_x86_64-dev-20150828 $Id: apas2aseg,v 1.1 2014/08/14 22:25:53 greve Exp $ Linux frames1.cmrr.umn.edu 3.10.0-1127.el7.x86_64 #1 SMP Tue Mar 31 23:36:51 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux mri_binarize --i aparc+aseg.mgz --o aseg.mgz --replace 1000 3 --replace 2000 42 --replace 1001 3 --replace 2001 42 --replace 1002 3 --replace 2002 42 --replace 1003 3 --replace 2003 42 --replace 1004 3 --replace 2004 42 --replace 1005 3 --replace 2005 42 --replace 1006 3 --replace 2006 42 --replace 1007 3 --replace 2007 42 --replace 1008 3 --replace 2008 42 --replace 1009 3 --replace 2009 42 --replace 1010 3 --replace 2010 42 --replace 1011 3 --replace 2011 42 --replace 1012 3 --replace 2012 42 --replace 1013 3 --replace 2013 42 --replace 1014 3 --replace 2014 42 --replace 1015 3 --replace 2015 42 --replace 1016 3 --replace 2016 42 --replace 1017 3 --replace 2017 42 --replace 1018 3 --replace 2018 42 --replace 1019 3 --replace 2019 42 --replace 1020 3 --replace 2020 42 --replace 1021 3 --replace 2021 42 --replace 1022 3 --replace 2022 42 --replace 1023 3 --replace 2023 42 --replace 1024 3 --replace 2024 42 --replace 1025 3 --replace 2025 42 --replace 1026 3 --replace 2026 42 --replace 1027 3 --replace 2027 42 --replace 1028 3 --replace 2028 42 --replace 1029 3 --replace 2029 42 --replace 1030 3 --replace 2030 42 --replace 1031 3 --replace 2031 42 --replace 1032 3 --replace 2032 42 --replace 1033 3 --replace 2033 42 --replace 1034 3 --replace 2034 42 --replace 1035 3 --replace 2035 42 $Id: mri_binarize.c,v 1.41 2014/08/17 17:47:29 greve Exp $ cwd /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri cmdline mri_binarize --i aparc+aseg.mgz --o aseg.mgz --replace 1000 3 --replace 2000 42 --replace 1001 3 --replace 2001 42 --replace 1002 3 --replace 2002 42 --replace 1003 3 --replace 2003 42 --replace 1004 3 --replace 2004 42 --replace 1005 3 --replace 2005 42 --replace 1006 3 --replace 2006 42 --replace 1007 3 --replace 2007 42 --replace 1008 3 --replace 2008 42 --replace 1009 3 --replace 2009 42 --replace 1010 3 --replace 2010 42 --replace 1011 3 --replace 2011 42 --replace 1012 3 --replace 2012 42 --replace 1013 3 --replace 2013 42 --replace 1014 3 --replace 2014 42 --replace 1015 3 --replace 2015 42 --replace 1016 3 --replace 2016 42 --replace 1017 3 --replace 2017 42 --replace 1018 3 --replace 2018 42 --replace 1019 3 --replace 2019 42 --replace 1020 3 --replace 2020 42 --replace 1021 3 --replace 2021 42 --replace 1022 3 --replace 2022 42 --replace 1023 3 --replace 2023 42 --replace 1024 3 --replace 2024 42 --replace 1025 3 --replace 2025 42 --replace 1026 3 --replace 2026 42 --replace 1027 3 --replace 2027 42 --replace 1028 3 --replace 2028 42 --replace 1029 3 --replace 2029 42 --replace 1030 3 --replace 2030 42 --replace 1031 3 --replace 2031 42 --replace 1032 3 --replace 2032 42 --replace 1033 3 --replace 2033 42 --replace 1034 3 --replace 2034 42 --replace 1035 3 --replace 2035 42 sysname Linux hostname frames1.cmrr.umn.edu machine x86_64 user isaaca input aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output aseg.mgz Binarizing based on threshold min -infinity max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Replacing 72 1: 1000 3 2: 2000 42 3: 1001 3 4: 2001 42 5: 1002 3 6: 2002 42 7: 1003 3 8: 2003 42 9: 1004 3 10: 2004 42 11: 1005 3 12: 2005 42 13: 1006 3 14: 2006 42 15: 1007 3 16: 2007 42 17: 1008 3 18: 2008 42 19: 1009 3 20: 2009 42 21: 1010 3 22: 2010 42 23: 1011 3 24: 2011 42 25: 1012 3 26: 2012 42 27: 1013 3 28: 2013 42 29: 1014 3 30: 2014 42 31: 1015 3 32: 2015 42 33: 1016 3 34: 2016 42 35: 1017 3 36: 2017 42 37: 1018 3 38: 2018 42 39: 1019 3 40: 2019 42 41: 1020 3 42: 2020 42 43: 1021 3 44: 2021 42 45: 1022 3 46: 2022 42 47: 1023 3 48: 2023 42 49: 1024 3 50: 2024 42 51: 1025 3 52: 2025 42 53: 1026 3 54: 2026 42 55: 1027 3 56: 2027 42 57: 1028 3 58: 2028 42 59: 1029 3 60: 2029 42 61: 1030 3 62: 2030 42 63: 1031 3 64: 2031 42 65: 1032 3 66: 2032 42 67: 1033 3 68: 2033 42 69: 1034 3 70: 2034 42 71: 1035 3 72: 2035 42 Found 0 values in range Counting number of voxels in first frame Found 0 voxels in final mask Count: 0 0.000000 16777216 0.000000 mri_binarize done Started at Mon May 11 01:25:28 CDT 2020 Ended at Mon May 11 01:25:33 CDT 2020 Apas2aseg-Run-Time-Sec 5 apas2aseg Done #-------------------------------------------- #@# ASeg Stats Mon May 11 01:25:33 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1 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 /opt/local/freesurfer-6.0/x86_64/ASegStatsLUT.txt --subject subject7_V1 $Id: mri_segstats.c,v 1.117 2015/07/02 15:52:06 fischl 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 /opt/local/freesurfer-6.0/x86_64/ASegStatsLUT.txt --subject subject7_V1 sysname Linux hostname frames1.cmrr.umn.edu machine x86_64 user isaaca UseRobust 0 atlas_icv (eTIV) = 1576049 mm^3 (det: 1.236069 ) Computing euler number orig.nofix lheno = -22, rheno = -26 orig.nofix lhholes = 12, rhholes = 14 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 249367.335 249428.000 diff= -60.7 pctdiff=-0.024 rhCtxGM: 237349.818 237706.000 diff= -356.2 pctdiff=-0.150 lhCtxWM: 230995.026 230911.500 diff= 83.5 pctdiff= 0.036 rhCtxWM: 216994.301 217423.500 diff= -429.2 pctdiff=-0.198 SubCortGMVol 60253.000 SupraTentVol 1010772.480 (1009395.000) diff=1377.480 pctdiff=0.136 SupraTentVolNotVent 997183.480 (995806.000) diff=1377.480 pctdiff=0.138 BrainSegVol 1187900.000 (1183807.000) diff=4093.000 pctdiff=0.345 BrainSegVolNotVent 1167134.000 (1165804.480) diff=1329.520 pctdiff=0.114 BrainSegVolNotVent 1167134.000 CerebellumVol 170761.000 VentChorVol 13589.000 3rd4th5thCSF 7177.000 CSFVol 3095.000, OptChiasmVol 556.000 MaskVol 1609937.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation Reporting on 45 segmentations Using PrintSegStat mri_segstats done #----------------------------------------- #@# WMParc Mon May 11 01:26:04 CDT 2020 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1 mri_aparc2aseg --s subject7_V1 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects subject subject7_V1 outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/aparc+aseg.mgz Reading lh white surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.white Reading lh pial surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.pial Loading lh annotations from /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.white Reading rh pial surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.pial Loading rh annotations from /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/ribbon.mgz Loading filled from /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/ribbon.mgz Ripping vertices labeled as unkown Ripped 7807 vertices from left hemi Ripped 7949 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 /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/aseg.mgz Loading Ctx Seg File /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/aparc+aseg.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- 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 = 933666 Used brute-force search on 66 voxels Fixing Parahip LH WM Found 9 clusters 0 k 1.000000 1 k 1.000000 2 k 1.000000 3 k 1319.000000 4 k 4.000000 5 k 1.000000 6 k 1.000000 7 k 1.000000 8 k 17.000000 Fixing Parahip RH WM Found 11 clusters 0 k 2.000000 1 k 1.000000 2 k 1.000000 3 k 1286.000000 4 k 3.000000 5 k 1.000000 6 k 5.000000 7 k 1.000000 8 k 1.000000 9 k 1.000000 10 k 16.000000 Writing output aseg to mri/wmparc.mgz mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject subject7_V1 --surf-wm-vol --ctab /opt/local/freesurfer-6.0/x86_64/WMParcStatsLUT.txt --etiv $Id: mri_segstats.c,v 1.117 2015/07/02 15:52:06 fischl 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 subject7_V1 --surf-wm-vol --ctab /opt/local/freesurfer-6.0/x86_64/WMParcStatsLUT.txt --etiv sysname Linux hostname frames1.cmrr.umn.edu machine x86_64 user isaaca UseRobust 0 atlas_icv (eTIV) = 1576049 mm^3 (det: 1.236069 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 249367.335 249428.000 diff= -60.7 pctdiff=-0.024 rhCtxGM: 237349.818 237706.000 diff= -356.2 pctdiff=-0.150 lhCtxWM: 230995.026 230911.500 diff= 83.5 pctdiff= 0.036 rhCtxWM: 216994.301 217423.500 diff= -429.2 pctdiff=-0.198 SubCortGMVol 60253.000 SupraTentVol 1010772.480 (1009395.000) diff=1377.480 pctdiff=0.136 SupraTentVolNotVent 997183.480 (995806.000) diff=1377.480 pctdiff=0.138 BrainSegVol 1187900.000 (1183807.000) diff=4093.000 pctdiff=0.345 BrainSegVolNotVent 1167134.000 (1165804.480) diff=1329.520 pctdiff=0.114 BrainSegVolNotVent 1167134.000 CerebellumVol 170761.000 VentChorVol 13589.000 3rd4th5thCSF 7177.000 CSFVol 3095.000, OptChiasmVol 556.000 MaskVol 1609937.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 390 segmentations Computing statistics for each segmentation Reporting on 70 segmentations Using PrintSegStat mri_segstats done /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/label #-------------------------------------------- #@# BA_exvivo Labels lh Mon May 11 01:31:34 CDT 2020 mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA1_exvivo.label --trgsubject subject7_V1 --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA2_exvivo.label --trgsubject subject7_V1 --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA3a_exvivo.label --trgsubject subject7_V1 --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA3b_exvivo.label --trgsubject subject7_V1 --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA4a_exvivo.label --trgsubject subject7_V1 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA4p_exvivo.label --trgsubject subject7_V1 --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA6_exvivo.label --trgsubject subject7_V1 --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA44_exvivo.label --trgsubject subject7_V1 --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA45_exvivo.label --trgsubject subject7_V1 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.V1_exvivo.label --trgsubject subject7_V1 --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.V2_exvivo.label --trgsubject subject7_V1 --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.MT_exvivo.label --trgsubject subject7_V1 --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject subject7_V1 --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject subject7_V1 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface Waiting for PID 23920 of (23920 23923 23926 23929 23932 23935 23938 23941 23944 23947 23950 23953 23956 23959) to complete... Waiting for PID 23923 of (23920 23923 23926 23929 23932 23935 23938 23941 23944 23947 23950 23953 23956 23959) to complete... Waiting for PID 23926 of (23920 23923 23926 23929 23932 23935 23938 23941 23944 23947 23950 23953 23956 23959) to complete... Waiting for PID 23929 of (23920 23923 23926 23929 23932 23935 23938 23941 23944 23947 23950 23953 23956 23959) to complete... Waiting for PID 23932 of (23920 23923 23926 23929 23932 23935 23938 23941 23944 23947 23950 23953 23956 23959) to complete... Waiting for PID 23935 of (23920 23923 23926 23929 23932 23935 23938 23941 23944 23947 23950 23953 23956 23959) to complete... Waiting for PID 23938 of (23920 23923 23926 23929 23932 23935 23938 23941 23944 23947 23950 23953 23956 23959) to complete... Waiting for PID 23941 of (23920 23923 23926 23929 23932 23935 23938 23941 23944 23947 23950 23953 23956 23959) to complete... Waiting for PID 23944 of (23920 23923 23926 23929 23932 23935 23938 23941 23944 23947 23950 23953 23956 23959) to complete... Waiting for PID 23947 of (23920 23923 23926 23929 23932 23935 23938 23941 23944 23947 23950 23953 23956 23959) to complete... Waiting for PID 23950 of (23920 23923 23926 23929 23932 23935 23938 23941 23944 23947 23950 23953 23956 23959) to complete... Waiting for PID 23953 of (23920 23923 23926 23929 23932 23935 23938 23941 23944 23947 23950 23953 23956 23959) to complete... Waiting for PID 23956 of (23920 23923 23926 23929 23932 23935 23938 23941 23944 23947 23950 23953 23956 23959) to complete... Waiting for PID 23959 of (23920 23923 23926 23929 23932 23935 23938 23941 23944 23947 23950 23953 23956 23959) to complete... mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA1_exvivo.label --trgsubject subject7_V1 --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./lh.BA1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 142219 Number of reverse mapping hits = 294 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4423 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA2_exvivo.label --trgsubject subject7_V1 --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA2_exvivo.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./lh.BA2_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 142219 Number of reverse mapping hits = 786 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8695 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA3a_exvivo.label --trgsubject subject7_V1 --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./lh.BA3a_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 142219 Number of reverse mapping hits = 98 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4175 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA3b_exvivo.label --trgsubject subject7_V1 --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./lh.BA3b_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 142219 Number of reverse mapping hits = 319 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6302 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA4a_exvivo.label --trgsubject subject7_V1 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./lh.BA4a_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 142219 Number of reverse mapping hits = 284 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 6068 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA4p_exvivo.label --trgsubject subject7_V1 --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./lh.BA4p_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 142219 Number of reverse mapping hits = 123 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4193 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA6_exvivo.label --trgsubject subject7_V1 --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA6_exvivo.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./lh.BA6_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 142219 Number of reverse mapping hits = 940 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 14529 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA44_exvivo.label --trgsubject subject7_V1 --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA44_exvivo.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./lh.BA44_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 142219 Number of reverse mapping hits = 393 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4574 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA45_exvivo.label --trgsubject subject7_V1 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA45_exvivo.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./lh.BA45_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 142219 Number of reverse mapping hits = 677 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 4099 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.V1_exvivo.label --trgsubject subject7_V1 --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.V1_exvivo.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./lh.V1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 142219 Number of reverse mapping hits = 1937 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 6578 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.V2_exvivo.label --trgsubject subject7_V1 --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.V2_exvivo.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./lh.V2_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 142219 Number of reverse mapping hits = 4257 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 12371 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.MT_exvivo.label --trgsubject subject7_V1 --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.MT_exvivo.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./lh.MT_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 142219 Number of reverse mapping hits = 782 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2800 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject subject7_V1 --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./lh.entorhinal_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 1290 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1290 nlabel points Performing mapping from target back to the source label 142219 Number of reverse mapping hits = 117 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1407 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject subject7_V1 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./lh.perirhinal_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 142219 Number of reverse mapping hits = 112 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1311 mri_label2label: Done PIDs (23920 23923 23926 23929 23932 23935 23938 23941 23944 23947 23950 23953 23956 23959) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 24163 of (24163 24166 24169 24172 24175 24178 24181 24184 24187 24190 24193 24196 24199 24202) to complete... Waiting for PID 24166 of (24163 24166 24169 24172 24175 24178 24181 24184 24187 24190 24193 24196 24199 24202) to complete... Waiting for PID 24169 of (24163 24166 24169 24172 24175 24178 24181 24184 24187 24190 24193 24196 24199 24202) to complete... Waiting for PID 24172 of (24163 24166 24169 24172 24175 24178 24181 24184 24187 24190 24193 24196 24199 24202) to complete... Waiting for PID 24175 of (24163 24166 24169 24172 24175 24178 24181 24184 24187 24190 24193 24196 24199 24202) to complete... Waiting for PID 24178 of (24163 24166 24169 24172 24175 24178 24181 24184 24187 24190 24193 24196 24199 24202) to complete... Waiting for PID 24181 of (24163 24166 24169 24172 24175 24178 24181 24184 24187 24190 24193 24196 24199 24202) to complete... Waiting for PID 24184 of (24163 24166 24169 24172 24175 24178 24181 24184 24187 24190 24193 24196 24199 24202) to complete... Waiting for PID 24187 of (24163 24166 24169 24172 24175 24178 24181 24184 24187 24190 24193 24196 24199 24202) to complete... Waiting for PID 24190 of (24163 24166 24169 24172 24175 24178 24181 24184 24187 24190 24193 24196 24199 24202) to complete... Waiting for PID 24193 of (24163 24166 24169 24172 24175 24178 24181 24184 24187 24190 24193 24196 24199 24202) to complete... Waiting for PID 24196 of (24163 24166 24169 24172 24175 24178 24181 24184 24187 24190 24193 24196 24199 24202) to complete... Waiting for PID 24199 of (24163 24166 24169 24172 24175 24178 24181 24184 24187 24190 24193 24196 24199 24202) to complete... Waiting for PID 24202 of (24163 24166 24169 24172 24175 24178 24181 24184 24187 24190 24193 24196 24199 24202) to complete... mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./lh.BA1_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 142219 Number of reverse mapping hits = 72 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1086 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./lh.BA2_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 142219 Number of reverse mapping hits = 196 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2288 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./lh.BA3a_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 142219 Number of reverse mapping hits = 31 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1535 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./lh.BA3b_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 142219 Number of reverse mapping hits = 110 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2106 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./lh.BA4a_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 142219 Number of reverse mapping hits = 111 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2430 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./lh.BA4p_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 142219 Number of reverse mapping hits = 43 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1592 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./lh.BA6_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 142219 Number of reverse mapping hits = 390 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 7425 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./lh.BA44_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 142219 Number of reverse mapping hits = 201 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 2113 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./lh.BA45_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 142219 Number of reverse mapping hits = 202 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1353 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./lh.V1_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 142219 Number of reverse mapping hits = 1413 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 4818 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./lh.V2_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 142219 Number of reverse mapping hits = 1858 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 5192 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./lh.MT_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 142219 Number of reverse mapping hits = 185 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 698 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./lh.entorhinal_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 470 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 470 nlabel points Performing mapping from target back to the source label 142219 Number of reverse mapping hits = 68 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 538 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/lh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./lh.perirhinal_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 450 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 450 nlabel points Performing mapping from target back to the source label 142219 Number of reverse mapping hits = 71 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 521 mri_label2label: Done PIDs (24163 24166 24169 24172 24175 24178 24181 24184 24187 24190 24193 24196 24199 24202) completed and logs appended. mris_label2annot --s subject7_V1 --hemi lh --ctab /opt/local/freesurfer-6.0/x86_64/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.entorhinal_exvivo.label --l lh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose Reading ctab /opt/local/freesurfer-6.0/x86_64/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.19 2013/11/19 18:50:56 greve Exp $ cwd /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/label cmdline mris_label2annot --s subject7_V1 --hemi lh --ctab /opt/local/freesurfer-6.0/x86_64/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.entorhinal_exvivo.label --l lh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose sysname Linux hostname frames1.cmrr.umn.edu machine x86_64 user isaaca subject subject7_V1 hemi lh SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects ColorTable /opt/local/freesurfer-6.0/x86_64/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 98763 unhit vertices Writing annot to /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/label/lh.BA_exvivo.annot mris_label2annot --s subject7_V1 --hemi lh --ctab /opt/local/freesurfer-6.0/x86_64/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose Reading ctab /opt/local/freesurfer-6.0/x86_64/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.19 2013/11/19 18:50:56 greve Exp $ cwd /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/label cmdline mris_label2annot --s subject7_V1 --hemi lh --ctab /opt/local/freesurfer-6.0/x86_64/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose sysname Linux hostname frames1.cmrr.umn.edu machine x86_64 user isaaca subject subject7_V1 hemi lh SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects ColorTable /opt/local/freesurfer-6.0/x86_64/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 117206 unhit vertices Writing annot to /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/label/lh.BA_exvivo.thresh.annot mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.stats -b -a ./lh.BA_exvivo.annot -c ./BA_exvivo.ctab subject7_V1 lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/wm.mgz... reading input surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.white... reading input pial surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.pial... reading input white surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 254114 Total vertex volume 250037 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /opt/local/freesurfer-6.0/x86_64/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1576049 mm^3 (det: 1.236069 ) lhCtxGM: 249367.335 249428.000 diff= -60.7 pctdiff=-0.024 rhCtxGM: 237349.818 237706.000 diff= -356.2 pctdiff=-0.150 lhCtxWM: 230995.026 230911.500 diff= 83.5 pctdiff= 0.036 rhCtxWM: 216994.301 217423.500 diff= -429.2 pctdiff=-0.198 SubCortGMVol 60253.000 SupraTentVol 1010772.480 (1009395.000) diff=1377.480 pctdiff=0.136 SupraTentVolNotVent 997183.480 (995806.000) diff=1377.480 pctdiff=0.138 BrainSegVol 1187900.000 (1183807.000) diff=4093.000 pctdiff=0.345 BrainSegVolNotVent 1167134.000 (1165804.480) diff=1329.520 pctdiff=0.114 BrainSegVolNotVent 1167134.000 CerebellumVol 170761.000 VentChorVol 13589.000 3rd4th5thCSF 7177.000 CSFVol 3095.000, OptChiasmVol 556.000 MaskVol 1609937.000 1135 585 1526 2.039 0.613 0.109 0.025 13 1.2 BA1_exvivo 4507 2893 6568 2.213 0.603 0.099 0.022 38 3.9 BA2_exvivo 944 593 789 1.737 0.462 0.122 0.023 8 0.9 BA3a_exvivo 2270 1447 2749 1.705 0.769 0.095 0.018 18 1.7 BA3b_exvivo 1486 878 2340 2.384 0.532 0.101 0.019 11 1.2 BA4a_exvivo 1043 692 1538 2.434 0.403 0.087 0.020 4 0.8 BA4p_exvivo 8559 5582 18790 2.944 0.581 0.117 0.023 84 7.9 BA6_exvivo 2496 1671 5130 2.815 0.407 0.110 0.019 25 2.0 BA44_exvivo 3124 2047 5843 2.510 0.651 0.118 0.022 36 2.6 BA45_exvivo 4224 2700 3822 1.469 0.480 0.110 0.021 37 3.6 V1_exvivo 9997 6190 12447 2.010 0.564 0.141 0.034 133 13.9 V2_exvivo 2549 1648 4371 2.551 0.493 0.117 0.024 25 2.4 MT_exvivo 510 305 698 2.937 0.711 0.150 0.076 10 1.7 perirhinal_exvivo 612 397 1388 3.259 0.725 0.086 0.018 3 0.4 entorhinal_exvivo mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab subject7_V1 lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/wm.mgz... reading input surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.white... reading input pial surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.pial... reading input white surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 254114 Total vertex volume 250037 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /opt/local/freesurfer-6.0/x86_64/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1576049 mm^3 (det: 1.236069 ) lhCtxGM: 249367.335 249428.000 diff= -60.7 pctdiff=-0.024 rhCtxGM: 237349.818 237706.000 diff= -356.2 pctdiff=-0.150 lhCtxWM: 230995.026 230911.500 diff= 83.5 pctdiff= 0.036 rhCtxWM: 216994.301 217423.500 diff= -429.2 pctdiff=-0.198 SubCortGMVol 60253.000 SupraTentVol 1010772.480 (1009395.000) diff=1377.480 pctdiff=0.136 SupraTentVolNotVent 997183.480 (995806.000) diff=1377.480 pctdiff=0.138 BrainSegVol 1187900.000 (1183807.000) diff=4093.000 pctdiff=0.345 BrainSegVolNotVent 1167134.000 (1165804.480) diff=1329.520 pctdiff=0.114 BrainSegVolNotVent 1167134.000 CerebellumVol 170761.000 VentChorVol 13589.000 3rd4th5thCSF 7177.000 CSFVol 3095.000, OptChiasmVol 556.000 MaskVol 1609937.000 736 350 945 2.010 0.582 0.119 0.027 10 0.9 BA1_exvivo 1694 1070 2508 2.267 0.444 0.084 0.014 9 1.0 BA2_exvivo 797 495 625 1.702 0.458 0.127 0.025 7 0.8 BA3a_exvivo 1392 919 1121 1.240 0.296 0.069 0.011 5 0.6 BA3b_exvivo 1445 851 2255 2.458 0.549 0.091 0.016 9 1.0 BA4a_exvivo 883 592 1247 2.375 0.402 0.097 0.022 4 0.7 BA4p_exvivo 4599 2947 9607 2.820 0.605 0.114 0.024 47 4.2 BA6_exvivo 1614 1092 3519 2.876 0.356 0.115 0.019 18 1.4 BA44_exvivo 1142 743 2781 2.888 0.535 0.125 0.027 14 1.1 BA45_exvivo 4507 2862 4122 1.475 0.481 0.114 0.023 42 4.3 V1_exvivo 4907 3055 5335 1.840 0.487 0.144 0.037 65 7.4 V2_exvivo 667 426 1019 2.478 0.389 0.106 0.021 5 0.5 MT_exvivo 247 147 324 2.886 0.667 0.154 0.059 5 0.6 perirhinal_exvivo 383 235 993 3.406 0.616 0.091 0.050 4 1.0 entorhinal_exvivo #-------------------------------------------- #@# BA_exvivo Labels rh Mon May 11 01:32:46 CDT 2020 mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA1_exvivo.label --trgsubject subject7_V1 --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA2_exvivo.label --trgsubject subject7_V1 --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA3a_exvivo.label --trgsubject subject7_V1 --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA3b_exvivo.label --trgsubject subject7_V1 --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA4a_exvivo.label --trgsubject subject7_V1 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA4p_exvivo.label --trgsubject subject7_V1 --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA6_exvivo.label --trgsubject subject7_V1 --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA44_exvivo.label --trgsubject subject7_V1 --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA45_exvivo.label --trgsubject subject7_V1 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.V1_exvivo.label --trgsubject subject7_V1 --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.V2_exvivo.label --trgsubject subject7_V1 --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.MT_exvivo.label --trgsubject subject7_V1 --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject subject7_V1 --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject subject7_V1 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface Waiting for PID 24605 of (24605 24608 24611 24614 24617 24622 24626 24629 24632 24635 24638 24641 24644 24647) to complete... Waiting for PID 24608 of (24605 24608 24611 24614 24617 24622 24626 24629 24632 24635 24638 24641 24644 24647) to complete... Waiting for PID 24611 of (24605 24608 24611 24614 24617 24622 24626 24629 24632 24635 24638 24641 24644 24647) to complete... Waiting for PID 24614 of (24605 24608 24611 24614 24617 24622 24626 24629 24632 24635 24638 24641 24644 24647) to complete... Waiting for PID 24617 of (24605 24608 24611 24614 24617 24622 24626 24629 24632 24635 24638 24641 24644 24647) to complete... Waiting for PID 24622 of (24605 24608 24611 24614 24617 24622 24626 24629 24632 24635 24638 24641 24644 24647) to complete... Waiting for PID 24626 of (24605 24608 24611 24614 24617 24622 24626 24629 24632 24635 24638 24641 24644 24647) to complete... Waiting for PID 24629 of (24605 24608 24611 24614 24617 24622 24626 24629 24632 24635 24638 24641 24644 24647) to complete... Waiting for PID 24632 of (24605 24608 24611 24614 24617 24622 24626 24629 24632 24635 24638 24641 24644 24647) to complete... Waiting for PID 24635 of (24605 24608 24611 24614 24617 24622 24626 24629 24632 24635 24638 24641 24644 24647) to complete... Waiting for PID 24638 of (24605 24608 24611 24614 24617 24622 24626 24629 24632 24635 24638 24641 24644 24647) to complete... Waiting for PID 24641 of (24605 24608 24611 24614 24617 24622 24626 24629 24632 24635 24638 24641 24644 24647) to complete... Waiting for PID 24644 of (24605 24608 24611 24614 24617 24622 24626 24629 24632 24635 24638 24641 24644 24647) to complete... Waiting for PID 24647 of (24605 24608 24611 24614 24617 24622 24626 24629 24632 24635 24638 24641 24644 24647) to complete... mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA1_exvivo.label --trgsubject subject7_V1 --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA1_exvivo.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./rh.BA1_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 136618 Number of reverse mapping hits = 285 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4247 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA2_exvivo.label --trgsubject subject7_V1 --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA2_exvivo.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./rh.BA2_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 136618 Number of reverse mapping hits = 390 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 7077 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA3a_exvivo.label --trgsubject subject7_V1 --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./rh.BA3a_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 136618 Number of reverse mapping hits = 73 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4053 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA3b_exvivo.label --trgsubject subject7_V1 --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./rh.BA3b_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 136618 Number of reverse mapping hits = 234 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 4756 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA4a_exvivo.label --trgsubject subject7_V1 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./rh.BA4a_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 136618 Number of reverse mapping hits = 169 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 5916 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA4p_exvivo.label --trgsubject subject7_V1 --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./rh.BA4p_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 136618 Number of reverse mapping hits = 82 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4555 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA6_exvivo.label --trgsubject subject7_V1 --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA6_exvivo.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./rh.BA6_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 136618 Number of reverse mapping hits = 616 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 12872 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA44_exvivo.label --trgsubject subject7_V1 --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA44_exvivo.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./rh.BA44_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 136618 Number of reverse mapping hits = 952 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 7864 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA45_exvivo.label --trgsubject subject7_V1 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA45_exvivo.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./rh.BA45_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 136618 Number of reverse mapping hits = 889 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 6244 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.V1_exvivo.label --trgsubject subject7_V1 --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.V1_exvivo.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./rh.V1_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 136618 Number of reverse mapping hits = 984 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 5711 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.V2_exvivo.label --trgsubject subject7_V1 --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.V2_exvivo.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./rh.V2_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 136618 Number of reverse mapping hits = 1996 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 10012 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.MT_exvivo.label --trgsubject subject7_V1 --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.MT_exvivo.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./rh.MT_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 136618 Number of reverse mapping hits = 488 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2420 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject subject7_V1 --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./rh.entorhinal_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 1038 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1038 nlabel points Performing mapping from target back to the source label 136618 Number of reverse mapping hits = 73 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1111 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject subject7_V1 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./rh.perirhinal_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 136618 Number of reverse mapping hits = 62 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 814 mri_label2label: Done PIDs (24605 24608 24611 24614 24617 24622 24626 24629 24632 24635 24638 24641 24644 24647) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 24906 of (24906 24909 24912 24915 24918 24921 24924 24927 24930 24933 24936 24939 24942 24945) to complete... Waiting for PID 24909 of (24906 24909 24912 24915 24918 24921 24924 24927 24930 24933 24936 24939 24942 24945) to complete... Waiting for PID 24912 of (24906 24909 24912 24915 24918 24921 24924 24927 24930 24933 24936 24939 24942 24945) to complete... Waiting for PID 24915 of (24906 24909 24912 24915 24918 24921 24924 24927 24930 24933 24936 24939 24942 24945) to complete... Waiting for PID 24918 of (24906 24909 24912 24915 24918 24921 24924 24927 24930 24933 24936 24939 24942 24945) to complete... Waiting for PID 24921 of (24906 24909 24912 24915 24918 24921 24924 24927 24930 24933 24936 24939 24942 24945) to complete... Waiting for PID 24924 of (24906 24909 24912 24915 24918 24921 24924 24927 24930 24933 24936 24939 24942 24945) to complete... Waiting for PID 24927 of (24906 24909 24912 24915 24918 24921 24924 24927 24930 24933 24936 24939 24942 24945) to complete... Waiting for PID 24930 of (24906 24909 24912 24915 24918 24921 24924 24927 24930 24933 24936 24939 24942 24945) to complete... Waiting for PID 24933 of (24906 24909 24912 24915 24918 24921 24924 24927 24930 24933 24936 24939 24942 24945) to complete... Waiting for PID 24936 of (24906 24909 24912 24915 24918 24921 24924 24927 24930 24933 24936 24939 24942 24945) to complete... Waiting for PID 24939 of (24906 24909 24912 24915 24918 24921 24924 24927 24930 24933 24936 24939 24942 24945) to complete... Waiting for PID 24942 of (24906 24909 24912 24915 24918 24921 24924 24927 24930 24933 24936 24939 24942 24945) to complete... Waiting for PID 24945 of (24906 24909 24912 24915 24918 24921 24924 24927 24930 24933 24936 24939 24942 24945) to complete... mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./rh.BA1_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 136618 Number of reverse mapping hits = 117 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 993 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./rh.BA2_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 136618 Number of reverse mapping hits = 114 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2802 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./rh.BA3a_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 136618 Number of reverse mapping hits = 22 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1720 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./rh.BA3b_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 136618 Number of reverse mapping hits = 100 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2283 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./rh.BA4a_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 136618 Number of reverse mapping hits = 46 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1434 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./rh.BA4p_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 136618 Number of reverse mapping hits = 16 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1505 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./rh.BA6_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 136618 Number of reverse mapping hits = 240 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 7199 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./rh.BA44_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 136618 Number of reverse mapping hits = 377 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1389 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./rh.BA45_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 136618 Number of reverse mapping hits = 134 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1312 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./rh.V1_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 136618 Number of reverse mapping hits = 636 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 3868 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./rh.V2_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 136618 Number of reverse mapping hits = 899 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 4336 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./rh.MT_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/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 136618 Number of reverse mapping hits = 80 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 348 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./rh.entorhinal_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 694 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 694 nlabel points Performing mapping from target back to the source label 136618 Number of reverse mapping hits = 30 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 724 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject subject7_V1 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/server1/data/freesurfer_workingdir/subjects/fsaverage/label/rh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = subject7_V1 trglabel = ./rh.perirhinal_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects FREESURFER_HOME /opt/local/freesurfer-6.0/x86_64 Loading source label. Found 291 points in source label. Starting surface-based mapping Reading source registration /home/server1/data/freesurfer_workingdir/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.white Reading target registration /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 291 nlabel points Performing mapping from target back to the source label 136618 Number of reverse mapping hits = 17 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 308 mri_label2label: Done PIDs (24906 24909 24912 24915 24918 24921 24924 24927 24930 24933 24936 24939 24942 24945) completed and logs appended. mris_label2annot --s subject7_V1 --hemi rh --ctab /opt/local/freesurfer-6.0/x86_64/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.entorhinal_exvivo.label --l rh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose Reading ctab /opt/local/freesurfer-6.0/x86_64/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.19 2013/11/19 18:50:56 greve Exp $ cwd /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/label cmdline mris_label2annot --s subject7_V1 --hemi rh --ctab /opt/local/freesurfer-6.0/x86_64/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.entorhinal_exvivo.label --l rh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose sysname Linux hostname frames1.cmrr.umn.edu machine x86_64 user isaaca subject subject7_V1 hemi rh SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects ColorTable /opt/local/freesurfer-6.0/x86_64/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 99117 unhit vertices Writing annot to /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/label/rh.BA_exvivo.annot mris_label2annot --s subject7_V1 --hemi rh --ctab /opt/local/freesurfer-6.0/x86_64/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose Reading ctab /opt/local/freesurfer-6.0/x86_64/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.19 2013/11/19 18:50:56 greve Exp $ cwd /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/label cmdline mris_label2annot --s subject7_V1 --hemi rh --ctab /opt/local/freesurfer-6.0/x86_64/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose sysname Linux hostname frames1.cmrr.umn.edu machine x86_64 user isaaca subject subject7_V1 hemi rh SUBJECTS_DIR /home/server1/data/freesurfer_workingdir/subjects ColorTable /opt/local/freesurfer-6.0/x86_64/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 116163 unhit vertices Writing annot to /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/label/rh.BA_exvivo.thresh.annot mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.stats -b -a ./rh.BA_exvivo.annot -c ./BA_exvivo.ctab subject7_V1 rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/wm.mgz... reading input surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.white... reading input pial surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.pial... reading input white surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 241169 Total vertex volume 237015 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /opt/local/freesurfer-6.0/x86_64/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1576049 mm^3 (det: 1.236069 ) lhCtxGM: 249367.335 249428.000 diff= -60.7 pctdiff=-0.024 rhCtxGM: 237349.818 237706.000 diff= -356.2 pctdiff=-0.150 lhCtxWM: 230995.026 230911.500 diff= 83.5 pctdiff= 0.036 rhCtxWM: 216994.301 217423.500 diff= -429.2 pctdiff=-0.198 SubCortGMVol 60253.000 SupraTentVol 1010772.480 (1009395.000) diff=1377.480 pctdiff=0.136 SupraTentVolNotVent 997183.480 (995806.000) diff=1377.480 pctdiff=0.138 BrainSegVol 1187900.000 (1183807.000) diff=4093.000 pctdiff=0.345 BrainSegVolNotVent 1167134.000 (1165804.480) diff=1329.520 pctdiff=0.114 BrainSegVolNotVent 1167134.000 CerebellumVol 170761.000 VentChorVol 13589.000 3rd4th5thCSF 7177.000 CSFVol 3095.000, OptChiasmVol 556.000 MaskVol 1609937.000 984 489 1671 2.446 0.446 0.104 0.021 9 1.0 BA1_exvivo 3271 2144 4461 2.052 0.478 0.096 0.016 21 2.0 BA2_exvivo 905 587 710 1.663 0.461 0.124 0.024 7 0.8 BA3a_exvivo 1922 1172 2102 1.565 0.673 0.086 0.016 13 1.3 BA3b_exvivo 1430 822 2204 2.335 0.416 0.085 0.015 8 0.9 BA4a_exvivo 995 643 1324 2.140 0.303 0.068 0.011 3 0.4 BA4p_exvivo 7178 4757 14320 2.538 0.660 0.112 0.019 65 5.6 BA6_exvivo 4040 2660 7110 2.389 0.655 0.105 0.021 35 3.1 BA44_exvivo 3824 2579 7748 2.430 0.693 0.132 0.027 50 4.2 BA45_exvivo 3140 1967 3204 1.637 0.469 0.122 0.029 37 4.1 V1_exvivo 6938 4273 9135 2.026 0.706 0.130 0.033 95 9.6 V2_exvivo 2033 1342 3372 2.476 0.476 0.117 0.023 19 1.9 MT_exvivo 507 289 1092 3.380 0.794 0.126 0.059 9 1.6 perirhinal_exvivo 334 208 815 3.362 0.615 0.107 0.033 2 0.5 entorhinal_exvivo mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab subject7_V1 rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/mri/wm.mgz... reading input surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.white... reading input pial surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.pial... reading input white surface /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 241169 Total vertex volume 237015 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /opt/local/freesurfer-6.0/x86_64/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1576049 mm^3 (det: 1.236069 ) lhCtxGM: 249367.335 249428.000 diff= -60.7 pctdiff=-0.024 rhCtxGM: 237349.818 237706.000 diff= -356.2 pctdiff=-0.150 lhCtxWM: 230995.026 230911.500 diff= 83.5 pctdiff= 0.036 rhCtxWM: 216994.301 217423.500 diff= -429.2 pctdiff=-0.198 SubCortGMVol 60253.000 SupraTentVol 1010772.480 (1009395.000) diff=1377.480 pctdiff=0.136 SupraTentVolNotVent 997183.480 (995806.000) diff=1377.480 pctdiff=0.138 BrainSegVol 1187900.000 (1183807.000) diff=4093.000 pctdiff=0.345 BrainSegVolNotVent 1167134.000 (1165804.480) diff=1329.520 pctdiff=0.114 BrainSegVolNotVent 1167134.000 CerebellumVol 170761.000 VentChorVol 13589.000 3rd4th5thCSF 7177.000 CSFVol 3095.000, OptChiasmVol 556.000 MaskVol 1609937.000 747 335 1181 2.393 0.486 0.096 0.021 7 0.6 BA1_exvivo 1769 1181 2451 1.996 0.455 0.095 0.015 11 1.1 BA2_exvivo 780 506 564 1.610 0.359 0.131 0.024 6 0.7 BA3a_exvivo 1495 960 1263 1.300 0.373 0.076 0.013 7 0.8 BA3b_exvivo 904 478 1404 2.405 0.448 0.093 0.017 6 0.6 BA4a_exvivo 797 538 1084 2.122 0.266 0.068 0.012 2 0.3 BA4p_exvivo 4330 2844 8824 2.551 0.663 0.115 0.020 40 3.3 BA6_exvivo 1270 872 3069 2.675 0.551 0.116 0.019 15 1.1 BA44_exvivo 938 639 2368 2.844 0.558 0.145 0.036 16 1.4 BA45_exvivo 2961 1855 2957 1.618 0.466 0.121 0.028 35 3.8 V1_exvivo 3657 2228 4472 1.865 0.599 0.140 0.039 55 5.6 V2_exvivo 320 212 505 2.257 0.392 0.108 0.015 2 0.3 MT_exvivo 266 160 700 3.462 0.712 0.112 0.033 3 0.3 perirhinal_exvivo 221 134 646 3.437 0.528 0.090 0.016 1 0.1 entorhinal_exvivo #-------------------------------------------- #@# Segmentation of brainstem substructures Mon May 11 01:33:58 CDT 2020 /opt/local/freesurfer-6.0/x86_64/bin/segmentBS.sh /opt/local/freesurfer-6.0/x86_64/MCRv80 /opt/local/freesurfer-6.0/x86_64 subject7_V1 /home/server1/data/freesurfer_workingdir/subjects See log file: /home/server1/data/freesurfer_workingdir/subjects/subject7_V1/scripts/brainstem-structures.log #------------------------------------------ Started at Sun May 10 20:55:29 CDT 2020 Ended at Mon May 11 01:43:39 CDT 2020 #@#%# recon-all-run-time-hours 4.803 recon-all -s subject7_V1 finished without error at Mon May 11 01:43:39 CDT 2020