Sat Dec 10 12:30:14 EST 2016 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002 /usr/local/freesurfer/bin/recon-all -i /shared_data2/sneha/4RTNI/1_S_5002/t1_mprage/2011-02-14_15_43_50.0/S110040/4RTNI_1_S_5002_MR_t1_mprage__br_raw_20110526134557719_133_S110040_I237658.nii -i /shared_data2/sneha/4RTNI/1_S_5002/t1_mprage_S3_DIS3D/2011-02-14_15_43_50.0/S110042/4RTNI_1_S_5002_MR_t1_mprage_S3_DIS3D_br_raw_20110526134108854_83_S110042_I237662.nii -FLAIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/reorientFlair/1_S_5002/2011-02-14/4RTNI_1_S_5002_MR_t2_flair_br_raw_20110526134544495_36_S110043_I237664.nii -s 1_S_5002 subjid 1_S_5002 setenv SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux TRON 3.8.0-44-generic #66~precise1-Ubuntu SMP Tue Jul 15 04:01:04 UTC 2014 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 1804890 maxlocks unlimited maxsignal 1804890 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 231111108 228000408 3110700 0 1411188 201090820 -/+ buffers/cache: 25498400 205612708 Swap: 31255548 290180 30965368 ######################################## program versions used $Id: recon-all,v 1.482 2014/08/26 20:36:16 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:15-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:15-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:15-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:15-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:15-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:15-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:15-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:16-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:16-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:16-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:16-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:16-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:16-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:16-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002 mri_convert /shared_data2/sneha/4RTNI/1_S_5002/t1_mprage/2011-02-14_15_43_50.0/S110040/4RTNI_1_S_5002_MR_t1_mprage__br_raw_20110526134557719_133_S110040_I237658.nii /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/orig/001.mgz mri_convert /shared_data2/sneha/4RTNI/1_S_5002/t1_mprage/2011-02-14_15_43_50.0/S110040/4RTNI_1_S_5002_MR_t1_mprage__br_raw_20110526134557719_133_S110040_I237658.nii /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/orig/001.mgz INFO: using NIfTI-1 qform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /shared_data2/sneha/4RTNI/1_S_5002/t1_mprage/2011-02-14_15_43_50.0/S110040/4RTNI_1_S_5002_MR_t1_mprage__br_raw_20110526134557719_133_S110040_I237658.nii... INFO: this is an unsiged short. I'll try to read it, but it might not work if there are values over 32k TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/orig/001.mgz... /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002 mri_convert /shared_data2/sneha/4RTNI/1_S_5002/t1_mprage_S3_DIS3D/2011-02-14_15_43_50.0/S110042/4RTNI_1_S_5002_MR_t1_mprage_S3_DIS3D_br_raw_20110526134108854_83_S110042_I237662.nii /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/orig/002.mgz mri_convert /shared_data2/sneha/4RTNI/1_S_5002/t1_mprage_S3_DIS3D/2011-02-14_15_43_50.0/S110042/4RTNI_1_S_5002_MR_t1_mprage_S3_DIS3D_br_raw_20110526134108854_83_S110042_I237662.nii /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/orig/002.mgz INFO: using NIfTI-1 qform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /shared_data2/sneha/4RTNI/1_S_5002/t1_mprage_S3_DIS3D/2011-02-14_15_43_50.0/S110042/4RTNI_1_S_5002_MR_t1_mprage_S3_DIS3D_br_raw_20110526134108854_83_S110042_I237662.nii... INFO: this is an unsiged short. I'll try to read it, but it might not work if there are values over 32k TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/orig/002.mgz... #-------------------------------------------- #@# T2/FLAIR Input Sat Dec 10 12:30:34 EST 2016 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002 mri_convert --no_scale 1 /shared_data2/sneha/4RTNI_processed/FreeSurfer/reorientFlair/1_S_5002/2011-02-14/4RTNI_1_S_5002_MR_t2_flair_br_raw_20110526134544495_36_S110043_I237664.nii /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/orig/FLAIRraw.mgz mri_convert --no_scale 1 /shared_data2/sneha/4RTNI_processed/FreeSurfer/reorientFlair/1_S_5002/2011-02-14/4RTNI_1_S_5002_MR_t2_flair_br_raw_20110526134544495_36_S110043_I237664.nii /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/orig/FLAIRraw.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /shared_data2/sneha/4RTNI_processed/FreeSurfer/reorientFlair/1_S_5002/2011-02-14/4RTNI_1_S_5002_MR_t2_flair_br_raw_20110526134544495_36_S110043_I237664.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/orig/FLAIRraw.mgz... #------------------------------------------ Started at Sat Dec 10 12:30:14 EST 2016 Ended at Sat Dec 10 12:30:44 EST 2016 #@#%# recon-all-run-time-hours 0.009 recon-all -s 1_S_5002 finished without error at Sat Dec 10 12:30:45 EST 2016 New invocation of recon-all Sat Dec 10 12:30:45 EST 2016 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002 /usr/local/freesurfer/bin/recon-all -all -s 1_S_5002 -cw256 -bigventricles -3T -norm2-b 20 -norm2-n 5 -openmp 12 -qcache -mail snp2003@med.cornell.edu subjid 1_S_5002 setenv SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux TRON 3.8.0-44-generic #66~precise1-Ubuntu SMP Tue Jul 15 04:01:04 UTC 2014 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 1804890 maxlocks unlimited maxsignal 1804890 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 231111108 228013888 3097220 0 1411208 201120892 -/+ buffers/cache: 25481788 205629320 Swap: 31255548 290180 30965368 ######################################## program versions used $Id: recon-all,v 1.482 2014/08/26 20:36:16 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:45-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 12 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/12/10-17:30:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### -cw256 option is now persistent (remove with -clean-cw256) #-------------------------------------------- #@# MotionCor Sat Dec 10 12:30:51 EST 2016 Found 2 runs /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/orig/001.mgz /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/orig/002.mgz Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002 mri_robust_template --mov /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/orig/001.mgz /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/orig/002.mgz --average 1 --template /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/orig/001-iscale.txt /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/orig/002-iscale.txt --subsample 200 --lta /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/orig/001.lta /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/orig/002.lta $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ --mov: Using /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/orig/001.mgz as movable/source volume. --mov: Using /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/orig/002.mgz as movable/source volume. Total: 2 input volumes --average: Using method 1 for template computation. --template: Using /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/rawavg.mgz as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no iterations)! --iscale: Enableing intensity scaling! --iscaleout: Will perform intensity scaling and output results --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms reading source '/shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/orig/001.mgz'... converting source '/shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/orig/001.mgz' to bspline ... MRItoBSpline degree 3 reading source '/shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/orig/002.mgz'... converting source '/shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/orig/002.mgz' to bspline ... MRItoBSpline degree 3 MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : [init] ========================= TP 2 to TP 1 ============================== Register TP 2 ( /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/orig/002.mgz ) to TP 1 ( /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/orig/001.mgz ) - Max Resolution used: 2 -- gpS ( 40 , 60 , 64 ) -- gpT ( 40 , 60 , 64 ) - running loop to estimate saturation parameter: mapping movs and creating initial template... allow intensity scaling using median Writing final template: /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/rawavg.mgz Writing final transforms (warps etc.)... Determinant( lta[ 0 ]) : 1 Determinant( lta[ 1 ]) : 1 registration took 3 minutes and 42 seconds. Thank you for using RobustTemplate! If you find it useful and use it for a publication, please cite: Within-Subject Template Estimation for Unbiased Longitudinal Image Analysis M. Reuter, N.J. Schmansky, H.D. Rosas, B. Fischl. NeuroImage 2012. http://dx.doi.org/10.1016/j.neuroimage.2012.02.084 http://reuter.mit.edu/papers/reuter-long12.pdf /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002 mri_convert /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/rawavg.mgz /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/orig.mgz -rt cubic --conform --cw256 mri_convert /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/rawavg.mgz /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/orig.mgz -rt cubic --conform --cw256 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) Original Data has (1, 1, 1) mm size and (160, 240, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using MRItoBSpline degree 3 writing to /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/orig.mgz... mri_add_xform_to_header -c /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/transforms/talairach.xfm /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/orig.mgz /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Sat Dec 10 12:35:08 EST 2016 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm --atlas 3T18yoSchwartzReactN32_as_orig cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Sat Dec 10 12:39:07 EST 2016 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.8060, pval=0.8469 >= threshold=0.0050) awk -f /usr/local/freesurfer/bin/extract_talairach_avi_QA.awk /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/transforms/talairach_avi.log tal_QC_AZS /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/transforms/talairach_avi.log TalAviQA: 0.96417 z-score: -3 #-------------------------------------------- #@# Nu Intensity Correction Sat Dec 10 12:39:07 EST 2016 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --proto-iters 1000 --distance 50 --n 1 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --proto-iters 1000 --distance 50 --n 1 nIters 1 $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux TRON 3.8.0-44-generic #66~precise1-Ubuntu SMP Tue Jul 15 04:01:04 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux Sat Dec 10 12:39:07 EST 2016 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 tmpdir is ./tmp.mri_nu_correct.mni.25932 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.25932/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.25932/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.25932/nu0.mnc... -------------------------------------------------------- Iteration 1 Sat Dec 10 12:39:12 EST 2016 nu_correct -clobber ./tmp.mri_nu_correct.mni.25932/nu0.mnc ./tmp.mri_nu_correct.mni.25932/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.25932/0/ -iterations 1000 -distance 50 [sneha@TRON:/shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/] [2016-12-10 12:39:12] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.25932/0/ ./tmp.mri_nu_correct.mni.25932/nu0.mnc ./tmp.mri_nu_correct.mni.25932/nu1.imp Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Number of iterations: 57 CV of field change: 0.000979092 [sneha@TRON:/shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/] [2016-12-10 12:41:30] running: /usr/local/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.25932/nu0.mnc ./tmp.mri_nu_correct.mni.25932/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.25932/nu1.mnc --min -1 --o ./tmp.mri_nu_correct.mni.25932/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.25932/nu1.mnc --min -1 --o ./tmp.mri_nu_correct.mni.25932/ones.mgz sysname Linux hostname TRON machine x86_64 user sneha input ./tmp.mri_nu_correct.mni.25932/nu1.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.25932/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 Found 16777216 values in range Counting number of voxels Found 16777216 voxels in final mask mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.25932/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.25932/sum.junk --avgwf ./tmp.mri_nu_correct.mni.25932/input.mean.dat $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.25932/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.25932/sum.junk --avgwf ./tmp.mri_nu_correct.mni.25932/input.mean.dat sysname Linux hostname TRON machine x86_64 user sneha UseRobust 0 Loading ./tmp.mri_nu_correct.mni.25932/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 16777216.000 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.25932/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.25932/ones.mgz --i ./tmp.mri_nu_correct.mni.25932/nu1.mnc --sum ./tmp.mri_nu_correct.mni.25932/sum.junk --avgwf ./tmp.mri_nu_correct.mni.25932/output.mean.dat $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.25932/ones.mgz --i ./tmp.mri_nu_correct.mni.25932/nu1.mnc --sum ./tmp.mri_nu_correct.mni.25932/sum.junk --avgwf ./tmp.mri_nu_correct.mni.25932/output.mean.dat sysname Linux hostname TRON machine x86_64 user sneha UseRobust 0 Loading ./tmp.mri_nu_correct.mni.25932/ones.mgz Loading ./tmp.mri_nu_correct.mni.25932/nu1.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 16777216.000 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.25932/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.25932/nu1.mnc ./tmp.mri_nu_correct.mni.25932/nu1.mnc mul 1.02067535955685090172 Saving result to './tmp.mri_nu_correct.mni.25932/nu1.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.25932/nu1.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.25932/nu1.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.25932/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 14 seconds. mapping ( 7, 106) to ( 3, 110) Sat Dec 10 12:42:58 EST 2016 mri_nu_correct.mni done mri_add_xform_to_header -c /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Sat Dec 10 12:43:02 EST 2016 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.064 -0.013 -0.023 -244.820; -0.093 1.076 0.142 -413.767; -0.016 -0.132 1.175 -569.030; 0.000 0.000 0.000 1.000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 18 Starting OpenSpline(): npoints = 18 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 102 gm peak at 71 (71), valley at 56 (56) csf peak at 35, setting threshold to 59 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at -nan white matter peak found at 0 gm peak at 0 (0), valley at 30 (-10) csf peak at 0, setting threshold to 0 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 4 minutes and 23 seconds. #-------------------------------------------- #@# Skull Stripping Sat Dec 10 12:47:27 EST 2016 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri mri_em_register -skull nu.mgz /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta ======= NUMBER OF OPENMP THREADS = 12 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 5 reading 1 input volumes... logging results to talairach_with_skull.log reading '/usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=7.0 skull bounding box = (46, 56, 19) --> (211, 255, 219) using (101, 122, 119) as brain centroid... mean wm in atlas = 126, using box (81,97,94) --> (121, 146,143) to find MRI wm before smoothing, mri peak at 104 after smoothing, mri peak at 104, scaling input intensities by 1.212 scaling channel 0 by 1.21154 initial log_p = -4.7 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.697590 @ (-9.091, -9.091, -9.091) max log p = -4.499403 @ (4.545, -13.636, 4.545) max log p = -4.457431 @ (2.273, 6.818, 2.273) max log p = -4.447979 @ (-1.136, -3.409, -1.136) max log p = -4.422770 @ (2.841, 5.114, 2.841) max log p = -4.422770 @ (0.000, 0.000, 0.000) Found translation: (-0.6, -14.2, -0.6): log p = -4.423 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.3, old_max_log_p =-4.4 (thresh=-4.4) 1.064 0.000 0.000 -8.622; 0.000 1.226 0.161 -61.944; 0.000 -0.139 1.055 12.394; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.2, old_max_log_p =-4.3 (thresh=-4.2) 1.064 0.000 0.000 -8.622; 0.000 1.326 0.024 -60.850; 0.000 0.021 0.987 -1.943; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.2, old_max_log_p =-4.2 (thresh=-4.2) 1.064 0.000 0.000 -8.622; 0.000 1.326 0.024 -60.850; 0.000 0.021 0.987 -1.943; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.1, old_max_log_p =-4.2 (thresh=-4.2) 1.064 -0.000 0.002 -10.998; 0.000 1.299 0.087 -60.306; 0.003 -0.070 1.039 2.474; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 1.064 -0.000 0.002 -10.998; 0.000 1.299 0.087 -60.306; 0.003 -0.070 1.039 2.474; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 1.064 -0.010 -0.007 -8.661; 0.009 1.297 0.095 -62.509; 0.011 -0.081 1.039 2.256; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 1.064 0.000 -0.006 -10.617; -0.000 1.295 0.087 -60.112; 0.011 -0.070 1.039 1.819; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 1.064 0.000 -0.006 -10.617; -0.000 1.295 0.087 -60.112; 0.011 -0.070 1.039 1.819; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3481 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.06386 0.00047 -0.00618 -10.61668; -0.00010 1.29493 0.08652 -60.11179; 0.01141 -0.06986 1.03881 1.81905; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.06386 0.00047 -0.00618 -10.61668; -0.00010 1.29493 0.08652 -60.11179; 0.01141 -0.06986 1.03881 1.81905; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.064 0.000 -0.006 -10.617; -0.000 1.295 0.087 -60.112; 0.011 -0.070 1.039 1.819; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -4.1 (old=-4.7) transform before final EM align: 1.064 0.000 -0.006 -10.617; -0.000 1.295 0.087 -60.112; 0.011 -0.070 1.039 1.819; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 382743 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.06386 0.00047 -0.00618 -10.61668; -0.00010 1.29493 0.08652 -60.11179; 0.01141 -0.06986 1.03881 1.81905; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.06386 0.00047 -0.00618 -10.61668; -0.00010 1.29493 0.08652 -60.11179; 0.01141 -0.06986 1.03881 1.81905; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 012: -log(p) = 4.5 tol 0.000000 final transform: 1.064 0.000 -0.006 -10.617; -0.000 1.295 0.087 -60.112; 0.011 -0.070 1.039 1.819; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 1364 minutes and 36 seconds. mri_watershed -T1 -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=128 y=144 z=100 r=82 first estimation of the main basin volume: 2394015 voxels Looking for seedpoints 2 found in the cerebellum 15 found in the rest of the brain global maximum in x=94, y=139, z=100, Imax=255 CSF=17, 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=19343707877 voxels, voxel volume =1.000 = 19343707877 mmm3 = 19343708.160 cm3 done. PostAnalyze...Basin Prior 71 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=128,y=131, z=106, r=10260 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=32 , nb = 45583 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=24 , nb = 1139604922 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=22 , nb = 1134412316 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=31 , nb = 1131775478 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=33 , nb = 1077338370 OTHER CSF_MIN=0, CSF_intensity=9, CSF_MAX=56 , nb = 1065402432 (2) Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 32, 27, 14, 95 after analyzing : 20, 27, 27, 44 RIGHT_CER before analyzing : 24, 19, 0, 97 after analyzing : 19, 23, 25, 41 LEFT_CER before analyzing : 22, 28, 38, 69 after analyzing : 22, 34, 38, 42 RIGHT_BRAIN before analyzing : 31, 26, 14, 95 after analyzing : 19, 26, 26, 43 LEFT_BRAIN before analyzing : 33, 27, 14, 95 after analyzing : 20, 27, 27, 44 OTHER before analyzing : 56, 74, 80, 94 after analyzing : 56, 78, 80, 82 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...72 iterations *********************VALIDATION********************* curvature mean = -0.014, std = 0.011 curvature mean = 68.349, std = 8.369 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 4.46, sigma = 5.90 after rotation: sse = 4.46, sigma = 5.90 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 4.84, its var is 6.91 before Erosion-Dilatation 0.83% of inacurate vertices after Erosion-Dilatation 0.00% 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...49 iterations mri_strip_skull: done peeling brain Brain Size = 1532403 voxels, voxel volume = 1.000 mm3 = 1532403 mmm3 = 1532.403 cm3 ****************************** Saving brainmask.auto.mgz done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Sun Dec 11 11:32:50 EST 2016 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta ======= NUMBER OF OPENMP THREADS = 12 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 14.9 or > 790.2 total sample mean = 84.4 (994 zeros) ************************************************ spacing=8, using 2772 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2772, passno 0, spacing 8 resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=14.0 skull bounding box = (59, 75, 28) --> (199, 189, 198) using (106, 113, 113) as brain centroid... mean wm in atlas = 107, using box (89,99,92) --> (123, 126,133) to find MRI wm before smoothing, mri peak at 104 after smoothing, mri peak at 104, scaling input intensities by 1.029 scaling channel 0 by 1.02885 initial log_p = -4.3 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.188315 @ (-9.091, -9.091, -9.091) max log p = -3.942395 @ (4.545, -4.545, 4.545) max log p = -3.876617 @ (2.273, -2.273, 2.273) max log p = -3.839444 @ (-1.136, -1.136, -1.136) max log p = -3.809469 @ (0.568, 0.568, 0.568) max log p = -3.809469 @ (0.000, 0.000, 0.000) Found translation: (-2.8, -16.5, -2.8): log p = -3.809 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.7, old_max_log_p =-3.8 (thresh=-3.8) 1.000 0.000 0.000 -2.841; 0.000 1.140 0.131 -49.566; 0.000 -0.150 0.991 18.400; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.7, old_max_log_p =-3.7 (thresh=-3.7) 1.000 0.000 0.000 -2.841; 0.000 1.140 0.131 -49.566; 0.000 -0.150 0.991 18.400; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.6, old_max_log_p =-3.7 (thresh=-3.7) 0.999 -0.037 -0.005 2.826; 0.033 1.134 0.162 -54.502; 0.000 -0.196 1.023 21.119; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.6, old_max_log_p =-3.6 (thresh=-3.6) 0.999 -0.006 0.033 -5.467; 0.000 1.156 0.164 -55.311; -0.032 -0.191 1.004 26.723; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.6, old_max_log_p =-3.6 (thresh=-3.6) 0.997 -0.041 0.011 1.894; 0.032 1.156 0.181 -62.337; -0.016 -0.210 1.001 27.429; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.6, old_max_log_p =-3.6 (thresh=-3.6) 0.997 -0.041 0.011 1.894; 0.032 1.156 0.181 -62.337; -0.016 -0.210 1.001 27.429; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2772 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.99700 -0.04058 0.01116 1.89384; 0.03232 1.15647 0.18111 -62.33698; -0.01573 -0.20975 1.00145 27.42894; 0.00000 0.00000 0.00000 1.00000; nsamples 2772 Quasinewton: input matrix 0.99700 -0.04058 0.01116 1.89384; 0.03232 1.15647 0.18111 -62.33698; -0.01573 -0.20975 1.00145 27.42894; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.997 -0.041 0.011 1.894; 0.032 1.156 0.181 -62.337; -0.016 -0.210 1.001 27.429; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.6 (old=-4.3) transform before final EM align: 0.997 -0.041 0.011 1.894; 0.032 1.156 0.181 -62.337; -0.016 -0.210 1.001 27.429; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 312841 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.99700 -0.04058 0.01116 1.89384; 0.03232 1.15647 0.18111 -62.33698; -0.01573 -0.20975 1.00145 27.42894; 0.00000 0.00000 0.00000 1.00000; nsamples 312841 Quasinewton: input matrix 0.99700 -0.04058 0.01116 1.89384; 0.03232 1.15647 0.18111 -62.33698; -0.01573 -0.20975 1.00145 27.42894; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = 4.1 tol 0.000000 final transform: 0.997 -0.041 0.011 1.894; 0.032 1.156 0.181 -62.337; -0.016 -0.210 1.001 27.429; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 723 minutes and 39 seconds. #-------------------------------------- #@# CA Normalize Sun Dec 11 23:36:29 EST 2016 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=14.0 skull bounding box = (59, 75, 28) --> (199, 189, 198) using (106, 113, 113) as brain centroid... mean wm in atlas = 107, using box (89,99,92) --> (123, 126,133) to find MRI wm before smoothing, mri peak at 104 after smoothing, mri peak at 104, scaling input intensities by 1.029 scaling channel 0 by 1.02885 using 244171 sample points... INFO: compute sample coordinates transform 0.997 -0.041 0.011 1.894; 0.032 1.156 0.181 -62.337; -0.016 -0.210 1.001 27.429; 0.000 0.000 0.000 1.000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (128, 79, 33) --> (196, 175, 196) Left_Cerebral_White_Matter: limiting intensities to 125.0 --> 255.0 6 of 7 (85.7%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (64, 81, 32) --> (129, 178, 196) Right_Cerebral_White_Matter: limiting intensities to 102.0 --> 255.0 0 of 9 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (132, 153, 60) --> (181, 191, 112) finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (85, 154, 57) --> (131, 192, 113) finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (114, 146, 94) --> (146, 205, 124) using 16 total control points for intensity normalization... bias field = 0.977 +- 0.061 0 of 10 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (128, 79, 33) --> (196, 175, 196) Left_Cerebral_White_Matter: limiting intensities to 81.0 --> 246.0 0 of 89 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (64, 81, 32) --> (129, 178, 196) Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 246.0 0 of 73 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (132, 153, 60) --> (181, 191, 112) finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (85, 154, 57) --> (131, 192, 113) finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (114, 146, 94) --> (146, 205, 124) Brain_Stem: limiting intensities to 118.0 --> 246.0 16 of 17 (94.1%) samples deleted using 179 total control points for intensity normalization... bias field = 1.026 +- 0.088 0 of 163 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (128, 79, 33) --> (196, 175, 196) Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 230.0 0 of 114 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (64, 81, 32) --> (129, 178, 196) Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 230.0 0 of 126 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (132, 153, 60) --> (181, 191, 112) finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (85, 154, 57) --> (131, 192, 113) finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (114, 146, 94) --> (146, 205, 124) Brain_Stem: limiting intensities to 95.0 --> 230.0 16 of 40 (40.0%) samples deleted using 280 total control points for intensity normalization... bias field = 1.006 +- 0.068 1 of 264 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 3 minutes and 3 seconds. #-------------------------------------- #@# CA Reg Sun Dec 11 23:39:32 EST 2016 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri mri_ca_register -bigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.m3z handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log ======= NUMBER OF OPENMP THREADS = 12 ======= reading input volume 'norm.mgz'... reading GCA '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.19 (predicted orig area = 6.7) label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 registering ventricular system... rms increased (dt=0.4500) - undoing step... rms increased (dt=0.1500) - undoing step... rms increased (dt=0.1000) - undoing step... rms increased (dt=0.0500) - undoing step... **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=1.010, neg=0, invalid=96777 0005: dt=129.472000, rms=0.855 (15.341%), neg=0, invalid=96777 0006: dt=295.936000, rms=0.800 (6.454%), neg=0, invalid=96777 0007: dt=221.952000, rms=0.778 (2.732%), neg=0, invalid=96777 0008: dt=110.976000, rms=0.769 (1.125%), neg=0, invalid=96777 0009: dt=129.472000, rms=0.764 (0.773%), neg=0, invalid=96777 0010: dt=295.936000, rms=0.757 (0.848%), neg=0, invalid=96777 0011: dt=92.480000, rms=0.752 (0.630%), neg=0, invalid=96777 0012: dt=517.888000, rms=0.747 (0.654%), neg=0, invalid=96777 0013: dt=92.480000, rms=0.743 (0.549%), neg=0, invalid=96777 0014: dt=129.472000, rms=0.742 (0.116%), neg=0, invalid=96777 0015: dt=129.472000, rms=0.741 (0.200%), neg=0, invalid=96777 0016: dt=129.472000, rms=0.739 (0.251%), neg=0, invalid=96777 0017: dt=129.472000, rms=0.737 (0.331%), neg=0, invalid=96777 0018: dt=129.472000, rms=0.734 (0.358%), neg=0, invalid=96777 0019: dt=129.472000, rms=0.731 (0.422%), neg=0, invalid=96777 0020: dt=129.472000, rms=0.728 (0.368%), neg=0, invalid=96777 0021: dt=129.472000, rms=0.725 (0.378%), neg=0, invalid=96777 0022: dt=129.472000, rms=0.723 (0.327%), neg=0, invalid=96777 0023: dt=129.472000, rms=0.721 (0.347%), neg=0, invalid=96777 0024: dt=129.472000, rms=0.719 (0.275%), neg=0, invalid=96777 0025: dt=129.472000, rms=0.718 (0.147%), neg=0, invalid=96777 0026: dt=129.472000, rms=0.716 (0.189%), neg=0, invalid=96777 0027: dt=129.472000, rms=0.715 (0.157%), neg=0, invalid=96777 0028: dt=129.472000, rms=0.714 (0.164%), neg=0, invalid=96777 0029: dt=129.472000, rms=0.713 (0.156%), neg=0, invalid=96777 0030: dt=129.472000, rms=0.711 (0.189%), neg=0, invalid=96777 0031: dt=129.472000, rms=0.710 (0.154%), neg=0, invalid=96777 0032: dt=129.472000, rms=0.710 (0.087%), neg=0, invalid=96777 0033: dt=129.472000, rms=0.709 (0.087%), neg=0, invalid=96777 0034: dt=129.472000, rms=0.708 (0.110%), neg=0, invalid=96777 0035: dt=129.472000, rms=0.707 (0.183%), neg=0, invalid=96777 0036: dt=129.472000, rms=0.706 (0.124%), neg=0, invalid=96777 0037: dt=129.472000, rms=0.706 (0.047%), neg=0, invalid=96777 0038: dt=110.976000, rms=0.705 (0.067%), neg=0, invalid=96777 0039: dt=8.092000, rms=0.705 (-0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.705, neg=0, invalid=96777 0040: dt=92.480000, rms=0.705 (0.035%), neg=0, invalid=96777 0041: dt=517.888000, rms=0.704 (0.208%), neg=0, invalid=96777 0042: dt=129.472000, rms=0.703 (0.087%), neg=0, invalid=96777 0043: dt=129.472000, rms=0.703 (0.002%), neg=0, invalid=96777 0044: dt=129.472000, rms=0.703 (0.036%), neg=0, invalid=96777 0045: dt=129.472000, rms=0.702 (0.050%), neg=0, invalid=96777 0046: dt=129.472000, rms=0.702 (0.050%), neg=0, invalid=96777 0047: dt=129.472000, rms=0.702 (0.045%), neg=0, invalid=96777 0048: dt=129.472000, rms=0.701 (0.026%), neg=0, invalid=96777 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.710, neg=0, invalid=96777 0049: dt=145.152000, rms=0.700 (1.443%), neg=0, invalid=96777 0050: dt=36.288000, rms=0.697 (0.398%), neg=0, invalid=96777 0051: dt=145.152000, rms=0.687 (1.432%), neg=0, invalid=96777 0052: dt=20.736000, rms=0.685 (0.303%), neg=0, invalid=96777 0053: dt=36.288000, rms=0.684 (0.155%), neg=0, invalid=96777 0054: dt=36.288000, rms=0.682 (0.297%), neg=0, invalid=96777 0055: dt=36.288000, rms=0.679 (0.398%), neg=0, invalid=96777 0056: dt=36.288000, rms=0.675 (0.511%), neg=0, invalid=96777 0057: dt=36.288000, rms=0.671 (0.603%), neg=0, invalid=96777 0058: dt=36.288000, rms=0.667 (0.662%), neg=0, invalid=96777 0059: dt=36.288000, rms=0.663 (0.648%), neg=0, invalid=96777 0060: dt=36.288000, rms=0.658 (0.631%), neg=0, invalid=96777 0061: dt=36.288000, rms=0.655 (0.540%), neg=0, invalid=96777 0062: dt=36.288000, rms=0.652 (0.487%), neg=0, invalid=96777 0063: dt=36.288000, rms=0.648 (0.511%), neg=0, invalid=96777 0064: dt=36.288000, rms=0.646 (0.391%), neg=0, invalid=96777 0065: dt=36.288000, rms=0.643 (0.359%), neg=0, invalid=96777 0066: dt=36.288000, rms=0.641 (0.331%), neg=0, invalid=96777 0067: dt=36.288000, rms=0.640 (0.261%), neg=0, invalid=96777 0068: dt=36.288000, rms=0.638 (0.251%), neg=0, invalid=96777 0069: dt=36.288000, rms=0.637 (0.228%), neg=0, invalid=96777 0070: dt=36.288000, rms=0.635 (0.198%), neg=0, invalid=96777 0071: dt=36.288000, rms=0.634 (0.148%), neg=0, invalid=96777 0072: dt=36.288000, rms=0.634 (0.092%), neg=0, invalid=96777 0073: dt=36.288000, rms=0.633 (0.120%), neg=0, invalid=96777 0074: dt=36.288000, rms=0.632 (0.110%), neg=0, invalid=96777 0075: dt=36.288000, rms=0.632 (0.030%), neg=0, invalid=96777 0076: dt=36.288000, rms=0.632 (0.031%), neg=0, invalid=96777 0077: dt=36.288000, rms=0.632 (0.046%), neg=0, invalid=96777 0078: dt=36.288000, rms=0.631 (0.038%), neg=0, invalid=96777 0079: dt=36.288000, rms=0.631 (0.055%), neg=0, invalid=96777 0080: dt=36.288000, rms=0.631 (0.061%), neg=0, invalid=96777 0081: dt=36.288000, rms=0.631 (0.036%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.631, neg=0, invalid=96777 0082: dt=36.288000, rms=0.630 (0.034%), neg=0, invalid=96777 0083: dt=25.920000, rms=0.630 (0.015%), neg=0, invalid=96777 0084: dt=25.920000, rms=0.630 (0.003%), neg=0, invalid=96777 0085: dt=25.920000, rms=0.630 (-0.027%), neg=0, invalid=96777 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.662, neg=0, invalid=96777 0086: dt=0.400000, rms=0.662 (0.000%), neg=0, invalid=96777 0087: dt=0.000000, rms=0.662 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.662, neg=0, invalid=96777 0088: dt=0.000000, rms=0.662 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.757, neg=0, invalid=96777 0089: dt=4.566604, rms=0.736 (2.827%), neg=0, invalid=96777 0090: dt=2.666667, rms=0.734 (0.182%), neg=0, invalid=96777 0091: dt=2.666667, rms=0.734 (-0.034%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.734, neg=0, invalid=96777 0092: dt=0.000000, rms=0.734 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.835, neg=0, invalid=96777 0093: dt=1.444660, rms=0.827 (1.005%), neg=0, invalid=96777 0094: dt=1.792000, rms=0.819 (0.941%), neg=0, invalid=96777 0095: dt=0.534483, rms=0.818 (0.113%), neg=0, invalid=96777 0096: dt=0.534483, rms=0.818 (0.044%), neg=0, invalid=96777 0097: dt=0.534483, rms=0.818 (0.035%), neg=0, invalid=96777 0098: dt=0.534483, rms=0.818 (-0.021%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.818, neg=0, invalid=96777 0099: dt=1.537037, rms=0.816 (0.248%), neg=0, invalid=96777 0100: dt=0.000000, rms=0.816 (-0.001%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.732, neg=0, invalid=96777 0101: dt=0.320000, rms=0.716 (2.196%), neg=0, invalid=96777 0102: dt=0.000000, rms=0.715 (0.005%), neg=0, invalid=96777 0103: dt=0.050000, rms=0.715 (-0.321%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.715, neg=0, invalid=96777 0104: dt=0.000000, rms=0.715 (0.000%), neg=0, invalid=96777 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.08313 (15) Left_Lateral_Ventricle (4): linear fit = 0.55 x + 0.0 (1983 voxels, overlap=0.173) Left_Lateral_Ventricle (4): linear fit = 0.55 x + 0.0 (1983 voxels, peak = 13), gca=13.1 gca peak = 0.14022 (22) mri peak = 0.07918 (19) Right_Lateral_Ventricle (43): linear fit = 0.58 x + 0.0 (992 voxels, overlap=0.349) Right_Lateral_Ventricle (43): linear fit = 0.58 x + 0.0 (992 voxels, peak = 13), gca=12.9 gca peak = 0.24234 (100) mri peak = 0.06327 (90) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (295 voxels, overlap=1.003) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (295 voxels, peak = 100), gca=100.5 gca peak = 0.19192 (97) mri peak = 0.08418 (85) Left_Pallidum (13): linear fit = 0.85 x + 0.0 (287 voxels, overlap=0.044) Left_Pallidum (13): linear fit = 0.85 x + 0.0 (287 voxels, peak = 82), gca=82.0 gca peak = 0.24007 (63) mri peak = 0.05477 (67) Right_Hippocampus (53): linear fit = 1.05 x + 0.0 (479 voxels, overlap=0.711) Right_Hippocampus (53): linear fit = 1.05 x + 0.0 (479 voxels, peak = 66), gca=66.5 gca peak = 0.29892 (64) mri peak = 0.07551 (73) Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (265 voxels, overlap=0.875) Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (265 voxels, peak = 71), gca=71.4 gca peak = 0.12541 (104) mri peak = 0.06506 (105) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (52388 voxels, overlap=0.952) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (52388 voxels, peak = 105), gca=104.5 gca peak = 0.13686 (104) mri peak = 0.06473 (107) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (47564 voxels, overlap=0.904) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (47564 voxels, peak = 106), gca=105.6 gca peak = 0.11691 (63) mri peak = 0.03096 (68) Left_Cerebral_Cortex (3): linear fit = 1.09 x + 0.0 (10935 voxels, overlap=0.537) Left_Cerebral_Cortex (3): linear fit = 1.09 x + 0.0 (10935 voxels, peak = 68), gca=68.4 gca peak = 0.13270 (63) mri peak = 0.03095 (72) Right_Cerebral_Cortex (42): linear fit = 1.13 x + 0.0 (13169 voxels, overlap=0.473) Right_Cerebral_Cortex (42): linear fit = 1.13 x + 0.0 (13169 voxels, peak = 72), gca=71.5 gca peak = 0.15182 (70) mri peak = 0.08455 (95) Right_Caudate (50): linear fit = 1.33 x + 0.0 (528 voxels, overlap=0.015) Right_Caudate (50): linear fit = 1.33 x + 0.0 (528 voxels, peak = 93), gca=92.8 gca peak = 0.14251 (76) mri peak = 0.08082 (79) Left_Caudate (11): linear fit = 1.00 x + 0.0 (550 voxels, overlap=0.966) Left_Caudate (11): linear fit = 1.00 x + 0.0 (550 voxels, peak = 76), gca=76.0 gca peak = 0.12116 (60) mri peak = 0.03776 ( 9) Left_Cerebellum_Cortex (8): linear fit = 0.20 x + 0.0 (4156 voxels, overlap=0.001) Left_Cerebellum_Cortex (8): linear fit = 0.20 x + 0.0 (4156 voxels, peak = 12), gca=12.3 gca peak = 0.12723 (61) mri peak = 0.02193 (92) Right_Cerebellum_Cortex (47): linear fit = 1.51 x + 0.0 (6337 voxels, overlap=0.000) Right_Cerebellum_Cortex (47): linear fit = 1.51 x + 0.0 (6337 voxels, peak = 92), gca=92.4 gca peak = 0.22684 (88) mri peak = 0.05059 (99) Left_Cerebellum_White_Matter (7): linear fit = 1.12 x + 0.0 (3193 voxels, overlap=0.022) Left_Cerebellum_White_Matter (7): linear fit = 1.12 x + 0.0 (3193 voxels, peak = 98), gca=98.1 gca peak = 0.21067 (87) mri peak = 0.03463 (94) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (2968 voxels, overlap=0.730) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (2968 voxels, peak = 93), gca=92.7 gca peak = 0.25455 (62) mri peak = 0.06766 (69) Left_Amygdala (18): linear fit = 1.04 x + 0.0 (195 voxels, overlap=0.447) Left_Amygdala (18): linear fit = 1.04 x + 0.0 (195 voxels, peak = 65), gca=64.8 gca peak = 0.39668 (62) mri peak = 0.08780 (66) Right_Amygdala (54): linear fit = 1.05 x + 0.0 (211 voxels, overlap=0.981) Right_Amygdala (54): linear fit = 1.05 x + 0.0 (211 voxels, peak = 65), gca=65.4 gca peak = 0.10129 (93) mri peak = 0.05263 (100) Left_Thalamus_Proper (10): linear fit = 1.05 x + 0.0 (4397 voxels, overlap=0.905) Left_Thalamus_Proper (10): linear fit = 1.05 x + 0.0 (4397 voxels, peak = 98), gca=98.1 gca peak = 0.12071 (89) mri peak = 0.05832 (92) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (3197 voxels, overlap=0.987) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (3197 voxels, peak = 90), gca=90.3 gca peak = 0.13716 (82) mri peak = 0.04977 (92) Left_Putamen (12): linear fit = 1.07 x + 0.0 (1309 voxels, overlap=0.876) Left_Putamen (12): linear fit = 1.07 x + 0.0 (1309 voxels, peak = 87), gca=87.3 gca peak = 0.15214 (84) mri peak = 0.04840 (87) Right_Putamen (51): linear fit = 1.02 x + 0.0 (1916 voxels, overlap=1.001) Right_Putamen (51): linear fit = 1.02 x + 0.0 (1916 voxels, peak = 86), gca=86.1 gca peak = 0.08983 (85) mri peak = 0.07458 (92) Brain_Stem (16): linear fit = 1.09 x + 0.0 (6302 voxels, overlap=0.592) Brain_Stem (16): linear fit = 1.09 x + 0.0 (6302 voxels, peak = 92), gca=92.2 gca peak = 0.11809 (92) mri peak = 0.10115 (97) Right_VentralDC (60): linear fit = 1.05 x + 0.0 (538 voxels, overlap=0.619) Right_VentralDC (60): linear fit = 1.05 x + 0.0 (538 voxels, peak = 97), gca=97.1 gca peak = 0.12914 (94) mri peak = 0.08511 (98) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (630 voxels, overlap=0.726) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (630 voxels, peak = 104), gca=103.9 gca peak = 0.21100 (36) mri peak = 0.08469 (34) gca peak = 0.13542 (27) mri peak = 0.04341 (16) Fourth_Ventricle (15): linear fit = 0.79 x + 0.0 (645 voxels, overlap=1.000) Fourth_Ventricle (15): linear fit = 0.79 x + 0.0 (645 voxels, peak = 21), gca=21.2 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21802 (40) gca peak Left_Cerebellum_Cortex = 0.12116 (60) gca peak Third_Ventricle = 0.21100 (36) gca peak CSF = 0.17123 (45) gca peak Left_Accumbens_area = 0.25875 (69) gca peak Left_undetermined = 0.96240 (36) gca peak Left_vessel = 0.33262 (65) gca peak Left_choroid_plexus = 0.09846 (46) gca peak Right_Inf_Lat_Vent = 0.28113 (34) gca peak Right_Cerebellum_Cortex = 0.12723 (61) gca peak Right_Accumbens_area = 0.27120 (72) gca peak Right_vessel = 0.61915 (60) gca peak Right_choroid_plexus = 0.12775 (51) gca peak Fifth_Ventricle = 0.45329 (44) gca peak WM_hypointensities = 0.11729 (81) gca peak non_WM_hypointensities = 0.10912 (56) gca peak Optic_Chiasm = 0.33287 (75) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 1.08 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 0.64 x + 0.0 setting left cbm cortex = 1.08 x + 0.00 setting right cbm cortex = 1.08 x + 0.00 saving intensity scales to talairach.label_intensities.txt **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.738, neg=0, invalid=96777 0105: dt=32.368000, rms=0.732 (0.874%), neg=0, invalid=96777 0106: dt=32.368000, rms=0.728 (0.454%), neg=0, invalid=96777 0107: dt=32.368000, rms=0.726 (0.294%), neg=0, invalid=96777 0108: dt=8.092000, rms=0.726 (0.058%), neg=0, invalid=96777 0109: dt=1.734000, rms=0.726 (0.011%), neg=0, invalid=96777 0110: dt=0.054187, rms=0.726 (0.001%), neg=0, invalid=96777 0111: dt=0.027094, rms=0.726 (0.000%), neg=0, invalid=96777 0112: dt=0.006773, rms=0.726 (0.000%), neg=0, invalid=96777 0113: dt=0.000000, rms=0.726 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.726, neg=0, invalid=96777 0114: dt=0.000000, rms=0.726 (-0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.726, neg=0, invalid=96777 0115: dt=0.000000, rms=0.726 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.726, neg=0, invalid=96777 0116: dt=0.000000, rms=0.726 (-0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.726, neg=0, invalid=96777 0117: dt=0.000000, rms=0.726 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.726, neg=0, invalid=96777 0118: dt=0.000000, rms=0.726 (-0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.726, neg=0, invalid=96777 0119: dt=0.720000, rms=0.718 (1.085%), neg=0, invalid=96777 0120: dt=0.252000, rms=0.716 (0.363%), neg=0, invalid=96777 0121: dt=0.252000, rms=0.713 (0.353%), neg=0, invalid=96777 0122: dt=0.063000, rms=0.712 (0.086%), neg=0, invalid=96777 0123: dt=0.063000, rms=0.712 (0.087%), neg=0, invalid=96777 0124: dt=0.015750, rms=0.712 (0.023%), neg=0, invalid=96777 0125: dt=0.001969, rms=0.712 (0.003%), neg=0, invalid=96777 0126: dt=0.000984, rms=0.712 (0.001%), neg=0, invalid=96777 0127: dt=0.000492, rms=0.712 (0.001%), neg=0, invalid=96777 0128: dt=0.000000, rms=0.712 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.712, neg=0, invalid=96777 0129: dt=0.000540, rms=0.712 (0.001%), neg=0, invalid=96777 0130: dt=0.000000, rms=0.712 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.712, neg=0, invalid=96777 0131: dt=0.448000, rms=0.703 (1.255%), neg=0, invalid=96777 0132: dt=0.448000, rms=0.695 (1.109%), neg=0, invalid=96777 0133: dt=0.448000, rms=0.689 (0.983%), neg=0, invalid=96777 0134: dt=1.280000, rms=0.672 (2.469%), neg=0, invalid=96777 0135: dt=1.792000, rms=0.656 (2.345%), neg=0, invalid=96777 0136: dt=1.792000, rms=0.647 (1.379%), neg=0, invalid=96777 0137: dt=1.792000, rms=0.641 (0.893%), neg=0, invalid=96777 0138: dt=1.280000, rms=0.638 (0.457%), neg=0, invalid=96777 0139: dt=1.792000, rms=0.635 (0.526%), neg=0, invalid=96777 0140: dt=1.280000, rms=0.633 (0.291%), neg=0, invalid=96777 0141: dt=1.792000, rms=0.631 (0.353%), neg=0, invalid=96777 0142: dt=1.792000, rms=0.629 (0.290%), neg=0, invalid=96777 0143: dt=1.792000, rms=0.627 (0.250%), neg=0, invalid=96777 0144: dt=1.792000, rms=0.626 (0.205%), neg=0, invalid=96777 0145: dt=1.792000, rms=0.625 (0.183%), neg=0, invalid=96777 0146: dt=1.792000, rms=0.624 (0.157%), neg=0, invalid=96777 0147: dt=1.536000, rms=0.623 (0.117%), neg=0, invalid=96777 0148: dt=1.792000, rms=0.622 (0.128%), neg=0, invalid=96777 0149: dt=1.792000, rms=0.622 (0.114%), neg=0, invalid=96777 0150: dt=1.792000, rms=0.621 (0.101%), neg=0, invalid=96777 0151: dt=1.792000, rms=0.620 (0.092%), neg=0, invalid=96777 0152: dt=0.541667, rms=0.620 (0.024%), neg=0, invalid=96777 0153: dt=0.541667, rms=0.620 (0.025%), neg=0, invalid=96777 0154: dt=0.541667, rms=0.620 (0.046%), neg=0, invalid=96777 0155: dt=0.541667, rms=0.619 (0.067%), neg=0, invalid=96777 0156: dt=0.541667, rms=0.619 (0.073%), neg=0, invalid=96777 0157: dt=0.541667, rms=0.618 (0.086%), neg=0, invalid=96777 0158: dt=0.541667, rms=0.618 (0.096%), neg=0, invalid=96777 0159: dt=0.541667, rms=0.617 (0.100%), neg=0, invalid=96777 0160: dt=0.541667, rms=0.617 (0.103%), neg=0, invalid=96777 0161: dt=0.541667, rms=0.616 (0.100%), neg=0, invalid=96777 0162: dt=0.541667, rms=0.615 (0.094%), neg=0, invalid=96777 0163: dt=0.541667, rms=0.615 (0.085%), neg=0, invalid=96777 0164: dt=0.541667, rms=0.614 (0.082%), neg=0, invalid=96777 0165: dt=0.541667, rms=0.614 (0.073%), neg=0, invalid=96777 0166: dt=0.541667, rms=0.614 (0.061%), neg=0, invalid=96777 0167: dt=0.541667, rms=0.613 (0.054%), neg=0, invalid=96777 0168: dt=0.541667, rms=0.613 (0.043%), neg=0, invalid=96777 0169: dt=0.541667, rms=0.613 (0.000%), neg=0, invalid=96777 0170: dt=0.541667, rms=0.613 (-0.005%), neg=0, invalid=96777 0171: dt=0.000000, rms=0.613 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.613, neg=0, invalid=96777 0172: dt=0.448000, rms=0.612 (0.074%), neg=0, invalid=96777 0173: dt=1.792000, rms=0.611 (0.247%), neg=0, invalid=96777 0174: dt=1.792000, rms=0.610 (0.137%), neg=0, invalid=96777 0175: dt=1.792000, rms=0.610 (0.101%), neg=0, invalid=96777 0176: dt=1.280000, rms=0.609 (0.052%), neg=0, invalid=96777 0177: dt=1.280000, rms=0.609 (0.039%), neg=0, invalid=96777 0178: dt=1.280000, rms=0.609 (0.039%), neg=0, invalid=96777 0179: dt=0.640000, rms=0.609 (0.018%), neg=0, invalid=96777 0180: dt=0.640000, rms=0.608 (0.028%), neg=0, invalid=96777 0181: dt=0.640000, rms=0.608 (0.042%), neg=0, invalid=96777 0182: dt=0.640000, rms=0.608 (0.012%), neg=0, invalid=96777 0183: dt=0.640000, rms=0.608 (0.025%), neg=0, invalid=96777 0184: dt=0.640000, rms=0.608 (0.010%), neg=0, invalid=96777 0185: dt=0.640000, rms=0.608 (0.020%), neg=0, invalid=96777 0186: dt=0.640000, rms=0.608 (0.024%), neg=0, invalid=96777 0187: dt=0.640000, rms=0.608 (0.008%), neg=0, invalid=96777 0188: dt=1.792000, rms=0.607 (0.028%), neg=0, invalid=96777 0189: dt=1.792000, rms=0.607 (0.021%), neg=0, invalid=96777 0190: dt=0.896000, rms=0.607 (0.012%), neg=0, invalid=96777 0191: dt=0.896000, rms=0.607 (0.007%), neg=0, invalid=96777 0192: dt=0.896000, rms=0.607 (0.024%), neg=0, invalid=96777 0193: dt=0.896000, rms=0.607 (0.024%), neg=0, invalid=96777 0194: dt=0.896000, rms=0.607 (0.034%), neg=0, invalid=96777 0195: dt=0.896000, rms=0.606 (0.036%), neg=0, invalid=96777 0196: dt=0.448000, rms=0.606 (0.002%), neg=0, invalid=96777 0197: dt=0.448000, rms=0.606 (0.003%), neg=0, invalid=96777 0198: dt=0.448000, rms=0.606 (0.007%), neg=0, invalid=96777 0199: dt=0.448000, rms=0.606 (0.008%), neg=0, invalid=96777 0200: dt=0.448000, rms=0.606 (0.010%), neg=0, invalid=96777 0201: dt=0.448000, rms=0.606 (0.012%), neg=0, invalid=96777 0202: dt=0.448000, rms=0.606 (0.015%), neg=0, invalid=96777 0203: dt=0.448000, rms=0.606 (0.016%), neg=0, invalid=96777 0204: dt=0.448000, rms=0.606 (0.018%), neg=0, invalid=96777 0205: dt=0.448000, rms=0.606 (0.019%), neg=0, invalid=96777 0206: dt=0.448000, rms=0.606 (0.020%), neg=0, invalid=96777 0207: dt=0.448000, rms=0.606 (-0.000%), neg=0, invalid=96777 0208: dt=0.448000, rms=0.606 (0.003%), neg=0, invalid=96777 0209: dt=0.448000, rms=0.606 (0.004%), neg=0, invalid=96777 0210: dt=1.792000, rms=0.606 (0.006%), neg=0, invalid=96777 0211: dt=1.792000, rms=0.606 (0.010%), neg=0, invalid=96777 0212: dt=1.792000, rms=0.605 (0.008%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.597, neg=0, invalid=96777 0213: dt=0.112000, rms=0.591 (1.033%), neg=0, invalid=96777 0214: dt=0.007000, rms=0.591 (0.052%), neg=0, invalid=96777 0215: dt=0.112000, rms=0.586 (0.820%), neg=0, invalid=96777 0216: dt=0.007000, rms=0.585 (0.040%), neg=0, invalid=96777 0217: dt=0.007000, rms=0.585 (0.042%), neg=0, invalid=96777 0218: dt=0.007000, rms=0.585 (0.077%), neg=0, invalid=96777 0219: dt=0.007000, rms=0.584 (0.111%), neg=0, invalid=96777 0220: dt=0.007000, rms=0.583 (0.138%), neg=0, invalid=96777 0221: dt=0.007000, rms=0.582 (0.160%), neg=0, invalid=96777 0222: dt=0.007000, rms=0.581 (0.180%), neg=0, invalid=96777 0223: dt=0.007000, rms=0.580 (0.194%), neg=0, invalid=96777 0224: dt=0.007000, rms=0.579 (0.207%), neg=0, invalid=96777 0225: dt=0.007000, rms=0.578 (0.214%), neg=0, invalid=96777 0226: dt=0.007000, rms=0.577 (0.218%), neg=0, invalid=96777 0227: dt=0.007000, rms=0.576 (0.024%), neg=0, invalid=96777 0228: dt=0.007000, rms=0.576 (0.045%), neg=0, invalid=96777 0229: dt=0.007000, rms=0.576 (0.065%), neg=0, invalid=96777 0230: dt=0.007000, rms=0.575 (0.080%), neg=0, invalid=96777 0231: dt=0.007000, rms=0.575 (0.095%), neg=0, invalid=96777 0232: dt=0.007000, rms=0.574 (0.104%), neg=0, invalid=96777 0233: dt=0.007000, rms=0.573 (0.115%), neg=0, invalid=96777 0234: dt=0.007000, rms=0.573 (0.121%), neg=0, invalid=96777 0235: dt=0.007000, rms=0.572 (0.129%), neg=0, invalid=96777 0236: dt=0.007000, rms=0.571 (0.131%), neg=0, invalid=96777 0237: dt=0.007000, rms=0.571 (0.134%), neg=0, invalid=96777 0238: dt=0.007000, rms=0.570 (0.135%), neg=0, invalid=96777 0239: dt=0.007000, rms=0.569 (0.132%), neg=0, invalid=96777 0240: dt=0.007000, rms=0.568 (0.134%), neg=0, invalid=96777 0241: dt=0.007000, rms=0.568 (0.129%), neg=0, invalid=96777 0242: dt=0.007000, rms=0.567 (0.125%), neg=0, invalid=96777 0243: dt=0.007000, rms=0.566 (0.122%), neg=0, invalid=96777 0244: dt=0.007000, rms=0.565 (0.115%), neg=0, invalid=96777 0245: dt=0.007000, rms=0.565 (0.109%), neg=0, invalid=96777 0246: dt=0.007000, rms=0.564 (0.107%), neg=0, invalid=96777 0247: dt=0.007000, rms=0.564 (0.099%), neg=0, invalid=96777 0248: dt=0.007000, rms=0.563 (0.093%), neg=0, invalid=96777 0249: dt=0.007000, rms=0.563 (0.087%), neg=0, invalid=96777 0250: dt=0.007000, rms=0.562 (0.083%), neg=0, invalid=96777 0251: dt=0.007000, rms=0.562 (0.074%), neg=0, invalid=96777 0252: dt=0.007000, rms=0.561 (0.071%), neg=0, invalid=96777 0253: dt=0.007000, rms=0.561 (0.063%), neg=0, invalid=96777 0254: dt=0.007000, rms=0.561 (0.062%), neg=0, invalid=96777 0255: dt=0.007000, rms=0.560 (0.054%), neg=0, invalid=96777 0256: dt=0.007000, rms=0.560 (0.051%), neg=0, invalid=96777 0257: dt=0.007000, rms=0.560 (0.048%), neg=0, invalid=96777 0258: dt=0.007000, rms=0.560 (0.040%), neg=0, invalid=96777 0259: dt=0.007000, rms=0.559 (0.039%), neg=0, invalid=96777 0260: dt=0.007000, rms=0.559 (0.036%), neg=0, invalid=96777 0261: dt=0.007000, rms=0.559 (0.033%), neg=0, invalid=96777 0262: dt=0.007000, rms=0.559 (0.030%), neg=0, invalid=96777 0263: dt=0.007000, rms=0.559 (0.029%), neg=0, invalid=96777 0264: dt=0.007000, rms=0.559 (0.027%), neg=0, invalid=96777 0265: dt=0.007000, rms=0.558 (0.024%), neg=0, invalid=96777 0266: dt=0.007000, rms=0.558 (0.025%), neg=0, invalid=96777 0267: dt=0.007000, rms=0.558 (0.024%), neg=0, invalid=96777 0268: dt=0.112000, rms=0.558 (0.024%), neg=0, invalid=96777 0269: dt=0.112000, rms=0.558 (0.026%), neg=0, invalid=96777 0270: dt=0.014000, rms=0.558 (0.001%), neg=0, invalid=96777 0271: dt=0.014000, rms=0.558 (0.006%), neg=0, invalid=96777 0272: dt=0.014000, rms=0.558 (0.008%), neg=0, invalid=96777 0273: dt=0.014000, rms=0.558 (0.010%), neg=0, invalid=96777 0274: dt=0.014000, rms=0.558 (0.013%), neg=0, invalid=96777 0275: dt=0.014000, rms=0.558 (0.015%), neg=0, invalid=96777 0276: dt=0.014000, rms=0.557 (0.017%), neg=0, invalid=96777 0277: dt=0.014000, rms=0.557 (0.019%), neg=0, invalid=96777 0278: dt=0.014000, rms=0.557 (0.020%), neg=0, invalid=96777 0279: dt=0.014000, rms=0.557 (0.020%), neg=0, invalid=96777 0280: dt=0.007000, rms=0.557 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.557, neg=0, invalid=96777 0281: dt=0.007000, rms=0.557 (0.029%), neg=0, invalid=96777 0282: dt=0.125492, rms=0.554 (0.502%), neg=0, invalid=96777 0283: dt=0.112103, rms=0.552 (0.322%), neg=0, invalid=96777 0284: dt=0.112000, rms=0.551 (0.237%), neg=0, invalid=96777 0285: dt=0.112000, rms=0.550 (0.178%), neg=0, invalid=96777 0286: dt=0.028000, rms=0.550 (0.033%), neg=0, invalid=96777 0287: dt=0.028000, rms=0.550 (0.030%), neg=0, invalid=96777 0288: dt=0.028000, rms=0.549 (0.060%), neg=0, invalid=96777 0289: dt=0.028000, rms=0.549 (0.078%), neg=0, invalid=96777 0290: dt=0.028000, rms=0.548 (0.091%), neg=0, invalid=96777 0291: dt=0.028000, rms=0.548 (0.014%), neg=0, invalid=96777 0292: dt=0.028000, rms=0.548 (0.031%), neg=0, invalid=96777 0293: dt=0.028000, rms=0.548 (0.038%), neg=0, invalid=96777 0294: dt=0.028000, rms=0.548 (0.044%), neg=0, invalid=96777 0295: dt=0.028000, rms=0.548 (0.049%), neg=0, invalid=96777 0296: dt=0.028000, rms=0.547 (0.050%), neg=0, invalid=96777 0297: dt=0.028000, rms=0.547 (0.046%), neg=0, invalid=96777 0298: dt=0.028000, rms=0.547 (0.042%), neg=0, invalid=96777 0299: dt=0.028000, rms=0.547 (0.034%), neg=0, invalid=96777 0300: dt=0.028000, rms=0.546 (0.029%), neg=0, invalid=96777 0301: dt=0.028000, rms=0.546 (0.016%), neg=0, invalid=96777 0302: dt=0.028000, rms=0.546 (0.013%), neg=0, invalid=96777 0303: dt=0.000000, rms=0.546 (-0.002%), neg=0, invalid=96777 label assignment complete, 0 changed (0.00%) ********************************************************************************************* ********************************************************************************************* ********************************************************************************************* ********************* ALLOWING NEGATIVE NODES IN DEFORMATION ******************************** ********************************************************************************************* ********************************************************************************************* ********************************************************************************************* **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.544, neg=0, invalid=96777 0304: dt=13.872000, rms=0.544 (0.012%), neg=0, invalid=96777 0305: dt=5.780000, rms=0.544 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.544, neg=0, invalid=96777 0306: dt=110.976000, rms=0.543 (0.070%), neg=0, invalid=96777 0307: dt=73.984000, rms=0.543 (0.054%), neg=0, invalid=96777 0308: dt=73.984000, rms=0.543 (-0.015%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.543, neg=0, invalid=96777 0309: dt=31.104000, rms=0.541 (0.288%), neg=0, invalid=96777 0310: dt=25.920000, rms=0.541 (0.067%), neg=0, invalid=96777 0311: dt=25.920000, rms=0.541 (0.024%), neg=0, invalid=96777 0312: dt=25.920000, rms=0.541 (-0.121%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.541, neg=0, invalid=96777 0313: dt=36.288000, rms=0.538 (0.502%), neg=0, invalid=96777 0314: dt=36.288000, rms=0.537 (0.275%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0315: dt=25.920000, rms=0.536 (0.071%), neg=0, invalid=96777 0316: dt=25.920000, rms=0.536 (0.128%), neg=0, invalid=96777 0317: dt=25.920000, rms=0.535 (0.135%), neg=0, invalid=96777 0318: dt=25.920000, rms=0.534 (0.167%), neg=0, invalid=96777 0319: dt=25.920000, rms=0.533 (0.147%), neg=0, invalid=96777 0320: dt=25.920000, rms=0.532 (0.160%), neg=0, invalid=96777 0321: dt=25.920000, rms=0.532 (0.144%), neg=0, invalid=96777 0322: dt=25.920000, rms=0.531 (0.124%), neg=0, invalid=96777 0323: dt=25.920000, rms=0.530 (0.112%), neg=0, invalid=96777 0324: dt=124.416000, rms=0.530 (0.063%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 12 iterations, nbhd size=2, neg = 0 0325: dt=124.416000, rms=0.530 (-0.168%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.531, neg=0, invalid=96777 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0326: dt=25.600000, rms=0.527 (0.683%), neg=0, invalid=96777 iter 0, gcam->neg = 8 after 39 iterations, nbhd size=1, neg = 0 0327: dt=25.600000, rms=0.526 (0.230%), neg=0, invalid=96777 iter 0, gcam->neg = 44 after 32 iterations, nbhd size=2, neg = 0 0328: dt=25.600000, rms=0.525 (0.106%), neg=0, invalid=96777 iter 0, gcam->neg = 8 after 55 iterations, nbhd size=4, neg = 0 0329: dt=25.600000, rms=0.523 (0.430%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0330: dt=25.600000, rms=0.522 (0.155%), neg=0, invalid=96777 iter 0, gcam->neg = 92 after 64 iterations, nbhd size=4, neg = 0 0331: dt=25.600000, rms=0.520 (0.331%), neg=0, invalid=96777 iter 0, gcam->neg = 34 after 35 iterations, nbhd size=3, neg = 0 0332: dt=25.600000, rms=0.518 (0.398%), neg=0, invalid=96777 iter 0, gcam->neg = 12 after 7 iterations, nbhd size=1, neg = 0 0333: dt=25.600000, rms=0.516 (0.438%), neg=0, invalid=96777 iter 0, gcam->neg = 28 after 16 iterations, nbhd size=2, neg = 0 0334: dt=25.600000, rms=0.514 (0.377%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0335: dt=25.600000, rms=0.513 (0.239%), neg=0, invalid=96777 iter 0, gcam->neg = 54 after 70 iterations, nbhd size=3, neg = 0 0336: dt=25.600000, rms=0.511 (0.329%), neg=0, invalid=96777 iter 0, gcam->neg = 31 after 50 iterations, nbhd size=1, neg = 0 0337: dt=25.600000, rms=0.511 (-0.034%), neg=0, invalid=96777 0338: dt=25.600000, rms=0.510 (0.266%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0339: dt=11.200000, rms=0.509 (0.138%), neg=0, invalid=96777 0340: dt=11.200000, rms=0.509 (0.073%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0341: dt=11.200000, rms=0.508 (0.075%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0342: dt=11.200000, rms=0.508 (0.085%), neg=0, invalid=96777 iter 0, gcam->neg = 15 after 200 iterations, nbhd size=1, neg = 3 starting rms=0.007, neg=3, removing folds in lattice.... iter 1, dt=0.002000: new neg 0, old_neg 3, delta 3, rms=0.005 (19.162%) 0343: dt=11.200000, rms=0.508 (0.044%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 200 iterations, nbhd size=1, neg = 3 starting rms=0.006, neg=3, removing folds in lattice.... iter 1, dt=0.002000: new neg 0, old_neg 3, delta 3, rms=0.005 (17.054%) 0344: dt=11.200000, rms=0.507 (0.043%), neg=0, invalid=96777 iter 0, gcam->neg = 7 after 60 iterations, nbhd size=1, neg = 0 0345: dt=32.000000, rms=0.507 (0.033%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.507, neg=0, invalid=96777 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0346: dt=38.400000, rms=0.504 (0.703%), neg=0, invalid=96777 0347: dt=8.901408, rms=0.502 (0.229%), neg=0, invalid=96777 0348: dt=8.901408, rms=0.502 (0.166%), neg=0, invalid=96777 0349: dt=8.901408, rms=0.501 (0.201%), neg=0, invalid=96777 0350: dt=8.901408, rms=0.500 (0.206%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 0351: dt=8.901408, rms=0.499 (0.207%), neg=0, invalid=96777 0352: dt=8.901408, rms=0.498 (0.187%), neg=0, invalid=96777 0353: dt=8.901408, rms=0.497 (0.159%), neg=0, invalid=96777 0354: dt=8.901408, rms=0.496 (0.106%), neg=0, invalid=96777 0355: dt=8.901408, rms=0.496 (0.041%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0356: dt=38.400000, rms=0.495 (0.164%), neg=0, invalid=96777 0357: dt=11.200000, rms=0.495 (0.082%), neg=0, invalid=96777 0358: dt=11.200000, rms=0.495 (0.037%), neg=0, invalid=96777 0359: dt=11.200000, rms=0.494 (0.050%), neg=0, invalid=96777 0360: dt=11.200000, rms=0.494 (0.094%), neg=0, invalid=96777 0361: dt=11.200000, rms=0.494 (0.074%), neg=0, invalid=96777 0362: dt=11.200000, rms=0.493 (0.065%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.502, neg=0, invalid=96777 0363: dt=1.789474, rms=0.502 (0.020%), neg=0, invalid=96777 0364: dt=0.864000, rms=0.502 (0.006%), neg=0, invalid=96777 0365: dt=0.864000, rms=0.502 (-0.003%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.502, neg=0, invalid=96777 0366: dt=2.880000, rms=0.502 (0.037%), neg=0, invalid=96777 0367: dt=2.304000, rms=0.502 (0.017%), neg=0, invalid=96777 0368: dt=2.304000, rms=0.502 (0.005%), neg=0, invalid=96777 0369: dt=2.304000, rms=0.502 (-0.024%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.516, neg=0, invalid=96777 0370: dt=0.325000, rms=0.516 (0.015%), neg=0, invalid=96777 0371: dt=0.112000, rms=0.516 (0.005%), neg=0, invalid=96777 0372: dt=0.112000, rms=0.516 (-0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.516, neg=0, invalid=96777 iter 0, gcam->neg = 5 after 0 iterations, nbhd size=0, neg = 0 0373: dt=1.416667, rms=0.514 (0.241%), neg=0, invalid=96777 0374: dt=0.768000, rms=0.514 (0.036%), neg=0, invalid=96777 iter 0, gcam->neg = 8 after 1 iterations, nbhd size=0, neg = 0 0375: dt=0.768000, rms=0.514 (0.006%), neg=0, invalid=96777 iter 0, gcam->neg = 10 after 7 iterations, nbhd size=1, neg = 0 0376: dt=0.768000, rms=0.514 (-0.076%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.501, neg=0, invalid=96777 iter 0, gcam->neg = 1203 after 35 iterations, nbhd size=4, neg = 0 0377: dt=2.201235, rms=0.449 (10.234%), neg=0, invalid=96777 0378: dt=0.000438, rms=0.449 (0.001%), neg=0, invalid=96777 0379: dt=0.000438, rms=0.449 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.449, neg=0, invalid=96777 0380: dt=0.003000, rms=0.449 (0.004%), neg=0, invalid=96777 0381: dt=0.001750, rms=0.449 (0.002%), neg=0, invalid=96777 0382: dt=0.001750, rms=0.449 (0.000%), neg=0, invalid=96777 0383: dt=0.001750, rms=0.449 (-0.000%), neg=0, invalid=96777 label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.426, neg=0, invalid=96777 0384: dt=0.000000, rms=0.427 (-0.155%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.427, neg=0, invalid=96777 0385: dt=73.984000, rms=0.427 (0.020%), neg=0, invalid=96777 0386: dt=73.984000, rms=0.427 (0.002%), neg=0, invalid=96777 0387: dt=73.984000, rms=0.427 (0.002%), neg=0, invalid=96777 0388: dt=73.984000, rms=0.427 (-0.001%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.427, neg=0, invalid=96777 0389: dt=0.000000, rms=0.427 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.427, neg=0, invalid=96777 iter 0, gcam->neg = 1 after 12 iterations, nbhd size=2, neg = 0 0390: dt=82.944000, rms=0.427 (0.053%), neg=0, invalid=96777 0391: dt=145.152000, rms=0.426 (0.095%), neg=0, invalid=96777 0392: dt=25.920000, rms=0.426 (0.017%), neg=0, invalid=96777 0393: dt=25.920000, rms=0.426 (0.006%), neg=0, invalid=96777 0394: dt=25.920000, rms=0.426 (0.009%), neg=0, invalid=96777 0395: dt=25.920000, rms=0.426 (0.015%), neg=0, invalid=96777 0396: dt=25.920000, rms=0.426 (0.025%), neg=0, invalid=96777 0397: dt=25.920000, rms=0.426 (0.028%), neg=0, invalid=96777 0398: dt=25.920000, rms=0.426 (0.023%), neg=0, invalid=96777 0399: dt=25.920000, rms=0.426 (0.016%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.427, neg=0, invalid=96777 iter 0, gcam->neg = 1 after 21 iterations, nbhd size=3, neg = 0 0400: dt=6.400000, rms=0.427 (0.043%), neg=0, invalid=96777 0401: dt=1.200000, rms=0.427 (0.001%), neg=0, invalid=96777 0402: dt=1.200000, rms=0.427 (0.002%), neg=0, invalid=96777 0403: dt=1.200000, rms=0.427 (0.001%), neg=0, invalid=96777 0404: dt=1.200000, rms=0.427 (-0.007%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.427, neg=0, invalid=96777 iter 0, gcam->neg = 2 after 42 iterations, nbhd size=2, neg = 0 0405: dt=44.800000, rms=0.424 (0.568%), neg=0, invalid=96777 0406: dt=0.031463, rms=0.424 (0.000%), neg=0, invalid=96777 0407: dt=0.031463, rms=0.424 (0.000%), neg=0, invalid=96777 0408: dt=0.031463, rms=0.424 (0.001%), neg=0, invalid=96777 0409: dt=0.031463, rms=0.424 (0.001%), neg=0, invalid=96777 0410: dt=0.031463, rms=0.424 (0.002%), neg=0, invalid=96777 0411: dt=0.031463, rms=0.424 (0.002%), neg=0, invalid=96777 0412: dt=0.031463, rms=0.424 (0.002%), neg=0, invalid=96777 0413: dt=0.031463, rms=0.424 (0.003%), neg=0, invalid=96777 0414: dt=0.031463, rms=0.424 (0.003%), neg=0, invalid=96777 0415: dt=0.031463, rms=0.424 (0.003%), neg=0, invalid=96777 0416: dt=0.031463, rms=0.424 (0.003%), neg=0, invalid=96777 0417: dt=0.031463, rms=0.424 (0.003%), neg=0, invalid=96777 0418: dt=0.031463, rms=0.424 (0.003%), neg=0, invalid=96777 0419: dt=0.031463, rms=0.424 (0.003%), neg=0, invalid=96777 0420: dt=0.031463, rms=0.424 (0.004%), neg=0, invalid=96777 0421: dt=0.031463, rms=0.424 (0.004%), neg=0, invalid=96777 0422: dt=0.031463, rms=0.424 (0.004%), neg=0, invalid=96777 0423: dt=0.031463, rms=0.424 (0.004%), neg=0, invalid=96777 0424: dt=0.031463, rms=0.424 (0.004%), neg=0, invalid=96777 0425: dt=0.031463, rms=0.424 (0.004%), neg=0, invalid=96777 0426: dt=0.031463, rms=0.424 (0.004%), neg=0, invalid=96777 0427: dt=0.031463, rms=0.424 (0.004%), neg=0, invalid=96777 0428: dt=0.031463, rms=0.424 (0.004%), neg=0, invalid=96777 0429: dt=0.031463, rms=0.424 (0.004%), neg=0, invalid=96777 0430: dt=0.031463, rms=0.424 (0.004%), neg=0, invalid=96777 iter 0, gcam->neg = 10 after 200 iterations, nbhd size=4, neg = 1 starting rms=0.006, neg=1, removing folds in lattice.... iter 1, dt=0.000039: new neg 0, old_neg 1, delta 1, rms=0.005 (21.245%) 0431: dt=44.800000, rms=0.423 (0.270%), neg=0, invalid=96777 0432: dt=4.800000, rms=0.423 (0.051%), neg=0, invalid=96777 0433: dt=4.800000, rms=0.422 (0.040%), neg=0, invalid=96777 0434: dt=4.800000, rms=0.422 (0.059%), neg=0, invalid=96777 0435: dt=4.800000, rms=0.422 (0.063%), neg=0, invalid=96777 0436: dt=4.800000, rms=0.422 (0.068%), neg=0, invalid=96777 0437: dt=4.800000, rms=0.421 (0.080%), neg=0, invalid=96777 0438: dt=4.800000, rms=0.421 (0.090%), neg=0, invalid=96777 0439: dt=4.800000, rms=0.421 (0.089%), neg=0, invalid=96777 0440: dt=4.800000, rms=0.420 (0.084%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 0441: dt=38.400000, rms=0.420 (0.067%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.424, neg=0, invalid=96777 0442: dt=0.252000, rms=0.424 (0.002%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 16 iterations, nbhd size=2, neg = 0 0443: dt=3.456000, rms=0.424 (0.044%), neg=0, invalid=96777 0444: dt=0.015750, rms=0.424 (0.000%), neg=0, invalid=96777 0445: dt=0.015750, rms=0.424 (0.000%), neg=0, invalid=96777 0446: dt=0.015750, rms=0.424 (0.000%), neg=0, invalid=96777 0447: dt=0.015750, rms=0.424 (0.000%), neg=0, invalid=96777 0448: dt=0.015750, rms=0.424 (0.000%), neg=0, invalid=96777 0449: dt=0.015750, rms=0.424 (0.000%), neg=0, invalid=96777 0450: dt=0.015750, rms=0.424 (0.000%), neg=0, invalid=96777 0451: dt=0.015750, rms=0.424 (0.000%), neg=0, invalid=96777 0452: dt=0.015750, rms=0.424 (0.001%), neg=0, invalid=96777 0453: dt=0.015750, rms=0.424 (0.001%), neg=0, invalid=96777 0454: dt=0.015750, rms=0.424 (0.001%), neg=0, invalid=96777 0455: dt=0.015750, rms=0.424 (0.001%), neg=0, invalid=96777 0456: dt=0.015750, rms=0.424 (0.001%), neg=0, invalid=96777 0457: dt=0.015750, rms=0.424 (0.001%), neg=0, invalid=96777 0458: dt=0.015750, rms=0.424 (0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.424, neg=0, invalid=96777 iter 0, gcam->neg = 12 after 23 iterations, nbhd size=3, neg = 0 0459: dt=13.824000, rms=0.423 (0.279%), neg=0, invalid=96777 0460: dt=0.144000, rms=0.423 (0.001%), neg=0, invalid=96777 0461: dt=0.144000, rms=0.423 (0.003%), neg=0, invalid=96777 0462: dt=0.144000, rms=0.423 (0.006%), neg=0, invalid=96777 0463: dt=0.144000, rms=0.423 (0.009%), neg=0, invalid=96777 0464: dt=0.144000, rms=0.423 (0.011%), neg=0, invalid=96777 0465: dt=0.144000, rms=0.423 (0.013%), neg=0, invalid=96777 0466: dt=0.144000, rms=0.423 (0.015%), neg=0, invalid=96777 0467: dt=0.144000, rms=0.422 (0.016%), neg=0, invalid=96777 0468: dt=0.144000, rms=0.422 (0.017%), neg=0, invalid=96777 0469: dt=0.144000, rms=0.422 (0.017%), neg=0, invalid=96777 0470: dt=0.144000, rms=0.422 (0.018%), neg=0, invalid=96777 0471: dt=0.144000, rms=0.422 (0.018%), neg=0, invalid=96777 0472: dt=0.144000, rms=0.422 (0.018%), neg=0, invalid=96777 0473: dt=0.144000, rms=0.422 (0.017%), neg=0, invalid=96777 iter 0, gcam->neg = 132 after 56 iterations, nbhd size=3, neg = 0 0474: dt=36.864000, rms=0.421 (0.206%), neg=0, invalid=96777 0475: dt=0.000090, rms=0.421 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.429, neg=0, invalid=96777 0476: dt=0.000000, rms=0.429 (0.000%), neg=0, invalid=96777 0477: dt=0.100000, rms=0.429 (-0.110%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.429, neg=0, invalid=96777 0478: dt=0.000000, rms=0.429 (0.000%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.416, neg=0, invalid=96777 iter 0, gcam->neg = 729 after 41 iterations, nbhd size=4, neg = 0 0479: dt=0.951238, rms=0.400 (3.820%), neg=0, invalid=96777 0480: dt=0.000063, rms=0.400 (0.003%), neg=0, invalid=96777 0481: dt=0.000063, rms=0.400 (0.001%), neg=0, invalid=96777 0482: dt=0.000063, rms=0.400 (0.001%), neg=0, invalid=96777 0483: dt=0.000063, rms=0.400 (0.000%), neg=0, invalid=96777 0484: dt=0.000000, rms=0.400 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.400, neg=0, invalid=96777 0485: dt=0.000750, rms=0.400 (0.001%), neg=0, invalid=96777 0486: dt=0.001500, rms=0.400 (0.000%), neg=0, invalid=96777 0487: dt=0.001500, rms=0.400 (0.000%), neg=0, invalid=96777 0488: dt=0.001500, rms=0.400 (0.001%), neg=0, invalid=96777 0489: dt=0.001500, rms=0.400 (0.001%), neg=0, invalid=96777 0490: dt=0.001500, rms=0.400 (0.001%), neg=0, invalid=96777 0491: dt=0.001500, rms=0.400 (0.002%), neg=0, invalid=96777 0492: dt=0.001500, rms=0.400 (0.002%), neg=0, invalid=96777 0493: dt=0.001500, rms=0.400 (0.003%), neg=0, invalid=96777 0494: dt=0.001500, rms=0.400 (0.003%), neg=0, invalid=96777 0495: dt=0.001500, rms=0.400 (0.003%), neg=0, invalid=96777 0496: dt=0.001500, rms=0.400 (0.003%), neg=0, invalid=96777 0497: dt=0.001500, rms=0.400 (0.003%), neg=0, invalid=96777 0498: dt=0.001500, rms=0.400 (0.003%), neg=0, invalid=96777 0499: dt=0.001500, rms=0.400 (0.003%), neg=0, invalid=96777 writing output transformation to transforms/talairach.m3z... GCAMwrite registration took 3 hours, 36 minutes and 22 seconds. #-------------------------------------- #@# Remove Neck Mon Dec 12 03:15:54 EST 2016 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2008-03-26.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... removing structures at least 25 mm from brain... 11417661 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 1 minutes and 52 seconds. #-------------------------------------- #@# SkullLTA Mon Dec 12 03:17:47 EST 2016 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull_2.lta ======= NUMBER OF OPENMP THREADS = 12 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 5 using previously computed transform transforms/talairach.lta reading 1 input volumes... logging results to talairach_with_skull_2.log reading '/usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu_noneck.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=6.0 skull bounding box = (46, 56, 15) --> (211, 231, 222) using (101, 114, 119) as brain centroid... mean wm in atlas = 126, using box (81,92,93) --> (121, 135,144) to find MRI wm before smoothing, mri peak at 104 after smoothing, mri peak at 104, scaling input intensities by 1.212 scaling channel 0 by 1.21154 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.2, old_max_log_p =-4.3 (thresh=-4.3) 0.997 -0.041 0.011 1.894; 0.035 1.243 0.195 -76.096; -0.017 -0.223 1.065 22.418; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.2, old_max_log_p =-4.2 (thresh=-4.2) 1.072 -0.044 0.012 -7.396; 0.039 1.356 0.058 -69.839; -0.011 -0.055 1.000 5.541; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.2, old_max_log_p =-4.2 (thresh=-4.2) 1.072 -0.044 0.012 -7.396; 0.039 1.356 0.058 -69.839; -0.011 -0.055 1.000 5.541; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.2, old_max_log_p =-4.2 (thresh=-4.2) 1.050 -0.034 -0.052 1.104; 0.038 1.324 0.121 -74.114; 0.059 -0.151 1.030 6.112; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.2, old_max_log_p =-4.2 (thresh=-4.1) 1.069 -0.034 -0.053 -1.233; 0.039 1.293 0.152 -75.434; 0.056 -0.191 1.007 14.306; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.1, old_max_log_p =-4.2 (thresh=-4.1) 1.073 -0.024 -0.052 -2.816; 0.030 1.292 0.152 -74.165; 0.056 -0.191 1.009 14.091; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 1.073 -0.024 -0.052 -2.816; 0.030 1.292 0.152 -74.165; 0.056 -0.191 1.009 14.091; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3481 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.07327 -0.02366 -0.05196 -2.81608; 0.03016 1.29195 0.15194 -74.16481; 0.05633 -0.19114 1.00905 14.09093; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.07327 -0.02366 -0.05196 -2.81608; 0.03016 1.29195 0.15194 -74.16481; 0.05633 -0.19114 1.00905 14.09093; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.073 -0.024 -0.052 -2.816; 0.030 1.292 0.152 -74.165; 0.056 -0.191 1.009 14.091; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -4.1 (old=-4.3) transform before final EM align: 1.073 -0.024 -0.052 -2.816; 0.030 1.292 0.152 -74.165; 0.056 -0.191 1.009 14.091; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 382743 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.07327 -0.02366 -0.05196 -2.81608; 0.03016 1.29195 0.15194 -74.16481; 0.05633 -0.19114 1.00905 14.09093; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.07327 -0.02366 -0.05196 -2.81608; 0.03016 1.29195 0.15194 -74.16481; 0.05633 -0.19114 1.00905 14.09093; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = 4.5 tol 0.000000 final transform: 1.073 -0.024 -0.052 -2.816; 0.030 1.292 0.152 -74.165; 0.056 -0.191 1.009 14.091; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull_2.lta... registration took 1249 minutes and 21 seconds. #-------------------------------------- #@# SubCort Seg Tue Dec 13 00:07:08 EST 2016 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz sysname Linux hostname TRON machine x86_64 setenv SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL cd /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz relabeling unlikely voxels more than 0.5 sigmas from label mean, with sigma=0.0mm, wsize=0mm renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes... reading classifier array from /usr/local/freesurfer/average/RB_all_2008-03-26.gca... reading input volume from norm.mgz... average std[0] = 6.9 reading transform from transforms/talairach.m3z... Atlas used for the 3D morph was /usr/local/freesurfer/average/RB_all_2008-03-26.gca average std = 6.9 using min determinant for regularization = 4.7 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15151 (27) mri peak = 0.08205 (15) Left_Lateral_Ventricle (4): linear fit = 0.58 x + 0.0 (4874 voxels, overlap=0.069) Left_Lateral_Ventricle (4): linear fit = 0.58 x + 0.0 (4874 voxels, peak = 16), gca=15.8 gca peak = 0.14982 (20) mri peak = 0.10149 (16) Right_Lateral_Ventricle (43): linear fit = 0.64 x + 0.0 (3853 voxels, overlap=0.414) Right_Lateral_Ventricle (43): linear fit = 0.64 x + 0.0 (3853 voxels, peak = 13), gca=12.9 gca peak = 0.28003 (97) mri peak = 0.08765 (97) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (251 voxels, overlap=0.991) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (251 voxels, peak = 96), gca=95.5 gca peak = 0.18160 (96) mri peak = 0.10024 (93) Left_Pallidum (13): linear fit = 0.95 x + 0.0 (201 voxels, overlap=0.943) Left_Pallidum (13): linear fit = 0.95 x + 0.0 (201 voxels, peak = 92), gca=91.7 gca peak = 0.27536 (62) mri peak = 0.07144 (66) Right_Hippocampus (53): linear fit = 1.11 x + 0.0 (366 voxels, overlap=1.014) Right_Hippocampus (53): linear fit = 1.11 x + 0.0 (366 voxels, peak = 69), gca=68.5 gca peak = 0.32745 (63) mri peak = 0.07895 (67) Left_Hippocampus (17): linear fit = 1.05 x + 0.0 (228 voxels, overlap=1.016) Left_Hippocampus (17): linear fit = 1.05 x + 0.0 (228 voxels, peak = 66), gca=66.5 gca peak = 0.08597 (105) mri peak = 0.07072 (105) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (28768 voxels, overlap=0.881) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (28768 voxels, peak = 104), gca=104.5 gca peak = 0.09209 (106) mri peak = 0.06859 (107) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (28679 voxels, overlap=0.814) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (28679 voxels, peak = 108), gca=107.6 gca peak = 0.07826 (63) mri peak = 0.04160 (68) Left_Cerebral_Cortex (3): linear fit = 1.10 x + 0.0 (6739 voxels, overlap=0.693) Left_Cerebral_Cortex (3): linear fit = 1.10 x + 0.0 (6739 voxels, peak = 69), gca=69.0 gca peak = 0.08598 (64) mri peak = 0.03284 (74) Right_Cerebral_Cortex (42): linear fit = 1.11 x + 0.0 (7796 voxels, overlap=0.717) Right_Cerebral_Cortex (42): linear fit = 1.11 x + 0.0 (7796 voxels, peak = 71), gca=70.7 gca peak = 0.24164 (71) mri peak = 0.09408 (78) Right_Caudate (50): linear fit = 1.03 x + 0.0 (655 voxels, overlap=1.011) Right_Caudate (50): linear fit = 1.03 x + 0.0 (655 voxels, peak = 73), gca=73.5 gca peak = 0.18227 (75) mri peak = 0.09911 (79) Left_Caudate (11): linear fit = 1.01 x + 0.0 (503 voxels, overlap=1.000) Left_Caudate (11): linear fit = 1.01 x + 0.0 (503 voxels, peak = 76), gca=76.1 gca peak = 0.10629 (62) mri peak = 0.03436 (13) Left_Cerebellum_Cortex (8): linear fit = 1.17 x + 0.0 (2464 voxels, overlap=0.001) Left_Cerebellum_Cortex (8): linear fit = 1.17 x + 0.0 (2464 voxels, peak = 73), gca=72.8 gca peak = 0.11668 (59) mri peak = 0.03634 (66) Right_Cerebellum_Cortex (47): linear fit = 1.12 x + 0.0 (2415 voxels, overlap=0.347) Right_Cerebellum_Cortex (47): linear fit = 1.12 x + 0.0 (2415 voxels, peak = 66), gca=66.4 gca peak = 0.17849 (88) mri peak = 0.07071 (97) Left_Cerebellum_White_Matter (7): linear fit = 1.11 x + 0.0 (2489 voxels, overlap=0.254) Left_Cerebellum_White_Matter (7): linear fit = 1.11 x + 0.0 (2489 voxels, peak = 97), gca=97.2 gca peak = 0.16819 (86) mri peak = 0.07727 (94) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (2627 voxels, overlap=0.695) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (2627 voxels, peak = 92), gca=91.6 gca peak = 0.41688 (64) mri peak = 0.10000 (68) Left_Amygdala (18): linear fit = 1.11 x + 0.0 (188 voxels, overlap=0.776) Left_Amygdala (18): linear fit = 1.11 x + 0.0 (188 voxels, peak = 71), gca=70.7 gca peak = 0.42394 (62) mri peak = 0.10180 (64) Right_Amygdala (54): linear fit = 1.05 x + 0.0 (167 voxels, overlap=1.030) Right_Amygdala (54): linear fit = 1.05 x + 0.0 (167 voxels, peak = 65), gca=65.4 gca peak = 0.10041 (96) mri peak = 0.06169 (93) Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (3097 voxels, overlap=0.995) Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (3097 voxels, peak = 94), gca=93.6 gca peak = 0.13978 (88) mri peak = 0.07221 (88) Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (3110 voxels, overlap=0.951) Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (3110 voxels, peak = 87), gca=86.7 gca peak = 0.08514 (81) mri peak = 0.07538 (84) Left_Putamen (12): linear fit = 1.02 x + 0.0 (1297 voxels, overlap=0.830) Left_Putamen (12): linear fit = 1.02 x + 0.0 (1297 voxels, peak = 83), gca=83.0 gca peak = 0.09624 (82) mri peak = 0.06071 (88) Right_Putamen (51): linear fit = 1.02 x + 0.0 (1463 voxels, overlap=1.000) Right_Putamen (51): linear fit = 1.02 x + 0.0 (1463 voxels, peak = 84), gca=84.0 gca peak = 0.07543 (88) mri peak = 0.06324 (89) Brain_Stem (16): linear fit = 1.03 x + 0.0 (8701 voxels, overlap=0.765) Brain_Stem (16): linear fit = 1.03 x + 0.0 (8701 voxels, peak = 91), gca=91.1 gca peak = 0.12757 (95) mri peak = 0.07180 (96) Right_VentralDC (60): linear fit = 1.04 x + 0.0 (600 voxels, overlap=0.681) Right_VentralDC (60): linear fit = 1.04 x + 0.0 (600 voxels, peak = 99), gca=99.3 gca peak = 0.17004 (92) mri peak = 0.07450 (97) Left_VentralDC (28): linear fit = 1.04 x + 0.0 (714 voxels, overlap=0.888) Left_VentralDC (28): linear fit = 1.04 x + 0.0 (714 voxels, peak = 96), gca=96.1 gca peak = 0.21361 (36) mri peak = 0.12341 (21) Third_Ventricle (14): linear fit = 0.61 x + 0.0 (226 voxels, overlap=0.056) Third_Ventricle (14): linear fit = 0.61 x + 0.0 (226 voxels, peak = 22), gca=21.8 gca peak = 0.26069 (23) mri peak = 0.10758 (22) Fourth_Ventricle (15): linear fit = 0.89 x + 0.0 (199 voxels, overlap=0.554) Fourth_Ventricle (15): linear fit = 0.89 x + 0.0 (199 voxels, peak = 21), gca=20.6 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.31795 (35) gca peak Third_Ventricle = 0.21361 (36) gca peak CSF = 0.14367 (38) gca peak Left_Accumbens_area = 0.57033 (70) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65201 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.31129 (32) gca peak Right_Accumbens_area = 0.30219 (72) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.72939 (42) gca peak WM_hypointensities = 0.14821 (82) gca peak non_WM_hypointensities = 0.10354 (53) gca peak Optic_Chiasm = 0.34849 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.09 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.71 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.23042 (16) mri peak = 0.08205 (15) Left_Lateral_Ventricle (4): linear fit = 1.03 x + 0.0 (4874 voxels, overlap=0.985) Left_Lateral_Ventricle (4): linear fit = 1.03 x + 0.0 (4874 voxels, peak = 17), gca=16.6 gca peak = 0.22433 (13) mri peak = 0.10149 (16) Right_Lateral_Ventricle (43): linear fit = 1.03 x + 0.0 (3853 voxels, overlap=0.983) Right_Lateral_Ventricle (43): linear fit = 1.03 x + 0.0 (3853 voxels, peak = 13), gca=13.5 gca peak = 0.32721 (96) mri peak = 0.08765 (97) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (251 voxels, overlap=1.029) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (251 voxels, peak = 96), gca=96.5 gca peak = 0.16969 (93) mri peak = 0.10024 (93) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (201 voxels, overlap=1.003) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (201 voxels, peak = 93), gca=92.5 gca peak = 0.22439 (68) mri peak = 0.07144 (66) Right_Hippocampus (53): linear fit = 0.95 x + 0.0 (366 voxels, overlap=1.008) Right_Hippocampus (53): linear fit = 0.95 x + 0.0 (366 voxels, peak = 65), gca=64.9 gca peak = 0.24797 (70) mri peak = 0.07895 (67) Left_Hippocampus (17): linear fit = 1.04 x + 0.0 (228 voxels, overlap=1.013) Left_Hippocampus (17): linear fit = 1.04 x + 0.0 (228 voxels, peak = 73), gca=73.1 gca peak = 0.08412 (106) mri peak = 0.07072 (105) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (28768 voxels, overlap=0.883) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (28768 voxels, peak = 106), gca=106.0 gca peak = 0.08754 (107) mri peak = 0.06859 (107) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (28679 voxels, overlap=0.832) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (28679 voxels, peak = 106), gca=106.5 gca peak = 0.07194 (69) mri peak = 0.04160 (68) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (6739 voxels, overlap=0.904) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (6739 voxels, peak = 68), gca=68.0 gca peak = 0.07923 (70) mri peak = 0.03284 (74) Right_Cerebral_Cortex (42): linear fit = 1.03 x + 0.0 (7796 voxels, overlap=0.830) Right_Cerebral_Cortex (42): linear fit = 1.03 x + 0.0 (7796 voxels, peak = 72), gca=72.4 gca peak = 0.28591 (76) mri peak = 0.09408 (78) Right_Caudate (50): linear fit = 1.01 x + 0.0 (655 voxels, overlap=1.013) Right_Caudate (50): linear fit = 1.01 x + 0.0 (655 voxels, peak = 77), gca=77.1 gca peak = 0.18130 (76) mri peak = 0.09911 (79) Left_Caudate (11): linear fit = 1.00 x + 0.0 (503 voxels, overlap=1.000) Left_Caudate (11): linear fit = 1.00 x + 0.0 (503 voxels, peak = 76), gca=76.0 gca peak = 0.09058 (73) mri peak = 0.03436 (13) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (2464 voxels, overlap=0.001) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (2464 voxels, peak = 72), gca=71.9 gca peak = 0.11773 (67) mri peak = 0.03634 (66) Right_Cerebellum_Cortex (47): linear fit = 1.03 x + 0.0 (2415 voxels, overlap=0.815) Right_Cerebellum_Cortex (47): linear fit = 1.03 x + 0.0 (2415 voxels, peak = 69), gca=69.3 gca peak = 0.15790 (97) mri peak = 0.07071 (97) Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (2489 voxels, overlap=0.985) Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (2489 voxels, peak = 98), gca=98.5 gca peak = 0.16064 (92) mri peak = 0.07727 (94) Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (2627 voxels, overlap=0.985) Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (2627 voxels, peak = 93), gca=93.4 gca peak = 0.32835 (70) mri peak = 0.10000 (68) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (188 voxels, overlap=1.027) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (188 voxels, peak = 70), gca=70.0 gca peak = 0.34625 (66) mri peak = 0.10180 (64) Right_Amygdala (54): linear fit = 0.96 x + 0.0 (167 voxels, overlap=1.027) Right_Amygdala (54): linear fit = 0.96 x + 0.0 (167 voxels, peak = 64), gca=63.7 gca peak = 0.10391 (92) mri peak = 0.06169 (93) Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (3097 voxels, overlap=0.957) Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (3097 voxels, peak = 94), gca=94.3 gca peak = 0.10538 (84) mri peak = 0.07221 (88) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (3110 voxels, overlap=0.989) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (3110 voxels, peak = 85), gca=85.3 gca peak = 0.08410 (83) mri peak = 0.07538 (84) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1297 voxels, overlap=0.923) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1297 voxels, peak = 83), gca=82.6 gca peak = 0.10509 (78) mri peak = 0.06071 (88) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1463 voxels, overlap=0.991) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1463 voxels, peak = 78), gca=77.6 gca peak = 0.07195 (88) mri peak = 0.06324 (89) Brain_Stem (16): linear fit = 1.00 x + 0.0 (8701 voxels, overlap=0.837) Brain_Stem (16): linear fit = 1.00 x + 0.0 (8701 voxels, peak = 88), gca=87.6 gca peak = 0.13200 (99) mri peak = 0.07180 (96) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (600 voxels, overlap=0.813) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (600 voxels, peak = 99), gca=99.5 gca peak = 0.13348 (97) mri peak = 0.07450 (97) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (714 voxels, overlap=0.933) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (714 voxels, peak = 97), gca=97.5 gca peak = 0.22155 (27) mri peak = 0.12341 (21) Third_Ventricle (14): linear fit = 0.81 x + 0.0 (226 voxels, overlap=0.620) Third_Ventricle (14): linear fit = 0.81 x + 0.0 (226 voxels, peak = 22), gca=22.0 gca peak = 0.22371 (21) mri peak = 0.10758 (22) Fourth_Ventricle (15): linear fit = 0.89 x + 0.0 (199 voxels, overlap=0.750) Fourth_Ventricle (15): linear fit = 0.89 x + 0.0 (199 voxels, peak = 19), gca=18.8 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.30831 (37) gca peak CSF = 0.19356 (27) gca peak Left_Accumbens_area = 0.57297 (71) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.63670 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.28428 (35) gca peak Right_Accumbens_area = 0.35686 (74) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.45329 (31) gca peak WM_hypointensities = 0.17489 (82) gca peak non_WM_hypointensities = 0.12291 (53) gca peak Optic_Chiasm = 0.34840 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.94 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 26465 gm and wm labels changed (%21 to gray, %79 to white out of all changed labels) 325 hippocampal voxels changed. 1 amygdala voxels changed. pass 1: 93465 changed. image ll: -2.220, PF=1.000 pass 2: 14732 changed. image ll: -2.217, PF=1.000 pass 3: 4249 changed. relabeling voxels using optimal scale estimates iter 1: nchanged = 9667 iter 2: nchanged = 1666 iter 3: nchanged = 520 iter 4: nchanged = 224 iter 5: nchanged = 99 iter 6: nchanged = 46 writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 178 minutes and 12 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/transforms/cc_up.lta 1_S_5002 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/transforms/cc_up.lta reading aseg from /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/aseg.auto_noCCseg.mgz reading norm from /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/norm.mgz 10210 voxels in left wm, 21154 in right wm, xrange [125, 131] searching rotation angles z=[-8 6], y=[-7 7] 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 searching scale 1 Z rot 6.2 global minimum found at slice 128.6, rotations (0.37, -0.51) final transformation (x=128.6, yr=0.366, zr=-0.509): 1.000 0.009 0.006 -2.272; -0.009 1.000 -0.000 6.153; -0.006 -0.000 1.000 43.824; 0.000 0.000 0.000 1.000; updating x range to be [125, 129] in xformed coordinates best xformed slice 127 cc center is found at 127 142 187 eigenvectors: -0.001 -0.000 1.000; 0.056 -0.998 -0.000; 0.998 0.056 0.001; error in mid anterior detected - correcting... writing aseg with callosum to /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/aseg.auto.mgz... corpus callosum matter segmentation took 0.8 minutes #-------------------------------------- #@# Merge ASeg Tue Dec 13 03:06:08 EST 2016 cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# Intensity Normalization2 Tue Dec 13 03:06:08 EST 2016 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri mri_normalize -b 20 -n 5 -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz using control point with intensity 20.0 below target. performing 3d normalization 5 times using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 422 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 5 times --------------------------------- 3d normalization pass 1 of 5 white matter peak found at 111 white matter peak found at 109 gm peak at 82 (82), valley at 35 (35) csf peak at 17, setting threshold to 60 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 5 white matter peak found at 111 white matter peak found at 110 gm peak at 77 (77), valley at 57 (57) csf peak at 17, setting threshold to 57 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 3 of 5 white matter peak found at 111 white matter peak found at 110 gm peak at 77 (77), valley at 57 (57) csf peak at 17, setting threshold to 57 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 4 of 5 white matter peak found at 111 white matter peak found at 110 gm peak at 77 (77), valley at 57 (57) csf peak at 17, setting threshold to 57 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 5 of 5 white matter peak found at 111 white matter peak found at 110 gm peak at 77 (77), valley at 57 (57) csf peak at 17, setting threshold to 57 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 10 minutes and 20 seconds. #-------------------------------------------- #@# Mask BFS Tue Dec 13 03:16:31 EST 2016 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1480751 voxels in mask (pct= 8.83) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Tue Dec 13 03:16:34 EST 2016 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 (106.0): 107.4 +- 5.6 [80.0 --> 125.0] GM (70.0) : 67.4 +- 11.3 [30.0 --> 96.0] setting bottom of white matter range to 78.8 setting top of gray matter range to 90.1 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 11714 sparsely connected voxels removed... thickening thin strands.... 20 segments, 4358 filled 707 bright non-wm voxels segmented. 7153 diagonally connected voxels added... white matter segmentation took 3.6 minutes writing output to wm.seg.mgz... mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 1.09 minutes reading wm segmentation from wm.seg.mgz... 53 voxels added to wm to prevent paths from MTL structures to cortex 1861 additional wm voxels added 0 additional wm voxels added SEG EDIT: 64902 voxels turned on, 34229 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+): 40 found - 40 modified | TOTAL: 40 pass 2 (xy+): 0 found - 40 modified | TOTAL: 40 pass 1 (xy-): 37 found - 37 modified | TOTAL: 77 pass 2 (xy-): 0 found - 37 modified | TOTAL: 77 pass 1 (yz+): 56 found - 56 modified | TOTAL: 133 pass 2 (yz+): 0 found - 56 modified | TOTAL: 133 pass 1 (yz-): 34 found - 34 modified | TOTAL: 167 pass 2 (yz-): 0 found - 34 modified | TOTAL: 167 pass 1 (xz+): 40 found - 40 modified | TOTAL: 207 pass 2 (xz+): 0 found - 40 modified | TOTAL: 207 pass 1 (xz-): 23 found - 23 modified | TOTAL: 230 pass 2 (xz-): 0 found - 23 modified | TOTAL: 230 Iteration Number : 1 pass 1 (+++): 53 found - 53 modified | TOTAL: 53 pass 2 (+++): 0 found - 53 modified | TOTAL: 53 pass 1 (+++): 42 found - 42 modified | TOTAL: 95 pass 2 (+++): 0 found - 42 modified | TOTAL: 95 pass 1 (+++): 38 found - 38 modified | TOTAL: 133 pass 2 (+++): 0 found - 38 modified | TOTAL: 133 pass 1 (+++): 56 found - 56 modified | TOTAL: 189 pass 2 (+++): 0 found - 56 modified | TOTAL: 189 Iteration Number : 1 pass 1 (++): 213 found - 213 modified | TOTAL: 213 pass 2 (++): 0 found - 213 modified | TOTAL: 213 pass 1 (+-): 220 found - 220 modified | TOTAL: 433 pass 2 (+-): 0 found - 220 modified | TOTAL: 433 pass 1 (--): 195 found - 195 modified | TOTAL: 628 pass 2 (--): 0 found - 195 modified | TOTAL: 628 pass 1 (-+): 201 found - 201 modified | TOTAL: 829 pass 2 (-+): 0 found - 201 modified | TOTAL: 829 Iteration Number : 2 pass 1 (xy+): 22 found - 22 modified | TOTAL: 22 pass 2 (xy+): 0 found - 22 modified | TOTAL: 22 pass 1 (xy-): 18 found - 18 modified | TOTAL: 40 pass 2 (xy-): 0 found - 18 modified | TOTAL: 40 pass 1 (yz+): 24 found - 24 modified | TOTAL: 64 pass 2 (yz+): 0 found - 24 modified | TOTAL: 64 pass 1 (yz-): 17 found - 17 modified | TOTAL: 81 pass 2 (yz-): 0 found - 17 modified | TOTAL: 81 pass 1 (xz+): 22 found - 22 modified | TOTAL: 103 pass 2 (xz+): 0 found - 22 modified | TOTAL: 103 pass 1 (xz-): 14 found - 14 modified | TOTAL: 117 pass 2 (xz-): 0 found - 14 modified | TOTAL: 117 Iteration Number : 2 pass 1 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 pass 1 (+++): 1 found - 1 modified | TOTAL: 5 pass 2 (+++): 0 found - 1 modified | TOTAL: 5 pass 1 (+++): 3 found - 3 modified | TOTAL: 8 pass 2 (+++): 0 found - 3 modified | TOTAL: 8 pass 1 (+++): 7 found - 7 modified | TOTAL: 15 pass 2 (+++): 0 found - 7 modified | TOTAL: 15 Iteration Number : 2 pass 1 (++): 6 found - 6 modified | TOTAL: 6 pass 2 (++): 0 found - 6 modified | TOTAL: 6 pass 1 (+-): 11 found - 11 modified | TOTAL: 17 pass 2 (+-): 0 found - 11 modified | TOTAL: 17 pass 1 (--): 13 found - 13 modified | TOTAL: 30 pass 2 (--): 0 found - 13 modified | TOTAL: 30 pass 1 (-+): 14 found - 14 modified | TOTAL: 44 pass 2 (-+): 0 found - 14 modified | TOTAL: 44 Iteration Number : 3 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 4 found - 4 modified | TOTAL: 7 pass 2 (xy-): 0 found - 4 modified | TOTAL: 7 pass 1 (yz+): 0 found - 0 modified | TOTAL: 7 pass 1 (yz-): 1 found - 1 modified | TOTAL: 8 pass 2 (yz-): 0 found - 1 modified | TOTAL: 8 pass 1 (xz+): 3 found - 3 modified | TOTAL: 11 pass 2 (xz+): 0 found - 3 modified | TOTAL: 11 pass 1 (xz-): 1 found - 1 modified | TOTAL: 12 pass 2 (xz-): 0 found - 1 modified | TOTAL: 12 Iteration Number : 3 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 (+++): 3 found - 3 modified | TOTAL: 5 pass 2 (+++): 0 found - 3 modified | TOTAL: 5 pass 1 (+++): 0 found - 0 modified | TOTAL: 5 Iteration Number : 3 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 (--): 2 found - 2 modified | TOTAL: 4 pass 2 (--): 0 found - 2 modified | TOTAL: 4 pass 1 (-+): 3 found - 3 modified | TOTAL: 7 pass 2 (-+): 0 found - 3 modified | TOTAL: 7 Iteration Number : 4 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 1 found - 1 modified | TOTAL: 3 pass 2 (xy-): 0 found - 1 modified | TOTAL: 3 pass 1 (yz+): 0 found - 0 modified | TOTAL: 3 pass 1 (yz-): 0 found - 0 modified | TOTAL: 3 pass 1 (xz+): 0 found - 0 modified | TOTAL: 3 pass 1 (xz-): 1 found - 1 modified | TOTAL: 4 pass 2 (xz-): 0 found - 1 modified | TOTAL: 4 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 Iteration Number : 5 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 : 5 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 5 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 1452 (out of 585893: 0.247827) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Tue Dec 13 03:21:24 EST 2016 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 0.997 -0.041 0.011 1.894; 0.032 1.156 0.181 -62.337; -0.016 -0.210 1.001 27.429; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 0.997 -0.041 0.011 1.894; 0.032 1.156 0.181 -62.337; -0.016 -0.210 1.001 27.429; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1521 (min = 350, max = 1400), aspect = 0.53 (min = 0.10, max = 0.75) need search nearby using seed (126, 100, 97), TAL = (2.0, -31.0, 28.0) talairach voxel to voxel transform 1.002 0.032 -0.017 0.568; -0.029 0.836 -0.151 56.327; 0.010 0.176 0.967 -15.583; 0.000 0.000 0.000 1.000; segmentation indicates cc at (126, 100, 97) --> (2.0, -31.0, 28.0) done. writing output to filled.mgz... filling took 1.2 minutes talairach cc position changed to (2.00, -31.00, 28.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, -31.00, 28.00) SRC: (110.31, 122.13, 96.78) search lh wm seed point around talairach space (-16.00, -31.00, 28.00), SRC: (146.38, 121.07, 97.13) 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 Tue Dec 13 03:22:39 EST 2016 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 3 found - 3 modified | TOTAL: 4 pass 2 (xy-): 0 found - 3 modified | TOTAL: 4 pass 1 (yz+): 3 found - 3 modified | TOTAL: 7 pass 2 (yz+): 0 found - 3 modified | TOTAL: 7 pass 1 (yz-): 1 found - 1 modified | TOTAL: 8 pass 2 (yz-): 0 found - 1 modified | TOTAL: 8 pass 1 (xz+): 1 found - 1 modified | TOTAL: 9 pass 2 (xz+): 0 found - 1 modified | TOTAL: 9 pass 1 (xz-): 3 found - 3 modified | TOTAL: 12 pass 2 (xz-): 0 found - 3 modified | TOTAL: 12 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 (-+): 1 found - 1 modified | TOTAL: 4 pass 2 (-+): 0 found - 1 modified | TOTAL: 4 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 = 16 (out of 277010: 0.005776) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 30: 14 vertices, 20 faces slice 40: 3464 vertices, 3659 faces slice 50: 11894 vertices, 12198 faces slice 60: 22083 vertices, 22453 faces slice 70: 33695 vertices, 34133 faces slice 80: 45526 vertices, 45918 faces slice 90: 57467 vertices, 57942 faces slice 100: 69795 vertices, 70297 faces slice 110: 82158 vertices, 82690 faces slice 120: 94072 vertices, 94613 faces slice 130: 105185 vertices, 105703 faces slice 140: 115266 vertices, 115727 faces slice 150: 123228 vertices, 123634 faces slice 160: 130645 vertices, 131045 faces slice 170: 136838 vertices, 137209 faces slice 180: 141879 vertices, 142229 faces slice 190: 144636 vertices, 144873 faces slice 200: 144870 vertices, 145058 faces slice 210: 144870 vertices, 145058 faces slice 220: 144870 vertices, 145058 faces slice 230: 144870 vertices, 145058 faces slice 240: 144870 vertices, 145058 faces slice 250: 144870 vertices, 145058 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 144870 voxel in cpt #1: X=-188 [v=144870,e=435174,f=290116] located at (-27.815939, -24.998068, -0.043687) For the whole surface: X=-188 [v=144870,e=435174,f=290116] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Tue Dec 13 03:22:57 EST 2016 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Tue Dec 13 03:23:04 EST 2016 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/scripts avg radius = 46.9 mm, total surface area = 73027 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.8 minutes Not saving sulc step 000: RMS=0.117 (target=0.015) step 005: RMS=0.088 (target=0.015) step 010: RMS=0.072 (target=0.015) step 015: RMS=0.063 (target=0.015) step 020: RMS=0.058 (target=0.015) step 025: RMS=0.055 (target=0.015) step 030: RMS=0.050 (target=0.015) step 035: RMS=0.048 (target=0.015) step 040: RMS=0.047 (target=0.015) step 045: RMS=0.045 (target=0.015) step 050: RMS=0.044 (target=0.015) step 055: RMS=0.043 (target=0.015) step 060: RMS=0.043 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Tue Dec 13 03:23:50 EST 2016 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.96 +- 0.58 (0.00-->8.66) (max @ vno 64629 --> 65765) face area 0.02 +- 0.03 (-0.38-->0.71) scaling brain by 0.315... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.459, avgs=0 005/300: dt: 0.9000, rms radial error=176.200, avgs=0 010/300: dt: 0.9000, rms radial error=175.644, avgs=0 015/300: dt: 0.9000, rms radial error=174.915, avgs=0 020/300: dt: 0.9000, rms radial error=174.084, avgs=0 025/300: dt: 0.9000, rms radial error=173.196, avgs=0 030/300: dt: 0.9000, rms radial error=172.276, avgs=0 035/300: dt: 0.9000, rms radial error=171.340, avgs=0 040/300: dt: 0.9000, rms radial error=170.397, avgs=0 045/300: dt: 0.9000, rms radial error=169.451, avgs=0 050/300: dt: 0.9000, rms radial error=168.506, avgs=0 055/300: dt: 0.9000, rms radial error=167.563, avgs=0 060/300: dt: 0.9000, rms radial error=166.625, avgs=0 065/300: dt: 0.9000, rms radial error=165.691, avgs=0 070/300: dt: 0.9000, rms radial error=164.762, avgs=0 075/300: dt: 0.9000, rms radial error=163.840, avgs=0 080/300: dt: 0.9000, rms radial error=162.923, avgs=0 085/300: dt: 0.9000, rms radial error=162.011, avgs=0 090/300: dt: 0.9000, rms radial error=161.103, avgs=0 095/300: dt: 0.9000, rms radial error=160.200, avgs=0 100/300: dt: 0.9000, rms radial error=159.301, avgs=0 105/300: dt: 0.9000, rms radial error=158.408, avgs=0 110/300: dt: 0.9000, rms radial error=157.519, avgs=0 115/300: dt: 0.9000, rms radial error=156.636, avgs=0 120/300: dt: 0.9000, rms radial error=155.757, avgs=0 125/300: dt: 0.9000, rms radial error=154.883, avgs=0 130/300: dt: 0.9000, rms radial error=154.014, avgs=0 135/300: dt: 0.9000, rms radial error=153.149, avgs=0 140/300: dt: 0.9000, rms radial error=152.289, avgs=0 145/300: dt: 0.9000, rms radial error=151.434, avgs=0 150/300: dt: 0.9000, rms radial error=150.583, avgs=0 155/300: dt: 0.9000, rms radial error=149.737, avgs=0 160/300: dt: 0.9000, rms radial error=148.896, avgs=0 165/300: dt: 0.9000, rms radial error=148.059, avgs=0 170/300: dt: 0.9000, rms radial error=147.227, avgs=0 175/300: dt: 0.9000, rms radial error=146.399, avgs=0 180/300: dt: 0.9000, rms radial error=145.576, avgs=0 185/300: dt: 0.9000, rms radial error=144.758, avgs=0 190/300: dt: 0.9000, rms radial error=143.944, avgs=0 195/300: dt: 0.9000, rms radial error=143.134, avgs=0 200/300: dt: 0.9000, rms radial error=142.329, avgs=0 205/300: dt: 0.9000, rms radial error=141.528, avgs=0 210/300: dt: 0.9000, rms radial error=140.732, avgs=0 215/300: dt: 0.9000, rms radial error=139.940, avgs=0 220/300: dt: 0.9000, rms radial error=139.153, avgs=0 225/300: dt: 0.9000, rms radial error=138.370, avgs=0 230/300: dt: 0.9000, rms radial error=137.591, avgs=0 235/300: dt: 0.9000, rms radial error=136.816, avgs=0 240/300: dt: 0.9000, rms radial error=136.046, avgs=0 245/300: dt: 0.9000, rms radial error=135.280, avgs=0 250/300: dt: 0.9000, rms radial error=134.519, avgs=0 255/300: dt: 0.9000, rms radial error=133.761, avgs=0 260/300: dt: 0.9000, rms radial error=133.008, avgs=0 265/300: dt: 0.9000, rms radial error=132.259, avgs=0 270/300: dt: 0.9000, rms radial error=131.514, avgs=0 275/300: dt: 0.9000, rms radial error=130.773, avgs=0 280/300: dt: 0.9000, rms radial error=130.037, avgs=0 285/300: dt: 0.9000, rms radial error=129.305, avgs=0 290/300: dt: 0.9000, rms radial error=128.576, avgs=0 295/300: dt: 0.9000, rms radial error=127.852, avgs=0 300/300: dt: 0.9000, rms radial error=127.132, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 17036.25 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 = 2891.38 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00002 epoch 3 (K=160.0), pass 1, starting sse = 319.86 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/10 = 0.00532 epoch 4 (K=640.0), pass 1, starting sse = 28.04 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.08/12 = 0.00650 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.09 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Tue Dec 13 03:29:14 EST 2016 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 1_S_5002 lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ before topology correction, eno=-188 (nv=144870, nf=290116, ne=435174, g=95) 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 9 iterations marking ambiguous vertices... 9726 ambiguous faces found in tessellation segmenting defects... 124 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 23 into 22 -merging segment 27 into 22 -merging segment 118 into 114 -merging segment 117 into 115 120 defects to be corrected 0 vertices coincident reading input surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.5075 (-4.7537) -vertex loglikelihood: -6.6560 (-3.3280) -normal dot loglikelihood: -3.5049 (-3.5049) -quad curv loglikelihood: -6.6669 (-3.3335) Total Loglikelihood : -26.3353 CORRECTING DEFECT 0 (vertices=75, convex hull=113) After retessellation of defect 0, euler #=-116 (138741,413421,274564) : difference with theory (-117) = -1 CORRECTING DEFECT 1 (vertices=11, convex hull=26) After retessellation of defect 1, euler #=-115 (138743,413432,274574) : difference with theory (-116) = -1 CORRECTING DEFECT 2 (vertices=18, convex hull=68) After retessellation of defect 2, euler #=-114 (138754,413489,274621) : difference with theory (-115) = -1 CORRECTING DEFECT 3 (vertices=23, convex hull=58) After retessellation of defect 3, euler #=-113 (138767,413549,274669) : difference with theory (-114) = -1 CORRECTING DEFECT 4 (vertices=73, convex hull=102) After retessellation of defect 4, euler #=-112 (138783,413642,274747) : difference with theory (-113) = -1 CORRECTING DEFECT 5 (vertices=18, convex hull=24) After retessellation of defect 5, euler #=-111 (138787,413661,274763) : difference with theory (-112) = -1 CORRECTING DEFECT 6 (vertices=9, convex hull=20) After retessellation of defect 6, euler #=-110 (138788,413670,274772) : difference with theory (-111) = -1 CORRECTING DEFECT 7 (vertices=24, convex hull=66) After retessellation of defect 7, euler #=-109 (138802,413740,274829) : difference with theory (-110) = -1 CORRECTING DEFECT 8 (vertices=34, convex hull=73) After retessellation of defect 8, euler #=-108 (138824,413832,274900) : difference with theory (-109) = -1 CORRECTING DEFECT 9 (vertices=25, convex hull=61) After retessellation of defect 9, euler #=-107 (138836,413893,274950) : difference with theory (-108) = -1 CORRECTING DEFECT 10 (vertices=47, convex hull=56) After retessellation of defect 10, euler #=-106 (138850,413961,275005) : difference with theory (-107) = -1 CORRECTING DEFECT 11 (vertices=28, convex hull=29) After retessellation of defect 11, euler #=-105 (138852,413973,275016) : difference with theory (-106) = -1 CORRECTING DEFECT 12 (vertices=16, convex hull=42) After retessellation of defect 12, euler #=-104 (138858,414007,275045) : difference with theory (-105) = -1 CORRECTING DEFECT 13 (vertices=88, convex hull=114) After retessellation of defect 13, euler #=-103 (138909,414211,275199) : difference with theory (-104) = -1 CORRECTING DEFECT 14 (vertices=33, convex hull=30) After retessellation of defect 14, euler #=-102 (138913,414234,275219) : difference with theory (-103) = -1 CORRECTING DEFECT 15 (vertices=26, convex hull=34) After retessellation of defect 15, euler #=-101 (138917,414259,275241) : difference with theory (-102) = -1 CORRECTING DEFECT 16 (vertices=26, convex hull=45) After retessellation of defect 16, euler #=-100 (138931,414319,275288) : difference with theory (-101) = -1 CORRECTING DEFECT 17 (vertices=16, convex hull=22) After retessellation of defect 17, euler #=-99 (138933,414332,275300) : difference with theory (-100) = -1 CORRECTING DEFECT 18 (vertices=19, convex hull=60) After retessellation of defect 18, euler #=-98 (138946,414394,275350) : difference with theory (-99) = -1 CORRECTING DEFECT 19 (vertices=122, convex hull=29) After retessellation of defect 19, euler #=-97 (138951,414417,275369) : difference with theory (-98) = -1 CORRECTING DEFECT 20 (vertices=19, convex hull=54) After retessellation of defect 20, euler #=-96 (138960,414463,275407) : difference with theory (-97) = -1 CORRECTING DEFECT 21 (vertices=62, convex hull=91) After retessellation of defect 21, euler #=-95 (138990,414589,275504) : difference with theory (-96) = -1 CORRECTING DEFECT 22 (vertices=811, convex hull=547) After retessellation of defect 22, euler #=-95 (139153,415379,276131) : difference with theory (-95) = 0 CORRECTING DEFECT 23 (vertices=35, convex hull=41) After retessellation of defect 23, euler #=-94 (139157,415404,276153) : difference with theory (-94) = 0 CORRECTING DEFECT 24 (vertices=28, convex hull=68) After retessellation of defect 24, euler #=-93 (139172,415474,276209) : difference with theory (-93) = 0 CORRECTING DEFECT 25 (vertices=7, convex hull=27) After retessellation of defect 25, euler #=-92 (139175,415491,276224) : difference with theory (-92) = 0 CORRECTING DEFECT 26 (vertices=51, convex hull=57) After retessellation of defect 26, euler #=-91 (139184,415540,276265) : difference with theory (-91) = 0 CORRECTING DEFECT 27 (vertices=318, convex hull=210) After retessellation of defect 27, euler #=-90 (139249,415835,276496) : difference with theory (-90) = 0 CORRECTING DEFECT 28 (vertices=80, convex hull=62) After retessellation of defect 28, euler #=-89 (139265,415908,276554) : difference with theory (-89) = 0 CORRECTING DEFECT 29 (vertices=42, convex hull=105) After retessellation of defect 29, euler #=-88 (139291,416029,276650) : difference with theory (-88) = 0 CORRECTING DEFECT 30 (vertices=42, convex hull=68) After retessellation of defect 30, euler #=-87 (139307,416106,276712) : difference with theory (-87) = 0 CORRECTING DEFECT 31 (vertices=63, convex hull=113) After retessellation of defect 31, euler #=-86 (139349,416282,276847) : difference with theory (-86) = 0 CORRECTING DEFECT 32 (vertices=29, convex hull=22) After retessellation of defect 32, euler #=-85 (139354,416303,276864) : difference with theory (-85) = 0 CORRECTING DEFECT 33 (vertices=41, convex hull=33) After retessellation of defect 33, euler #=-84 (139360,416333,276889) : difference with theory (-84) = 0 CORRECTING DEFECT 34 (vertices=32, convex hull=71) After retessellation of defect 34, euler #=-83 (139382,416429,276964) : difference with theory (-83) = 0 CORRECTING DEFECT 35 (vertices=10, convex hull=15) After retessellation of defect 35, euler #=-82 (139383,416435,276970) : difference with theory (-82) = 0 CORRECTING DEFECT 36 (vertices=104, convex hull=57) After retessellation of defect 36, euler #=-81 (139395,416502,277026) : difference with theory (-81) = 0 CORRECTING DEFECT 37 (vertices=117, convex hull=103) After retessellation of defect 37, euler #=-80 (139456,416729,277193) : difference with theory (-80) = 0 CORRECTING DEFECT 38 (vertices=9, convex hull=26) After retessellation of defect 38, euler #=-79 (139457,416739,277203) : difference with theory (-79) = 0 CORRECTING DEFECT 39 (vertices=17, convex hull=17) After retessellation of defect 39, euler #=-78 (139457,416742,277207) : difference with theory (-78) = 0 CORRECTING DEFECT 40 (vertices=35, convex hull=76) After retessellation of defect 40, euler #=-77 (139476,416833,277280) : difference with theory (-77) = 0 CORRECTING DEFECT 41 (vertices=9, convex hull=24) After retessellation of defect 41, euler #=-76 (139480,416852,277296) : difference with theory (-76) = 0 CORRECTING DEFECT 42 (vertices=20, convex hull=58) After retessellation of defect 42, euler #=-75 (139490,416898,277333) : difference with theory (-75) = 0 CORRECTING DEFECT 43 (vertices=21, convex hull=53) After retessellation of defect 43, euler #=-74 (139500,416947,277373) : difference with theory (-74) = 0 CORRECTING DEFECT 44 (vertices=70, convex hull=101) After retessellation of defect 44, euler #=-73 (139516,417043,277454) : difference with theory (-73) = 0 CORRECTING DEFECT 45 (vertices=48, convex hull=69) After retessellation of defect 45, euler #=-72 (139545,417154,277537) : difference with theory (-72) = 0 CORRECTING DEFECT 46 (vertices=93, convex hull=112) After retessellation of defect 46, euler #=-71 (139573,417289,277645) : difference with theory (-71) = 0 CORRECTING DEFECT 47 (vertices=25, convex hull=32) After retessellation of defect 47, euler #=-70 (139576,417310,277664) : difference with theory (-70) = 0 CORRECTING DEFECT 48 (vertices=71, convex hull=27) After retessellation of defect 48, euler #=-69 (139582,417336,277685) : difference with theory (-69) = 0 CORRECTING DEFECT 49 (vertices=27, convex hull=56) After retessellation of defect 49, euler #=-68 (139594,417393,277731) : difference with theory (-68) = 0 CORRECTING DEFECT 50 (vertices=73, convex hull=83) After retessellation of defect 50, euler #=-67 (139623,417516,277826) : difference with theory (-67) = 0 CORRECTING DEFECT 51 (vertices=38, convex hull=59) After retessellation of defect 51, euler #=-66 (139640,417588,277882) : difference with theory (-66) = 0 CORRECTING DEFECT 52 (vertices=21, convex hull=50) After retessellation of defect 52, euler #=-65 (139654,417650,277931) : difference with theory (-65) = 0 CORRECTING DEFECT 53 (vertices=62, convex hull=75) After retessellation of defect 53, euler #=-64 (139678,417753,278011) : difference with theory (-64) = 0 CORRECTING DEFECT 54 (vertices=39, convex hull=55) After retessellation of defect 54, euler #=-63 (139689,417808,278056) : difference with theory (-63) = 0 CORRECTING DEFECT 55 (vertices=13, convex hull=22) After retessellation of defect 55, euler #=-62 (139690,417818,278066) : difference with theory (-62) = 0 CORRECTING DEFECT 56 (vertices=147, convex hull=57) After retessellation of defect 56, euler #=-61 (139699,417866,278106) : difference with theory (-61) = 0 CORRECTING DEFECT 57 (vertices=9, convex hull=22) After retessellation of defect 57, euler #=-60 (139700,417877,278117) : difference with theory (-60) = 0 CORRECTING DEFECT 58 (vertices=39, convex hull=77) After retessellation of defect 58, euler #=-59 (139722,417976,278195) : difference with theory (-59) = 0 CORRECTING DEFECT 59 (vertices=26, convex hull=50) After retessellation of defect 59, euler #=-58 (139733,418028,278237) : difference with theory (-58) = 0 CORRECTING DEFECT 60 (vertices=6, convex hull=15) After retessellation of defect 60, euler #=-57 (139734,418033,278242) : difference with theory (-57) = 0 CORRECTING DEFECT 61 (vertices=7, convex hull=12) After retessellation of defect 61, euler #=-56 (139736,418041,278249) : difference with theory (-56) = 0 CORRECTING DEFECT 62 (vertices=112, convex hull=108) After retessellation of defect 62, euler #=-56 (139761,418168,278351) : difference with theory (-55) = 1 CORRECTING DEFECT 63 (vertices=7, convex hull=13) After retessellation of defect 63, euler #=-55 (139761,418172,278356) : difference with theory (-54) = 1 CORRECTING DEFECT 64 (vertices=20, convex hull=50) After retessellation of defect 64, euler #=-54 (139772,418221,278395) : difference with theory (-53) = 1 CORRECTING DEFECT 65 (vertices=64, convex hull=80) After retessellation of defect 65, euler #=-53 (139795,418327,278479) : difference with theory (-52) = 1 CORRECTING DEFECT 66 (vertices=357, convex hull=119) After retessellation of defect 66, euler #=-52 (139847,418536,278637) : difference with theory (-51) = 1 CORRECTING DEFECT 67 (vertices=18, convex hull=42) After retessellation of defect 67, euler #=-51 (139856,418576,278669) : difference with theory (-50) = 1 CORRECTING DEFECT 68 (vertices=17, convex hull=23) After retessellation of defect 68, euler #=-50 (139859,418591,278682) : difference with theory (-49) = 1 CORRECTING DEFECT 69 (vertices=13, convex hull=21) After retessellation of defect 69, euler #=-49 (139861,418606,278696) : difference with theory (-48) = 1 CORRECTING DEFECT 70 (vertices=8, convex hull=15) After retessellation of defect 70, euler #=-48 (139863,418614,278703) : difference with theory (-47) = 1 CORRECTING DEFECT 71 (vertices=16, convex hull=29) After retessellation of defect 71, euler #=-47 (139868,418634,278719) : difference with theory (-46) = 1 CORRECTING DEFECT 72 (vertices=31, convex hull=29) After retessellation of defect 72, euler #=-46 (139875,418663,278742) : difference with theory (-45) = 1 CORRECTING DEFECT 73 (vertices=66, convex hull=60) After retessellation of defect 73, euler #=-45 (139892,418734,278797) : difference with theory (-44) = 1 CORRECTING DEFECT 74 (vertices=12, convex hull=23) After retessellation of defect 74, euler #=-44 (139894,418745,278807) : difference with theory (-43) = 1 CORRECTING DEFECT 75 (vertices=5, convex hull=20) After retessellation of defect 75, euler #=-43 (139895,418754,278816) : difference with theory (-42) = 1 CORRECTING DEFECT 76 (vertices=32, convex hull=58) After retessellation of defect 76, euler #=-42 (139910,418821,278869) : difference with theory (-41) = 1 CORRECTING DEFECT 77 (vertices=34, convex hull=42) After retessellation of defect 77, euler #=-41 (139919,418864,278904) : difference with theory (-40) = 1 CORRECTING DEFECT 78 (vertices=52, convex hull=29) After retessellation of defect 78, euler #=-40 (139926,418898,278932) : difference with theory (-39) = 1 CORRECTING DEFECT 79 (vertices=49, convex hull=76) After retessellation of defect 79, euler #=-39 (139948,418992,279005) : difference with theory (-38) = 1 CORRECTING DEFECT 80 (vertices=19, convex hull=27) After retessellation of defect 80, euler #=-38 (139954,419015,279023) : difference with theory (-37) = 1 CORRECTING DEFECT 81 (vertices=147, convex hull=74) After retessellation of defect 81, euler #=-37 (139962,419065,279066) : difference with theory (-36) = 1 CORRECTING DEFECT 82 (vertices=38, convex hull=73) After retessellation of defect 82, euler #=-36 (139971,419125,279118) : difference with theory (-35) = 1 CORRECTING DEFECT 83 (vertices=128, convex hull=74) After retessellation of defect 83, euler #=-35 (139979,419184,279170) : difference with theory (-34) = 1 CORRECTING DEFECT 84 (vertices=81, convex hull=89) After retessellation of defect 84, euler #=-34 (140021,419350,279295) : difference with theory (-33) = 1 CORRECTING DEFECT 85 (vertices=24, convex hull=28) After retessellation of defect 85, euler #=-33 (140028,419379,279318) : difference with theory (-32) = 1 CORRECTING DEFECT 86 (vertices=41, convex hull=62) After retessellation of defect 86, euler #=-32 (140043,419446,279371) : difference with theory (-31) = 1 CORRECTING DEFECT 87 (vertices=51, convex hull=70) After retessellation of defect 87, euler #=-31 (140062,419535,279442) : difference with theory (-30) = 1 CORRECTING DEFECT 88 (vertices=33, convex hull=71) After retessellation of defect 88, euler #=-30 (140083,419625,279512) : difference with theory (-29) = 1 CORRECTING DEFECT 89 (vertices=12, convex hull=25) After retessellation of defect 89, euler #=-29 (140084,419638,279525) : difference with theory (-28) = 1 CORRECTING DEFECT 90 (vertices=35, convex hull=38) After retessellation of defect 90, euler #=-28 (140093,419674,279553) : difference with theory (-27) = 1 CORRECTING DEFECT 91 (vertices=66, convex hull=73) After retessellation of defect 91, euler #=-27 (140126,419802,279649) : difference with theory (-26) = 1 CORRECTING DEFECT 92 (vertices=29, convex hull=38) After retessellation of defect 92, euler #=-26 (140142,419866,279698) : difference with theory (-25) = 1 CORRECTING DEFECT 93 (vertices=36, convex hull=28) After retessellation of defect 93, euler #=-25 (140147,419888,279716) : difference with theory (-24) = 1 CORRECTING DEFECT 94 (vertices=7, convex hull=14) After retessellation of defect 94, euler #=-24 (140149,419898,279725) : difference with theory (-23) = 1 CORRECTING DEFECT 95 (vertices=27, convex hull=40) After retessellation of defect 95, euler #=-23 (140153,419920,279744) : difference with theory (-22) = 1 CORRECTING DEFECT 96 (vertices=42, convex hull=65) After retessellation of defect 96, euler #=-22 (140168,419988,279798) : difference with theory (-21) = 1 CORRECTING DEFECT 97 (vertices=29, convex hull=68) After retessellation of defect 97, euler #=-21 (140185,420066,279860) : difference with theory (-20) = 1 CORRECTING DEFECT 98 (vertices=76, convex hull=98) After retessellation of defect 98, euler #=-20 (140228,420246,279998) : difference with theory (-19) = 1 CORRECTING DEFECT 99 (vertices=25, convex hull=24) After retessellation of defect 99, euler #=-19 (140233,420266,280014) : difference with theory (-18) = 1 CORRECTING DEFECT 100 (vertices=19, convex hull=32) Warning - incorrect dp selected!!!!(-87.260075 >= -87.260077 ) After retessellation of defect 100, euler #=-18 (140236,420286,280032) : difference with theory (-17) = 1 CORRECTING DEFECT 101 (vertices=5, convex hull=18) After retessellation of defect 101, euler #=-17 (140236,420289,280036) : difference with theory (-16) = 1 CORRECTING DEFECT 102 (vertices=19, convex hull=41) After retessellation of defect 102, euler #=-16 (140244,420327,280067) : difference with theory (-15) = 1 CORRECTING DEFECT 103 (vertices=18, convex hull=21) After retessellation of defect 103, euler #=-15 (140248,420346,280083) : difference with theory (-14) = 1 CORRECTING DEFECT 104 (vertices=39, convex hull=88) After retessellation of defect 104, euler #=-14 (140273,420457,280170) : difference with theory (-13) = 1 CORRECTING DEFECT 105 (vertices=93, convex hull=29) After retessellation of defect 105, euler #=-13 (140277,420475,280185) : difference with theory (-12) = 1 CORRECTING DEFECT 106 (vertices=30, convex hull=37) After retessellation of defect 106, euler #=-12 (140282,420504,280210) : difference with theory (-11) = 1 CORRECTING DEFECT 107 (vertices=26, convex hull=54) After retessellation of defect 107, euler #=-11 (140299,420573,280263) : difference with theory (-10) = 1 CORRECTING DEFECT 108 (vertices=30, convex hull=32) After retessellation of defect 108, euler #=-10 (140303,420593,280280) : difference with theory (-9) = 1 CORRECTING DEFECT 109 (vertices=61, convex hull=51) After retessellation of defect 109, euler #=-9 (140311,420643,280323) : difference with theory (-8) = 1 CORRECTING DEFECT 110 (vertices=23, convex hull=28) After retessellation of defect 110, euler #=-9 (140313,420662,280340) : difference with theory (-7) = 2 CORRECTING DEFECT 111 (vertices=34, convex hull=72) After retessellation of defect 111, euler #=-8 (140335,420759,280416) : difference with theory (-6) = 2 CORRECTING DEFECT 112 (vertices=47, convex hull=83) After retessellation of defect 112, euler #=-6 (140358,420863,280499) : difference with theory (-5) = 1 CORRECTING DEFECT 113 (vertices=124, convex hull=106) After retessellation of defect 113, euler #=-4 (140399,421038,280635) : difference with theory (-4) = 0 CORRECTING DEFECT 114 (vertices=30, convex hull=77) After retessellation of defect 114, euler #=-3 (140408,421095,280684) : difference with theory (-3) = 0 CORRECTING DEFECT 115 (vertices=47, convex hull=74) After retessellation of defect 115, euler #=-2 (140430,421190,280758) : difference with theory (-2) = 0 CORRECTING DEFECT 116 (vertices=44, convex hull=87) After retessellation of defect 116, euler #=-1 (140453,421295,280841) : difference with theory (-1) = 0 CORRECTING DEFECT 117 (vertices=34, convex hull=71) After retessellation of defect 117, euler #=0 (140463,421356,280893) : difference with theory (0) = 0 CORRECTING DEFECT 118 (vertices=6, convex hull=21) After retessellation of defect 118, euler #=1 (140464,421365,280902) : difference with theory (1) = 0 CORRECTING DEFECT 119 (vertices=31, convex hull=57) After retessellation of defect 119, euler #=2 (140473,421413,280942) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.25 (0.07-->7.71) (max @ vno 79632 --> 87546) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.25 (0.07-->7.71) (max @ vno 79632 --> 87546) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 430 mutations (36.7%), 743 crossovers (63.3%), 410 vertices were eliminated building final representation... 4397 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=140473, nf=280942, ne=421413, g=0) writing corrected surface to /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 99.3 minutes 0 defective edges removing intersecting faces 000: 475 intersecting 001: 4 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 140473 - 421413 + 280942 = 2 --> 0 holes F =2V-4: 280942 = 280946-4 (0) 2E=3F: 842826 = 842826 (0) total defect index = 0 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 34 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Tue Dec 13 05:08:41 EST 2016 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs 1_S_5002 lh only generating white matter surface not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/filled.mgz... reading volume /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/brain.finalsurfs.mgz... reading volume /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/wm.mgz... 33253 bright wm thresholded. 849 bright non-wm voxels segmented. reading original surface position from /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.orig... computing class statistics... border white: 294157 voxels (1.75%) border gray 303787 voxels (1.81%) WM (93.0): 93.7 +- 9.1 [70.0 --> 110.0] GM (79.0) : 76.6 +- 12.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 56.4 (was 70) setting MAX_BORDER_WHITE to 110.1 (was 105) setting MIN_BORDER_WHITE to 69.0 (was 85) setting MAX_CSF to 43.8 (was 40) setting MAX_GRAY to 91.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 62.7 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 31.3 (was 40) repositioning cortical surface to gray/white boundary reading volume /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.80 +- 0.24 (0.02-->4.18) (max @ vno 56457 --> 139233) face area 0.27 +- 0.13 (0.00-->2.77) mean absolute distance = 0.92 +- 1.20 5236 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=101, GM=69 mean inside = 92.8, mean outside = 73.7 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group mean border=80.3, 176 (176) missing vertices, mean dist 0.1 [1.2 (%36.3)->0.8 (%63.7))] %42 local maxima, %53 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host= TRON, 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 0.89 +- 0.28 (0.06-->5.12) (max @ vno 64259 --> 139402) face area 0.27 +- 0.14 (0.00-->2.65) mean absolute distance = 0.51 +- 0.81 5739 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5640692.0, rms=10.52 001: dt: 0.5000, sse=7212617.0, rms=7.431 (0.000%) 002: dt: 0.5000, sse=7770127.5, rms=5.599 (0.000%) 003: dt: 0.5000, sse=8335441.5, rms=4.546 (0.000%) 004: dt: 0.5000, sse=8688126.0, rms=4.024 (0.000%) 005: dt: 0.5000, sse=8891018.0, rms=3.778 (0.000%) 006: dt: 0.5000, sse=9005217.0, rms=3.657 (0.000%) 007: dt: 0.5000, sse=9052171.0, rms=3.582 (0.000%) 008: dt: 0.5000, sse=9084771.0, rms=3.532 (0.000%) rms = 3.50, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=9070802.0, rms=3.502 (0.000%) 010: dt: 0.2500, sse=6091398.5, rms=2.633 (0.000%) 011: dt: 0.2500, sse=5734364.5, rms=2.362 (0.000%) rms = 2.32, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=5476848.0, rms=2.325 (0.000%) 013: dt: 0.1250, sse=5337191.0, rms=2.236 (0.000%) rms = 2.23, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=5281086.5, rms=2.229 (0.000%) positioning took 2.4 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 mean border=83.4, 268 (87) missing vertices, mean dist -0.3 [0.6 (%65.5)->0.3 (%34.5))] %63 local maxima, %32 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host= TRON, 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 0.88 +- 0.27 (0.06-->5.35) (max @ vno 64259 --> 139402) face area 0.33 +- 0.17 (0.00-->3.55) mean absolute distance = 0.35 +- 0.47 4411 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5887798.0, rms=4.87 015: dt: 0.5000, sse=6341922.0, rms=3.352 (0.000%) rms = 3.41, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=5877400.0, rms=2.741 (0.000%) 017: dt: 0.2500, sse=5704069.0, rms=2.322 (0.000%) 018: dt: 0.2500, sse=5577905.5, rms=2.134 (0.000%) 019: dt: 0.2500, sse=5533833.5, rms=2.048 (0.000%) rms = 2.00, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=5496133.5, rms=2.002 (0.000%) 021: dt: 0.1250, sse=5397765.0, rms=1.932 (0.000%) rms = 1.92, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=5362028.0, rms=1.921 (0.000%) positioning took 1.4 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group mean border=86.1, 232 (63) missing vertices, mean dist -0.2 [0.4 (%70.1)->0.2 (%29.9))] %81 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host= TRON, 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 0.87 +- 0.27 (0.08-->5.48) (max @ vno 64259 --> 139402) face area 0.32 +- 0.17 (0.00-->3.59) mean absolute distance = 0.27 +- 0.37 4035 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5665746.5, rms=3.97 023: dt: 0.5000, sse=6030610.0, rms=3.007 (0.000%) rms = 3.27, time step reduction 1 of 3 to 0.250... 024: dt: 0.2500, sse=5642203.0, rms=2.233 (0.000%) 025: dt: 0.2500, sse=5678493.5, rms=1.915 (0.000%) 026: dt: 0.2500, sse=5624183.0, rms=1.810 (0.000%) rms = 1.81, time step reduction 2 of 3 to 0.125... rms = 1.77, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=5565948.5, rms=1.771 (0.000%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group mean border=87.1, 250 (52) missing vertices, mean dist -0.1 [0.3 (%56.5)->0.2 (%43.5))] %86 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host= TRON, 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 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=5598934.0, rms=2.17 rms = 2.35, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=5700028.0, rms=1.630 (0.000%) 029: dt: 0.2500, sse=6031496.0, rms=1.339 (0.000%) rms = 1.34, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=6057311.0, rms=1.336 (0.000%) rms = 1.30, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=6077937.5, rms=1.301 (0.000%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group generating cortex label... 14 non-cortical segments detected only using segment with 2305 vertices erasing segment 1 (vno[0] = 57710) erasing segment 2 (vno[0] = 59016) erasing segment 3 (vno[0] = 101482) erasing segment 4 (vno[0] = 103471) erasing segment 5 (vno[0] = 104449) erasing segment 6 (vno[0] = 104472) erasing segment 7 (vno[0] = 106337) erasing segment 8 (vno[0] = 106351) erasing segment 9 (vno[0] = 107315) erasing segment 10 (vno[0] = 107328) erasing segment 11 (vno[0] = 107371) erasing segment 12 (vno[0] = 108249) erasing segment 13 (vno[0] = 139086) writing cortex label to /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/label/lh.cortex.label... writing curvature file /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.curv writing smoothed area to lh.area writing curvature file /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.area vertex spacing 0.87 +- 0.27 (0.03-->5.56) (max @ vno 64259 --> 139402) face area 0.32 +- 0.17 (0.00-->3.64) refinement took 9.0 minutes #-------------------------------------------- #@# Smooth2 lh Tue Dec 13 05:17:40 EST 2016 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 lh Tue Dec 13 05:17:48 EST 2016 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 47.2 mm, total surface area = 80434 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.124 (target=0.015) step 005: RMS=0.086 (target=0.015) step 010: RMS=0.065 (target=0.015) step 015: RMS=0.054 (target=0.015) step 020: RMS=0.047 (target=0.015) step 025: RMS=0.039 (target=0.015) step 030: RMS=0.033 (target=0.015) step 035: RMS=0.029 (target=0.015) step 040: RMS=0.025 (target=0.015) step 045: RMS=0.022 (target=0.015) step 050: RMS=0.020 (target=0.015) step 055: RMS=0.018 (target=0.015) step 060: RMS=0.017 (target=0.015) inflation complete. inflation took 0.9 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 186 vertices thresholded to be in k1 ~ [-0.89 0.35], k2 ~ [-0.24 0.15] total integrated curvature = 0.598*4pi (7.518) --> 0 handles ICI = 1.5, FI = 8.9, variation=153.966 135 vertices thresholded to be in [-0.05 0.02] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 114 vertices thresholded to be in [-0.22 0.16] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.016, std = 0.023 done. #----------------------------------------- #@# Curvature Stats lh Tue Dec 13 05:20:53 EST 2016 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 1_S_5002 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 [ 1_S_5002/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 [ 246 ] Gb_filter = 0 #-------------------------------------------- #@# Sphere lh Tue Dec 13 05:21:01 EST 2016 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... scaling brain by 0.298... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host= TRON, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.03 pass 1: epoch 2 of 3 starting distance error %18.96 unfolding complete - removing small folds... starting distance error %18.89 removing remaining folds... final distance error %18.91 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/lh.sphere spherical transformation took 0.99 hours #-------------------------------------------- #@# Surf Reg lh Tue Dec 13 06:20:30 EST 2016 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/scripts mris_register -curv ../surf/lh.sphere /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /usr/local/freesurfer/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= TRON, 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= TRON, 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 = 0.584 curvature mean = 0.030, std = 0.938 curvature mean = 0.026, std = 0.863 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 0.00) sse = 273573.0, tmin=1.1706 d=32.00 min @ (8.00, 8.00, 0.00) sse = 232717.2, tmin=2.3384 d=16.00 min @ (-4.00, -4.00, 4.00) sse = 206768.8, tmin=3.5189 d=8.00 min @ (0.00, 2.00, 0.00) sse = 195752.3, tmin=4.7945 d=4.00 min @ (0.00, 0.00, -1.00) sse = 195020.7, tmin=6.0866 d=2.00 min @ (0.00, 0.00, 0.50) sse = 194768.6, tmin=7.3875 d=1.00 min @ (0.25, 0.00, -0.25) sse = 194671.4, tmin=8.6578 d=0.50 min @ (-0.12, 0.00, 0.12) sse = 194660.7, tmin=9.9006 tol=1.0e+00, sigma=0.5, host= TRON, 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 9.90 min curvature mean = 0.005, std = 0.963 curvature mean = 0.010, std = 0.943 curvature mean = 0.001, std = 0.974 curvature mean = 0.004, std = 0.975 curvature mean = 0.000, std = 0.977 curvature mean = 0.001, std = 0.989 2 Reading smoothwm curvature mean = -0.028, std = 0.395 curvature mean = 0.003, std = 0.067 curvature mean = 0.049, std = 0.246 curvature mean = 0.003, std = 0.079 curvature mean = 0.022, std = 0.391 curvature mean = 0.003, std = 0.085 curvature mean = 0.013, std = 0.502 curvature mean = 0.003, std = 0.087 curvature mean = 0.006, std = 0.623 MRISregister() return, current seed 0 writing registered surface to ../surf/lh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white lh Tue Dec 13 06:51:32 EST 2016 mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white... writing curvature file ../surf/lh.jacobian_white #-------------------------------------------- #@# AvgCurv lh Tue Dec 13 06:51:35 EST 2016 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/scripts mrisp_paint -a 5 /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Tue Dec 13 06:51:38 EST 2016 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 1_S_5002 lh ../surf/lh.sphere.reg /usr/local/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/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... 1258 labels changed using aseg relabeling using gibbs priors... 000: 2912 changed, 140473 examined... 001: 688 changed, 12570 examined... 002: 183 changed, 3741 examined... 003: 66 changed, 1056 examined... 004: 31 changed, 397 examined... 005: 13 changed, 169 examined... 006: 3 changed, 72 examined... 007: 2 changed, 15 examined... 008: 3 changed, 15 examined... 009: 2 changed, 16 examined... 010: 0 changed, 10 examined... 253 labels changed using aseg 000: 126 total segments, 82 labels (395 vertices) changed 001: 47 total segments, 7 labels (17 vertices) changed 002: 40 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 38 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1597 vertices marked for relabeling... 1597 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 1 minutes and 33 seconds. #-------------------------------------------- #@# Make Pial Surf lh Tue Dec 13 06:53:12 EST 2016 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs 1_S_5002 lh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/filled.mgz... reading volume /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/brain.finalsurfs.mgz... reading volume /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/wm.mgz... 33253 bright wm thresholded. 849 bright non-wm voxels segmented. reading original surface position from /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.orig... computing class statistics... border white: 294157 voxels (1.75%) border gray 303787 voxels (1.81%) WM (93.0): 93.7 +- 9.1 [70.0 --> 110.0] GM (79.0) : 76.6 +- 12.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 56.4 (was 70) setting MAX_BORDER_WHITE to 110.1 (was 105) setting MIN_BORDER_WHITE to 69.0 (was 85) setting MAX_CSF to 43.8 (was 40) setting MAX_GRAY to 91.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 62.7 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 31.3 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=101, GM=69 mean inside = 92.8, mean outside = 73.7 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.80 +- 0.24 (0.02-->4.18) (max @ vno 56457 --> 139233) face area 0.27 +- 0.13 (0.00-->2.77) mean absolute distance = 0.92 +- 1.20 5293 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 2 with 111 points - only 0.00% unknown deleting segment 4 with 143 points - only 0.00% unknown deleting segment 5 with 15 points - only 0.00% unknown deleting segment 6 with 115 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 7 with 4 points - only 0.00% unknown mean border=80.3, 176 (176) missing vertices, mean dist 0.1 [1.2 (%36.4)->0.8 (%63.6))] %43 local maxima, %53 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host= TRON, 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 0.89 +- 0.27 (0.07-->5.08) (max @ vno 64259 --> 139402) face area 0.27 +- 0.14 (0.00-->2.62) mean absolute distance = 0.51 +- 0.80 5732 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5650097.0, rms=10.51 001: dt: 0.5000, sse=7235515.5, rms=7.427 (0.000%) 002: dt: 0.5000, sse=7794925.5, rms=5.597 (0.000%) 003: dt: 0.5000, sse=8363542.0, rms=4.547 (0.000%) 004: dt: 0.5000, sse=8717979.0, rms=4.026 (0.000%) 005: dt: 0.5000, sse=8927691.0, rms=3.782 (0.000%) 006: dt: 0.5000, sse=9038821.0, rms=3.660 (0.000%) 007: dt: 0.5000, sse=9088563.0, rms=3.584 (0.000%) rms = 3.53, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=9121331.0, rms=3.534 (0.000%) 009: dt: 0.2500, sse=6093093.5, rms=2.681 (0.000%) 010: dt: 0.2500, sse=5773956.0, rms=2.407 (0.000%) rms = 2.36, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=5514434.5, rms=2.364 (0.000%) 012: dt: 0.1250, sse=5367246.5, rms=2.275 (0.000%) rms = 2.26, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=5314476.0, rms=2.264 (0.000%) positioning took 2.3 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 17 points - only 0.00% unknown deleting segment 1 with 219 points - only 0.00% unknown deleting segment 4 with 27 points - only 0.00% unknown deleting segment 6 with 35 points - only 0.00% unknown deleting segment 7 with 73 points - only 0.00% unknown deleting segment 9 with 16 points - only 43.75% unknown removing 4 vertex label from ripped group deleting segment 10 with 4 points - only 0.00% unknown deleting segment 12 with 26 points - only 0.00% unknown deleting segment 13 with 12 points - only 0.00% unknown deleting segment 14 with 9 points - only 0.00% unknown mean border=83.4, 272 (85) missing vertices, mean dist -0.3 [0.6 (%65.6)->0.3 (%34.4))] %63 local maxima, %32 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host= TRON, 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 0.88 +- 0.27 (0.06-->5.37) (max @ vno 64259 --> 139402) face area 0.33 +- 0.17 (0.00-->3.38) mean absolute distance = 0.35 +- 0.47 4507 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5929978.5, rms=4.89 014: dt: 0.5000, sse=6412781.0, rms=3.364 (0.000%) rms = 3.42, time step reduction 1 of 3 to 0.250... 015: dt: 0.2500, sse=5934003.5, rms=2.758 (0.000%) 016: dt: 0.2500, sse=5760456.0, rms=2.343 (0.000%) 017: dt: 0.2500, sse=5626523.0, rms=2.156 (0.000%) 018: dt: 0.2500, sse=5593730.5, rms=2.074 (0.000%) rms = 2.03, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=5544575.0, rms=2.027 (0.000%) 020: dt: 0.1250, sse=5462362.0, rms=1.957 (0.000%) rms = 1.95, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=5423400.0, rms=1.947 (0.000%) positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 30 points - only 16.67% unknown deleting segment 1 with 307 points - only 0.00% unknown deleting segment 2 with 7 points - only 0.00% unknown deleting segment 3 with 11 points - only 0.00% unknown deleting segment 5 with 119 points - only 0.00% unknown deleting segment 7 with 18 points - only 50.00% unknown deleting segment 8 with 5 points - only 0.00% unknown deleting segment 10 with 26 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 11 with 3 points - only 0.00% unknown deleting segment 12 with 9 points - only 0.00% unknown mean border=86.1, 240 (59) missing vertices, mean dist -0.2 [0.4 (%70.2)->0.2 (%29.8))] %81 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host= TRON, 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 0.87 +- 0.27 (0.05-->5.47) (max @ vno 64259 --> 139402) face area 0.32 +- 0.17 (0.00-->3.46) mean absolute distance = 0.27 +- 0.37 3987 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5734971.5, rms=4.00 022: dt: 0.5000, sse=6094793.5, rms=3.016 (0.000%) rms = 3.29, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=5706364.0, rms=2.246 (0.000%) 024: dt: 0.2500, sse=5737659.5, rms=1.928 (0.000%) 025: dt: 0.2500, sse=5678309.0, rms=1.825 (0.000%) rms = 1.82, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=5643273.0, rms=1.821 (0.000%) 027: dt: 0.1250, sse=5531329.5, rms=1.743 (0.000%) rms = 1.74, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=5531329.5, rms=1.743 (0.000%) positioning took 1.3 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 15 points - only 0.00% unknown deleting segment 1 with 324 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 3 with 11 points - only 0.00% unknown deleting segment 4 with 11 points - only 0.00% unknown deleting segment 6 with 135 points - only 0.00% unknown deleting segment 7 with 42 points - only 21.43% unknown deleting segment 8 with 5 points - only 0.00% unknown deleting segment 9 with 26 points - only 0.00% unknown deleting segment 10 with 15 points - only 0.00% unknown mean border=87.1, 270 (53) missing vertices, mean dist -0.1 [0.3 (%57.2)->0.2 (%42.8))] %86 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host= TRON, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=5564584.0, rms=2.15 rms = 2.26, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=5737244.5, rms=1.613 (0.000%) 030: dt: 0.2500, sse=6085182.5, rms=1.329 (0.000%) rms = 1.34, time step reduction 2 of 3 to 0.125... rms = 1.32, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=6072862.0, rms=1.319 (0.000%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 4 with 14 points - only 57.14% unknown smoothing surface for 5 iterations... mean border=57.6, 240 (240) missing vertices, mean dist 1.9 [0.3 (%0.1)->2.2 (%99.9))] %36 local maxima, %46 large gradients and %14 min vals, 483 gradients ignored tol=1.0e-04, sigma=2.0, host= TRON, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=25909456.0, rms=29.43 001: dt: 0.5000, sse=20097376.0, rms=25.440 (0.000%) 002: dt: 0.5000, sse=15771473.0, rms=22.005 (0.000%) 003: dt: 0.5000, sse=12734259.0, rms=19.132 (0.000%) 004: dt: 0.5000, sse=10905046.0, rms=16.739 (0.000%) 005: dt: 0.5000, sse=9724475.0, rms=14.694 (0.000%) 006: dt: 0.5000, sse=9041309.0, rms=12.919 (0.000%) 007: dt: 0.5000, sse=8407859.0, rms=11.263 (0.000%) 008: dt: 0.5000, sse=8088251.5, rms=9.708 (0.000%) 009: dt: 0.5000, sse=7863700.5, rms=8.300 (0.000%) 010: dt: 0.5000, sse=7872647.0, rms=7.226 (0.000%) 011: dt: 0.5000, sse=7933416.5, rms=6.490 (0.000%) 012: dt: 0.5000, sse=8084107.0, rms=6.052 (0.000%) 013: dt: 0.5000, sse=8188761.0, rms=5.758 (0.000%) 014: dt: 0.5000, sse=8272993.5, rms=5.602 (0.000%) 015: dt: 0.5000, sse=8277897.0, rms=5.464 (0.000%) 016: dt: 0.5000, sse=8363155.0, rms=5.410 (0.000%) 017: dt: 0.5000, sse=8321890.0, rms=5.336 (0.000%) rms = 5.31, time step reduction 1 of 3 to 0.250... 018: dt: 0.5000, sse=8364816.5, rms=5.314 (0.000%) 019: dt: 0.2500, sse=5508314.5, rms=4.100 (0.000%) 020: dt: 0.2500, sse=5306697.5, rms=3.746 (0.000%) rms = 3.74, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=5065076.0, rms=3.739 (0.000%) 022: dt: 0.1250, sse=4573290.5, rms=3.261 (0.000%) 023: dt: 0.1250, sse=4505347.5, rms=3.186 (0.000%) rms = 3.18, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=4457851.0, rms=3.181 (0.000%) positioning took 3.9 minutes mean border=53.5, 650 (26) missing vertices, mean dist 0.2 [0.2 (%35.1)->0.5 (%64.9))] %55 local maxima, %30 large gradients and %10 min vals, 167 gradients ignored tol=1.0e-04, sigma=1.0, host= TRON, 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=5531527.0, rms=6.54 025: dt: 0.5000, sse=5782432.5, rms=5.573 (0.000%) 026: dt: 0.5000, sse=7366781.5, rms=5.495 (0.000%) rms = 5.66, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=5835053.5, rms=4.179 (0.000%) 028: dt: 0.2500, sse=5325648.5, rms=3.804 (0.000%) rms = 3.78, time step reduction 2 of 3 to 0.125... 029: dt: 0.2500, sse=5361512.5, rms=3.782 (0.000%) 030: dt: 0.1250, sse=4872415.0, rms=3.242 (0.000%) 031: dt: 0.1250, sse=4817570.0, rms=3.138 (0.000%) rms = 3.12, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=4777443.5, rms=3.121 (0.000%) positioning took 1.4 minutes mean border=51.1, 901 (16) missing vertices, mean dist 0.1 [0.2 (%35.2)->0.3 (%64.8))] %66 local maxima, %19 large gradients and %10 min vals, 181 gradients ignored tol=1.0e-04, sigma=0.5, host= TRON, 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=5074881.0, rms=4.50 rms = 5.47, time step reduction 1 of 3 to 0.250... 033: dt: 0.2500, sse=4822188.0, rms=3.681 (0.000%) 034: dt: 0.2500, sse=4831473.5, rms=3.416 (0.000%) rms = 3.40, time step reduction 2 of 3 to 0.125... 035: dt: 0.2500, sse=5057901.0, rms=3.405 (0.000%) 036: dt: 0.1250, sse=4799932.0, rms=3.051 (0.000%) 037: dt: 0.1250, sse=4774328.5, rms=2.971 (0.000%) rms = 2.96, time step reduction 3 of 3 to 0.062... 038: dt: 0.1250, sse=4758231.5, rms=2.960 (0.000%) positioning took 1.1 minutes mean border=50.1, 1639 (14) missing vertices, mean dist 0.1 [0.2 (%44.6)->0.2 (%55.4))] %67 local maxima, %18 large gradients and % 9 min vals, 140 gradients ignored tol=1.0e-04, sigma=0.2, host= TRON, 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 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=4800812.0, rms=3.25 rms = 4.61, time step reduction 1 of 3 to 0.250... 039: dt: 0.2500, sse=4710727.5, rms=2.972 (0.000%) rms = 2.95, time step reduction 2 of 3 to 0.125... 040: dt: 0.2500, sse=4939472.0, rms=2.953 (0.000%) 041: dt: 0.1250, sse=4798532.0, rms=2.826 (0.000%) 042: dt: 0.1250, sse=4807828.5, rms=2.775 (0.000%) rms = 2.76, time step reduction 3 of 3 to 0.062... 043: dt: 0.1250, sse=4814807.5, rms=2.764 (0.000%) positioning took 0.9 minutes writing curvature file /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.area.pial vertex spacing 0.95 +- 0.40 (0.04-->6.65) (max @ vno 109954 --> 110725) face area 0.37 +- 0.28 (0.00-->6.54) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 140473 vertices processed 25000 of 140473 vertices processed 50000 of 140473 vertices processed 75000 of 140473 vertices processed 100000 of 140473 vertices processed 125000 of 140473 vertices processed 0 of 140473 vertices processed 25000 of 140473 vertices processed 50000 of 140473 vertices processed 75000 of 140473 vertices processed 100000 of 140473 vertices processed 125000 of 140473 vertices processed thickness calculation complete, 132:157 truncations. 37394 vertices at 0 distance 102966 vertices at 1 distance 85209 vertices at 2 distance 31469 vertices at 3 distance 8141 vertices at 4 distance 2166 vertices at 5 distance 692 vertices at 6 distance 261 vertices at 7 distance 140 vertices at 8 distance 62 vertices at 9 distance 36 vertices at 10 distance 37 vertices at 11 distance 18 vertices at 12 distance 22 vertices at 13 distance 10 vertices at 14 distance 8 vertices at 15 distance 1 vertices at 16 distance 1 vertices at 17 distance 1 vertices at 18 distance 4 vertices at 19 distance 0 vertices at 20 distance writing curvature file /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.thickness positioning took 17.4 minutes #-------------------------------------------- #@# Surf Volume lh Tue Dec 13 07:10:35 EST 2016 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.volume lh.area.mid mul lh.thickness Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ] #-------------------------------------------- #@# Tessellate rh Tue Dec 13 07:10:35 EST 2016 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 4 found - 4 modified | TOTAL: 4 pass 2 (xy+): 0 found - 4 modified | TOTAL: 4 pass 1 (xy-): 4 found - 4 modified | TOTAL: 8 pass 2 (xy-): 0 found - 4 modified | TOTAL: 8 pass 1 (yz+): 2 found - 2 modified | TOTAL: 10 pass 2 (yz+): 0 found - 2 modified | TOTAL: 10 pass 1 (yz-): 0 found - 0 modified | TOTAL: 10 pass 1 (xz+): 0 found - 0 modified | TOTAL: 10 pass 1 (xz-): 5 found - 5 modified | TOTAL: 15 pass 2 (xz-): 0 found - 5 modified | TOTAL: 15 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 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 Iteration Number : 1 pass 1 (++): 2 found - 2 modified | TOTAL: 2 pass 2 (++): 0 found - 2 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 pass 1 (-+): 3 found - 3 modified | TOTAL: 6 pass 2 (-+): 0 found - 3 modified | TOTAL: 6 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+): 1 found - 1 modified | TOTAL: 1 pass 2 (xz+): 0 found - 1 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 26 (out of 289430: 0.008983) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 40: 1131 vertices, 1250 faces slice 50: 7093 vertices, 7327 faces slice 60: 15980 vertices, 16346 faces slice 70: 27307 vertices, 27742 faces slice 80: 39457 vertices, 39849 faces slice 90: 51159 vertices, 51547 faces slice 100: 63991 vertices, 64449 faces slice 110: 76122 vertices, 76587 faces slice 120: 88580 vertices, 89067 faces slice 130: 101192 vertices, 101646 faces slice 140: 112917 vertices, 113391 faces slice 150: 121959 vertices, 122338 faces slice 160: 130053 vertices, 130437 faces slice 170: 137147 vertices, 137485 faces slice 180: 143006 vertices, 143344 faces slice 190: 147265 vertices, 147519 faces slice 200: 148134 vertices, 148272 faces slice 210: 148134 vertices, 148272 faces slice 220: 148134 vertices, 148272 faces slice 230: 148134 vertices, 148272 faces slice 240: 148134 vertices, 148272 faces slice 250: 148134 vertices, 148272 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 148134 voxel in cpt #1: X=-138 [v=148134,e=444816,f=296544] located at (27.666363, -19.334185, 2.221556) For the whole surface: X=-138 [v=148134,e=444816,f=296544] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Tue Dec 13 07:10:54 EST 2016 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 rh Tue Dec 13 07:11:01 EST 2016 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/scripts avg radius = 46.6 mm, total surface area = 74452 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 1.0 minutes Not saving sulc step 000: RMS=0.115 (target=0.015) step 005: RMS=0.086 (target=0.015) step 010: RMS=0.068 (target=0.015) step 015: RMS=0.061 (target=0.015) step 020: RMS=0.055 (target=0.015) step 025: RMS=0.051 (target=0.015) step 030: RMS=0.048 (target=0.015) step 035: RMS=0.045 (target=0.015) step 040: RMS=0.044 (target=0.015) step 045: RMS=0.042 (target=0.015) step 050: RMS=0.041 (target=0.015) step 055: RMS=0.040 (target=0.015) step 060: RMS=0.040 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere rh Tue Dec 13 07:11:59 EST 2016 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.96 +- 0.56 (0.00-->6.54) (max @ vno 75382 --> 75393) face area 0.02 +- 0.03 (-0.29-->0.65) scaling brain by 0.312... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.563, avgs=0 005/300: dt: 0.9000, rms radial error=176.303, avgs=0 010/300: dt: 0.9000, rms radial error=175.747, avgs=0 015/300: dt: 0.9000, rms radial error=175.018, avgs=0 020/300: dt: 0.9000, rms radial error=174.187, avgs=0 025/300: dt: 0.9000, rms radial error=173.299, avgs=0 030/300: dt: 0.9000, rms radial error=172.379, avgs=0 035/300: dt: 0.9000, rms radial error=171.443, avgs=0 040/300: dt: 0.9000, rms radial error=170.499, avgs=0 045/300: dt: 0.9000, rms radial error=169.552, avgs=0 050/300: dt: 0.9000, rms radial error=168.607, avgs=0 055/300: dt: 0.9000, rms radial error=167.664, avgs=0 060/300: dt: 0.9000, rms radial error=166.725, avgs=0 065/300: dt: 0.9000, rms radial error=165.790, avgs=0 070/300: dt: 0.9000, rms radial error=164.859, avgs=0 075/300: dt: 0.9000, rms radial error=163.933, avgs=0 080/300: dt: 0.9000, rms radial error=163.012, avgs=0 085/300: dt: 0.9000, rms radial error=162.096, avgs=0 090/300: dt: 0.9000, rms radial error=161.184, avgs=0 095/300: dt: 0.9000, rms radial error=160.277, avgs=0 100/300: dt: 0.9000, rms radial error=159.376, avgs=0 105/300: dt: 0.9000, rms radial error=158.478, avgs=0 110/300: dt: 0.9000, rms radial error=157.586, avgs=0 115/300: dt: 0.9000, rms radial error=156.699, avgs=0 120/300: dt: 0.9000, rms radial error=155.816, avgs=0 125/300: dt: 0.9000, rms radial error=154.938, avgs=0 130/300: dt: 0.9000, rms radial error=154.065, avgs=0 135/300: dt: 0.9000, rms radial error=153.198, avgs=0 140/300: dt: 0.9000, rms radial error=152.335, avgs=0 145/300: dt: 0.9000, rms radial error=151.477, avgs=0 150/300: dt: 0.9000, rms radial error=150.623, avgs=0 155/300: dt: 0.9000, rms radial error=149.775, avgs=0 160/300: dt: 0.9000, rms radial error=148.930, avgs=0 165/300: dt: 0.9000, rms radial error=148.091, avgs=0 170/300: dt: 0.9000, rms radial error=147.256, avgs=0 175/300: dt: 0.9000, rms radial error=146.425, avgs=0 180/300: dt: 0.9000, rms radial error=145.600, avgs=0 185/300: dt: 0.9000, rms radial error=144.779, avgs=0 190/300: dt: 0.9000, rms radial error=143.962, avgs=0 195/300: dt: 0.9000, rms radial error=143.150, avgs=0 200/300: dt: 0.9000, rms radial error=142.342, avgs=0 205/300: dt: 0.9000, rms radial error=141.539, avgs=0 210/300: dt: 0.9000, rms radial error=140.740, avgs=0 215/300: dt: 0.9000, rms radial error=139.945, avgs=0 220/300: dt: 0.9000, rms radial error=139.155, avgs=0 225/300: dt: 0.9000, rms radial error=138.369, avgs=0 230/300: dt: 0.9000, rms radial error=137.588, avgs=0 235/300: dt: 0.9000, rms radial error=136.811, avgs=0 240/300: dt: 0.9000, rms radial error=136.039, avgs=0 245/300: dt: 0.9000, rms radial error=135.271, avgs=0 250/300: dt: 0.9000, rms radial error=134.507, avgs=0 255/300: dt: 0.9000, rms radial error=133.748, avgs=0 260/300: dt: 0.9000, rms radial error=132.992, avgs=0 265/300: dt: 0.9000, rms radial error=132.240, avgs=0 270/300: dt: 0.9000, rms radial error=131.493, avgs=0 275/300: dt: 0.9000, rms radial error=130.750, avgs=0 280/300: dt: 0.9000, rms radial error=130.011, avgs=0 285/300: dt: 0.9000, rms radial error=129.276, avgs=0 290/300: dt: 0.9000, rms radial error=128.545, avgs=0 295/300: dt: 0.9000, rms radial error=127.819, avgs=0 300/300: dt: 0.9000, rms radial error=127.096, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 17420.37 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00013 epoch 2 (K=40.0), pass 1, starting sse = 2921.49 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00001 epoch 3 (K=160.0), pass 1, starting sse = 319.29 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/11 = 0.00663 epoch 4 (K=640.0), pass 1, starting sse = 26.11 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.08/14 = 0.00548 final writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.12 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology rh Tue Dec 13 07:19:00 EST 2016 cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 1_S_5002 rh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ before topology correction, eno=-138 (nv=148134, nf=296544, ne=444816, g=70) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 7 iterations marking ambiguous vertices... 8757 ambiguous faces found in tessellation segmenting defects... 91 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 11 into 7 -merging segment 46 into 27 -merging segment 58 into 50 88 defects to be corrected 0 vertices coincident reading input surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.5786 (-4.7893) -vertex loglikelihood: -6.6658 (-3.3329) -normal dot loglikelihood: -3.5931 (-3.5931) -quad curv loglikelihood: -6.6658 (-3.3329) Total Loglikelihood : -26.5034 CORRECTING DEFECT 0 (vertices=39, convex hull=76) After retessellation of defect 0, euler #=-85 (142769,426182,283328) : difference with theory (-85) = 0 CORRECTING DEFECT 1 (vertices=31, convex hull=24) After retessellation of defect 1, euler #=-84 (142774,426204,283346) : difference with theory (-84) = 0 CORRECTING DEFECT 2 (vertices=90, convex hull=34) After retessellation of defect 2, euler #=-83 (142778,426228,283367) : difference with theory (-83) = 0 CORRECTING DEFECT 3 (vertices=32, convex hull=24) After retessellation of defect 3, euler #=-82 (142784,426258,283392) : difference with theory (-82) = 0 CORRECTING DEFECT 4 (vertices=30, convex hull=27) After retessellation of defect 4, euler #=-81 (142788,426278,283409) : difference with theory (-81) = 0 CORRECTING DEFECT 5 (vertices=48, convex hull=41) After retessellation of defect 5, euler #=-80 (142797,426316,283439) : difference with theory (-80) = 0 CORRECTING DEFECT 6 (vertices=36, convex hull=60) After retessellation of defect 6, euler #=-79 (142813,426386,283494) : difference with theory (-79) = 0 CORRECTING DEFECT 7 (vertices=135, convex hull=202) After retessellation of defect 7, euler #=-77 (142899,426749,283773) : difference with theory (-78) = -1 CORRECTING DEFECT 8 (vertices=26, convex hull=23) After retessellation of defect 8, euler #=-76 (142902,426768,283790) : difference with theory (-77) = -1 CORRECTING DEFECT 9 (vertices=9, convex hull=21) After retessellation of defect 9, euler #=-75 (142903,426777,283799) : difference with theory (-76) = -1 CORRECTING DEFECT 10 (vertices=36, convex hull=72) After retessellation of defect 10, euler #=-74 (142924,426869,283871) : difference with theory (-75) = -1 CORRECTING DEFECT 11 (vertices=46, convex hull=88) After retessellation of defect 11, euler #=-73 (142946,426974,283955) : difference with theory (-74) = -1 CORRECTING DEFECT 12 (vertices=8, convex hull=28) After retessellation of defect 12, euler #=-72 (142949,426989,283968) : difference with theory (-73) = -1 CORRECTING DEFECT 13 (vertices=41, convex hull=37) After retessellation of defect 13, euler #=-71 (142958,427027,283998) : difference with theory (-72) = -1 CORRECTING DEFECT 14 (vertices=288, convex hull=191) After retessellation of defect 14, euler #=-70 (143023,427325,284232) : difference with theory (-71) = -1 CORRECTING DEFECT 15 (vertices=52, convex hull=93) After retessellation of defect 15, euler #=-69 (143032,427388,284287) : difference with theory (-70) = -1 CORRECTING DEFECT 16 (vertices=41, convex hull=67) After retessellation of defect 16, euler #=-68 (143045,427456,284343) : difference with theory (-69) = -1 CORRECTING DEFECT 17 (vertices=63, convex hull=73) After retessellation of defect 17, euler #=-67 (143075,427579,284437) : difference with theory (-68) = -1 CORRECTING DEFECT 18 (vertices=6, convex hull=34) After retessellation of defect 18, euler #=-66 (143076,427592,284450) : difference with theory (-67) = -1 CORRECTING DEFECT 19 (vertices=56, convex hull=34) After retessellation of defect 19, euler #=-65 (143082,427624,284477) : difference with theory (-66) = -1 CORRECTING DEFECT 20 (vertices=11, convex hull=29) After retessellation of defect 20, euler #=-64 (143084,427637,284489) : difference with theory (-65) = -1 CORRECTING DEFECT 21 (vertices=9, convex hull=21) After retessellation of defect 21, euler #=-63 (143086,427648,284499) : difference with theory (-64) = -1 CORRECTING DEFECT 22 (vertices=5, convex hull=30) After retessellation of defect 22, euler #=-62 (143088,427661,284511) : difference with theory (-63) = -1 CORRECTING DEFECT 23 (vertices=6, convex hull=23) After retessellation of defect 23, euler #=-61 (143089,427675,284525) : difference with theory (-62) = -1 CORRECTING DEFECT 24 (vertices=7, convex hull=16) After retessellation of defect 24, euler #=-60 (143090,427681,284531) : difference with theory (-61) = -1 CORRECTING DEFECT 25 (vertices=5, convex hull=15) After retessellation of defect 25, euler #=-59 (143091,427687,284537) : difference with theory (-60) = -1 CORRECTING DEFECT 26 (vertices=1336, convex hull=536) After retessellation of defect 26, euler #=-59 (143186,428258,285013) : difference with theory (-59) = 0 CORRECTING DEFECT 27 (vertices=26, convex hull=69) After retessellation of defect 27, euler #=-58 (143195,428313,285060) : difference with theory (-58) = 0 CORRECTING DEFECT 28 (vertices=61, convex hull=100) After retessellation of defect 28, euler #=-57 (143212,428408,285139) : difference with theory (-57) = 0 CORRECTING DEFECT 29 (vertices=15, convex hull=23) After retessellation of defect 29, euler #=-56 (143214,428422,285152) : difference with theory (-56) = 0 CORRECTING DEFECT 30 (vertices=6, convex hull=31) After retessellation of defect 30, euler #=-55 (143215,428435,285165) : difference with theory (-55) = 0 CORRECTING DEFECT 31 (vertices=34, convex hull=46) After retessellation of defect 31, euler #=-54 (143228,428492,285210) : difference with theory (-54) = 0 CORRECTING DEFECT 32 (vertices=16, convex hull=66) After retessellation of defect 32, euler #=-53 (143240,428553,285260) : difference with theory (-53) = 0 CORRECTING DEFECT 33 (vertices=64, convex hull=28) After retessellation of defect 33, euler #=-53 (143243,428576,285280) : difference with theory (-52) = 1 CORRECTING DEFECT 34 (vertices=43, convex hull=66) After retessellation of defect 34, euler #=-52 (143257,428646,285337) : difference with theory (-51) = 1 CORRECTING DEFECT 35 (vertices=30, convex hull=43) After retessellation of defect 35, euler #=-51 (143266,428690,285373) : difference with theory (-50) = 1 CORRECTING DEFECT 36 (vertices=21, convex hull=26) Warning - incorrect dp selected!!!!(-91.888631 >= -91.888637 ) After retessellation of defect 36, euler #=-50 (143267,428699,285382) : difference with theory (-49) = 1 CORRECTING DEFECT 37 (vertices=92, convex hull=65) After retessellation of defect 37, euler #=-49 (143284,428775,285442) : difference with theory (-48) = 1 CORRECTING DEFECT 38 (vertices=19, convex hull=24) After retessellation of defect 38, euler #=-48 (143288,428792,285456) : difference with theory (-47) = 1 CORRECTING DEFECT 39 (vertices=25, convex hull=40) After retessellation of defect 39, euler #=-47 (143304,428853,285502) : difference with theory (-46) = 1 CORRECTING DEFECT 40 (vertices=20, convex hull=35) After retessellation of defect 40, euler #=-46 (143313,428897,285538) : difference with theory (-45) = 1 CORRECTING DEFECT 41 (vertices=11, convex hull=22) After retessellation of defect 41, euler #=-45 (143316,428911,285550) : difference with theory (-44) = 1 CORRECTING DEFECT 42 (vertices=36, convex hull=80) After retessellation of defect 42, euler #=-44 (143333,428997,285620) : difference with theory (-43) = 1 CORRECTING DEFECT 43 (vertices=348, convex hull=192) After retessellation of defect 43, euler #=-43 (143460,429484,285981) : difference with theory (-42) = 1 CORRECTING DEFECT 44 (vertices=24, convex hull=57) After retessellation of defect 44, euler #=-42 (143471,429535,286022) : difference with theory (-41) = 1 CORRECTING DEFECT 45 (vertices=48, convex hull=25) After retessellation of defect 45, euler #=-41 (143473,429550,286036) : difference with theory (-40) = 1 CORRECTING DEFECT 46 (vertices=43, convex hull=35) After retessellation of defect 46, euler #=-40 (143477,429571,286054) : difference with theory (-39) = 1 CORRECTING DEFECT 47 (vertices=53, convex hull=60) After retessellation of defect 47, euler #=-39 (143486,429619,286094) : difference with theory (-38) = 1 CORRECTING DEFECT 48 (vertices=64, convex hull=81) After retessellation of defect 48, euler #=-37 (143511,429729,286181) : difference with theory (-37) = 0 CORRECTING DEFECT 49 (vertices=102, convex hull=94) After retessellation of defect 49, euler #=-36 (143544,429865,286285) : difference with theory (-36) = 0 CORRECTING DEFECT 50 (vertices=162, convex hull=111) After retessellation of defect 50, euler #=-35 (143604,430099,286460) : difference with theory (-35) = 0 CORRECTING DEFECT 51 (vertices=38, convex hull=54) After retessellation of defect 51, euler #=-34 (143620,430168,286514) : difference with theory (-34) = 0 CORRECTING DEFECT 52 (vertices=134, convex hull=46) After retessellation of defect 52, euler #=-33 (143629,430216,286554) : difference with theory (-33) = 0 CORRECTING DEFECT 53 (vertices=14, convex hull=20) After retessellation of defect 53, euler #=-32 (143629,430221,286560) : difference with theory (-32) = 0 CORRECTING DEFECT 54 (vertices=7, convex hull=11) After retessellation of defect 54, euler #=-31 (143629,430222,286562) : difference with theory (-31) = 0 CORRECTING DEFECT 55 (vertices=35, convex hull=21) After retessellation of defect 55, euler #=-30 (143632,430235,286573) : difference with theory (-30) = 0 CORRECTING DEFECT 56 (vertices=219, convex hull=103) After retessellation of defect 56, euler #=-29 (143678,430424,286717) : difference with theory (-29) = 0 CORRECTING DEFECT 57 (vertices=16, convex hull=22) After retessellation of defect 57, euler #=-28 (143681,430438,286729) : difference with theory (-28) = 0 CORRECTING DEFECT 58 (vertices=61, convex hull=67) After retessellation of defect 58, euler #=-27 (143704,430542,286811) : difference with theory (-27) = 0 CORRECTING DEFECT 59 (vertices=18, convex hull=34) After retessellation of defect 59, euler #=-26 (143707,430564,286831) : difference with theory (-26) = 0 CORRECTING DEFECT 60 (vertices=22, convex hull=74) After retessellation of defect 60, euler #=-25 (143722,430638,286891) : difference with theory (-25) = 0 CORRECTING DEFECT 61 (vertices=15, convex hull=32) After retessellation of defect 61, euler #=-24 (143726,430664,286914) : difference with theory (-24) = 0 CORRECTING DEFECT 62 (vertices=200, convex hull=53) After retessellation of defect 62, euler #=-23 (143734,430704,286947) : difference with theory (-23) = 0 CORRECTING DEFECT 63 (vertices=19, convex hull=33) After retessellation of defect 63, euler #=-22 (143738,430732,286972) : difference with theory (-22) = 0 CORRECTING DEFECT 64 (vertices=44, convex hull=98) After retessellation of defect 64, euler #=-21 (143762,430842,287059) : difference with theory (-21) = 0 CORRECTING DEFECT 65 (vertices=23, convex hull=52) After retessellation of defect 65, euler #=-20 (143771,430891,287100) : difference with theory (-20) = 0 CORRECTING DEFECT 66 (vertices=96, convex hull=124) After retessellation of defect 66, euler #=-19 (143823,431101,287259) : difference with theory (-19) = 0 CORRECTING DEFECT 67 (vertices=59, convex hull=77) After retessellation of defect 67, euler #=-18 (143852,431219,287349) : difference with theory (-18) = 0 CORRECTING DEFECT 68 (vertices=20, convex hull=20) After retessellation of defect 68, euler #=-17 (143855,431236,287364) : difference with theory (-17) = 0 CORRECTING DEFECT 69 (vertices=7, convex hull=16) After retessellation of defect 69, euler #=-16 (143857,431244,287371) : difference with theory (-16) = 0 CORRECTING DEFECT 70 (vertices=15, convex hull=23) After retessellation of defect 70, euler #=-15 (143858,431254,287381) : difference with theory (-15) = 0 CORRECTING DEFECT 71 (vertices=32, convex hull=63) After retessellation of defect 71, euler #=-14 (143867,431305,287424) : difference with theory (-14) = 0 CORRECTING DEFECT 72 (vertices=21, convex hull=47) After retessellation of defect 72, euler #=-13 (143872,431334,287449) : difference with theory (-13) = 0 CORRECTING DEFECT 73 (vertices=8, convex hull=28) After retessellation of defect 73, euler #=-12 (143873,431345,287460) : difference with theory (-12) = 0 CORRECTING DEFECT 74 (vertices=14, convex hull=20) After retessellation of defect 74, euler #=-11 (143875,431360,287474) : difference with theory (-11) = 0 CORRECTING DEFECT 75 (vertices=19, convex hull=19) After retessellation of defect 75, euler #=-10 (143876,431365,287479) : difference with theory (-10) = 0 CORRECTING DEFECT 76 (vertices=35, convex hull=72) After retessellation of defect 76, euler #=-9 (143888,431428,287531) : difference with theory (-9) = 0 CORRECTING DEFECT 77 (vertices=6, convex hull=27) After retessellation of defect 77, euler #=-8 (143889,431439,287542) : difference with theory (-8) = 0 CORRECTING DEFECT 78 (vertices=35, convex hull=69) After retessellation of defect 78, euler #=-7 (143911,431534,287616) : difference with theory (-7) = 0 CORRECTING DEFECT 79 (vertices=57, convex hull=91) After retessellation of defect 79, euler #=-6 (143939,431662,287717) : difference with theory (-6) = 0 CORRECTING DEFECT 80 (vertices=21, convex hull=44) After retessellation of defect 80, euler #=-5 (143946,431698,287747) : difference with theory (-5) = 0 CORRECTING DEFECT 81 (vertices=16, convex hull=13) After retessellation of defect 81, euler #=-4 (143946,431702,287752) : difference with theory (-4) = 0 CORRECTING DEFECT 82 (vertices=22, convex hull=43) After retessellation of defect 82, euler #=-3 (143955,431745,287787) : difference with theory (-3) = 0 CORRECTING DEFECT 83 (vertices=39, convex hull=77) After retessellation of defect 83, euler #=-2 (143971,431820,287847) : difference with theory (-2) = 0 CORRECTING DEFECT 84 (vertices=14, convex hull=26) After retessellation of defect 84, euler #=-1 (143973,431836,287862) : difference with theory (-1) = 0 CORRECTING DEFECT 85 (vertices=86, convex hull=112) After retessellation of defect 85, euler #=0 (144018,432022,288004) : difference with theory (0) = 0 CORRECTING DEFECT 86 (vertices=27, convex hull=53) After retessellation of defect 86, euler #=1 (144029,432077,288049) : difference with theory (1) = 0 CORRECTING DEFECT 87 (vertices=6, convex hull=15) After retessellation of defect 87, euler #=2 (144029,432081,288054) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.87 +- 0.24 (0.06-->8.78) (max @ vno 92183 --> 96843) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.87 +- 0.24 (0.06-->8.78) (max @ vno 92183 --> 96843) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 300 mutations (37.2%), 506 crossovers (62.8%), 399 vertices were eliminated building final representation... 4105 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=144029, nf=288054, ne=432081, g=0) writing corrected surface to /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 94.2 minutes 0 defective edges removing intersecting faces 000: 418 intersecting 001: 29 intersecting 002: 9 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 144029 - 432081 + 288054 = 2 --> 0 holes F =2V-4: 288054 = 288058-4 (0) 2E=3F: 864162 = 864162 (0) total defect index = 0 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 49 intersecting 001: 4 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Tue Dec 13 08:53:25 EST 2016 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs 1_S_5002 rh only generating white matter surface not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/filled.mgz... reading volume /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/brain.finalsurfs.mgz... reading volume /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/wm.mgz... 34342 bright wm thresholded. 849 bright non-wm voxels segmented. reading original surface position from /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.orig... computing class statistics... border white: 294157 voxels (1.75%) border gray 303787 voxels (1.81%) WM (93.0): 93.7 +- 8.8 [70.0 --> 110.0] GM (79.0) : 76.2 +- 13.5 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 54.5 (was 70) setting MAX_BORDER_WHITE to 108.8 (was 105) setting MIN_BORDER_WHITE to 68.0 (was 85) setting MAX_CSF to 40.9 (was 40) setting MAX_GRAY to 91.2 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 61.2 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 27.4 (was 40) repositioning cortical surface to gray/white boundary reading volume /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.80 +- 0.23 (0.01-->3.97) (max @ vno 88688 --> 97969) face area 0.27 +- 0.13 (0.00-->2.96) mean absolute distance = 0.88 +- 1.18 5510 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=100, GM=68 mean inside = 91.8, mean outside = 72.8 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... 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 2 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=80.6, 214 (214) missing vertices, mean dist 0.1 [1.0 (%40.6)->0.8 (%59.4))] %47 local maxima, %49 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host= TRON, 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 0.89 +- 0.27 (0.06-->4.22) (max @ vno 88688 --> 97969) face area 0.27 +- 0.14 (0.00-->2.69) mean absolute distance = 0.51 +- 0.82 6196 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5650536.0, rms=10.20 001: dt: 0.5000, sse=7306216.0, rms=7.107 (0.000%) 002: dt: 0.5000, sse=7863930.0, rms=5.344 (0.000%) 003: dt: 0.5000, sse=8463036.0, rms=4.401 (0.000%) 004: dt: 0.5000, sse=8769653.0, rms=3.960 (0.000%) 005: dt: 0.5000, sse=9071969.0, rms=3.731 (0.000%) 006: dt: 0.5000, sse=9115268.0, rms=3.632 (0.000%) 007: dt: 0.5000, sse=9268109.0, rms=3.562 (0.000%) rms = 3.54, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=9217288.0, rms=3.541 (0.000%) 009: dt: 0.2500, sse=6141563.0, rms=2.629 (0.000%) 010: dt: 0.2500, sse=5779503.0, rms=2.343 (0.000%) rms = 2.30, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=5525779.5, rms=2.301 (0.000%) 012: dt: 0.1250, sse=5371610.5, rms=2.205 (0.000%) rms = 2.20, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=5319320.0, rms=2.197 (0.000%) positioning took 2.3 minutes inhibiting deformation at non-cortical midline structures... removing 2 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 mean border=83.2, 229 (96) missing vertices, mean dist -0.3 [0.7 (%62.4)->0.3 (%37.6))] %62 local maxima, %33 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host= TRON, 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 0.87 +- 0.27 (0.08-->4.15) (max @ vno 88688 --> 97969) face area 0.33 +- 0.17 (0.00-->3.41) mean absolute distance = 0.41 +- 0.54 5373 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5868469.0, rms=4.60 014: dt: 0.5000, sse=6444509.5, rms=3.326 (0.000%) rms = 3.37, time step reduction 1 of 3 to 0.250... 015: dt: 0.2500, sse=5969305.5, rms=2.740 (0.000%) 016: dt: 0.2500, sse=5810611.0, rms=2.330 (0.000%) 017: dt: 0.2500, sse=5669455.5, rms=2.129 (0.000%) 018: dt: 0.2500, sse=5647450.0, rms=2.034 (0.000%) rms = 1.99, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=5603194.5, rms=1.991 (0.000%) 020: dt: 0.1250, sse=5522640.0, rms=1.919 (0.000%) rms = 1.91, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=5484914.5, rms=1.906 (0.000%) positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=85.8, 197 (66) missing vertices, mean dist -0.2 [0.5 (%66.5)->0.3 (%33.5))] %77 local maxima, %18 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host= TRON, 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 0.87 +- 0.26 (0.06-->4.09) (max @ vno 88688 --> 97969) face area 0.32 +- 0.17 (0.00-->3.03) mean absolute distance = 0.32 +- 0.42 4287 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5805149.5, rms=3.99 022: dt: 0.5000, sse=6231955.5, rms=2.955 (0.000%) rms = 3.20, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=5855053.0, rms=2.267 (0.000%) 024: dt: 0.2500, sse=5884761.0, rms=1.927 (0.000%) 025: dt: 0.2500, sse=5809571.0, rms=1.824 (0.000%) rms = 1.80, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=5780069.0, rms=1.803 (0.000%) 027: dt: 0.1250, sse=5665437.5, rms=1.730 (0.000%) rms = 1.73, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=5626517.0, rms=1.728 (0.000%) positioning took 1.3 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=86.9, 208 (51) missing vertices, mean dist -0.1 [0.4 (%57.0)->0.3 (%43.0))] %84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host= TRON, 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 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=5683482.0, rms=2.32 029: dt: 0.5000, sse=7776121.0, rms=2.192 (0.000%) rms = 2.91, time step reduction 1 of 3 to 0.250... 030: dt: 0.2500, sse=6827687.0, rms=1.544 (0.000%) rms = 1.52, time step reduction 2 of 3 to 0.125... 031: dt: 0.2500, sse=6320476.0, rms=1.521 (0.000%) 032: dt: 0.1250, sse=6361387.0, rms=1.343 (0.000%) rms = 1.31, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=6379178.0, rms=1.307 (0.000%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 16 non-cortical segments detected only using segment with 2110 vertices erasing segment 1 (vno[0] = 75935) erasing segment 2 (vno[0] = 93154) erasing segment 3 (vno[0] = 94265) erasing segment 4 (vno[0] = 102201) erasing segment 5 (vno[0] = 103178) erasing segment 6 (vno[0] = 103227) erasing segment 7 (vno[0] = 103263) erasing segment 8 (vno[0] = 104262) erasing segment 9 (vno[0] = 105361) erasing segment 10 (vno[0] = 105407) erasing segment 11 (vno[0] = 105432) erasing segment 12 (vno[0] = 106471) erasing segment 13 (vno[0] = 109427) erasing segment 14 (vno[0] = 109445) erasing segment 15 (vno[0] = 143299) writing cortex label to /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/label/rh.cortex.label... writing curvature file /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.curv writing smoothed area to rh.area writing curvature file /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.area vertex spacing 0.87 +- 0.26 (0.04-->4.22) (max @ vno 87419 --> 88571) face area 0.32 +- 0.16 (0.00-->3.14) refinement took 9.4 minutes #-------------------------------------------- #@# Smooth2 rh Tue Dec 13 09:02:50 EST 2016 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 rh Tue Dec 13 09:02:58 EST 2016 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 46.8 mm, total surface area = 81702 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.124 (target=0.015) step 005: RMS=0.086 (target=0.015) step 010: RMS=0.064 (target=0.015) step 015: RMS=0.054 (target=0.015) step 020: RMS=0.046 (target=0.015) step 025: RMS=0.038 (target=0.015) step 030: RMS=0.032 (target=0.015) step 035: RMS=0.028 (target=0.015) step 040: RMS=0.024 (target=0.015) step 045: RMS=0.021 (target=0.015) step 050: RMS=0.019 (target=0.015) step 055: RMS=0.017 (target=0.015) step 060: RMS=0.016 (target=0.015) inflation complete. inflation took 1.0 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 177 vertices thresholded to be in k1 ~ [-0.19 0.74], k2 ~ [-0.08 0.06] total integrated curvature = 0.585*4pi (7.349) --> 0 handles ICI = 1.5, FI = 10.0, variation=167.875 110 vertices thresholded to be in [-0.01 0.01] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 137 vertices thresholded to be in [-0.12 0.29] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.016, std = 0.024 done. #----------------------------------------- #@# Curvature Stats rh Tue Dec 13 09:06:19 EST 2016 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 1_S_5002 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 [ 1_S_5002/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 [ 257 ] Gb_filter = 0 WARN: S lookup min: -0.340586 WARN: S explicit min: 0.000000 vertex = 141 #-------------------------------------------- #@# Sphere rh Tue Dec 13 09:06:27 EST 2016 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... scaling brain by 0.294... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host= TRON, 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 %19.09 pass 1: epoch 2 of 3 starting distance error %19.05 unfolding complete - removing small folds... starting distance error %18.99 removing remaining folds... final distance error %19.01 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/rh.sphere spherical transformation took 1.02 hours #-------------------------------------------- #@# Surf Reg rh Tue Dec 13 10:07:23 EST 2016 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/scripts mris_register -curv ../surf/rh.sphere /usr/local/freesurfer/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /usr/local/freesurfer/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= TRON, 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= TRON, 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 = 0.578 curvature mean = 0.033, std = 0.924 curvature mean = 0.026, std = 0.861 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 0.00, 16.00) sse = 426601.0, tmin=1.3987 d=32.00 min @ (-8.00, -8.00, -8.00) sse = 269980.0, tmin=2.7690 d=16.00 min @ (-4.00, 0.00, 4.00) sse = 255971.6, tmin=4.1753 d=8.00 min @ (2.00, 2.00, -2.00) sse = 237410.4, tmin=5.5890 d=4.00 min @ (1.00, 0.00, 1.00) sse = 233936.8, tmin=7.1072 d=2.00 min @ (-0.50, -0.50, -0.50) sse = 233145.8, tmin=8.5548 d=1.00 min @ (0.00, 0.00, 0.25) sse = 232937.2, tmin=10.0296 d=0.50 min @ (0.00, 0.12, 0.00) sse = 232918.0, tmin=11.5093 tol=1.0e+00, sigma=0.5, host= TRON, 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 11.51 min curvature mean = 0.005, std = 0.949 curvature mean = 0.010, std = 0.942 curvature mean = -0.000, std = 0.959 curvature mean = 0.004, std = 0.974 curvature mean = -0.003, std = 0.960 curvature mean = 0.001, std = 0.989 2 Reading smoothwm curvature mean = -0.028, std = 0.324 curvature mean = 0.005, std = 0.070 curvature mean = 0.061, std = 0.302 curvature mean = 0.005, std = 0.083 curvature mean = 0.027, std = 0.475 curvature mean = 0.005, std = 0.089 curvature mean = 0.015, std = 0.611 curvature mean = 0.005, std = 0.092 curvature mean = 0.005, std = 0.727 MRISregister() return, current seed 0 writing registered surface to ../surf/rh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white rh Tue Dec 13 10:46:39 EST 2016 mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white... writing curvature file ../surf/rh.jacobian_white #-------------------------------------------- #@# AvgCurv rh Tue Dec 13 10:46:44 EST 2016 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/scripts mrisp_paint -a 5 /usr/local/freesurfer/average/rh.average.curvature.filled.buckner40.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /usr/local/freesurfer/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc rh Tue Dec 13 10:46:47 EST 2016 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 1_S_5002 rh ../surf/rh.sphere.reg /usr/local/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/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... 1226 labels changed using aseg relabeling using gibbs priors... 000: 2960 changed, 144029 examined... 001: 759 changed, 12782 examined... 002: 155 changed, 4187 examined... 003: 53 changed, 960 examined... 004: 23 changed, 326 examined... 005: 11 changed, 143 examined... 006: 5 changed, 65 examined... 007: 1 changed, 31 examined... 008: 0 changed, 8 examined... 131 labels changed using aseg 000: 105 total segments, 67 labels (429 vertices) changed 001: 38 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 32 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1822 vertices marked for relabeling... 1822 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 1 minutes and 39 seconds. #-------------------------------------------- #@# Make Pial Surf rh Tue Dec 13 10:48:27 EST 2016 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs 1_S_5002 rh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/filled.mgz... reading volume /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/brain.finalsurfs.mgz... reading volume /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/wm.mgz... 34342 bright wm thresholded. 849 bright non-wm voxels segmented. reading original surface position from /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.orig... computing class statistics... border white: 294157 voxels (1.75%) border gray 303787 voxels (1.81%) WM (93.0): 93.7 +- 8.8 [70.0 --> 110.0] GM (79.0) : 76.2 +- 13.5 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 54.5 (was 70) setting MAX_BORDER_WHITE to 108.8 (was 105) setting MIN_BORDER_WHITE to 68.0 (was 85) setting MAX_CSF to 40.9 (was 40) setting MAX_GRAY to 91.2 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 61.2 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 27.4 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=100, GM=68 mean inside = 91.8, mean outside = 72.8 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.80 +- 0.23 (0.01-->3.97) (max @ vno 88688 --> 97969) face area 0.27 +- 0.13 (0.00-->2.96) mean absolute distance = 0.89 +- 1.18 5376 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 23 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 13 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 5 with 2 points - only 0.00% unknown deleting segment 6 with 42 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 10 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 11 with 3 points - only 0.00% unknown deleting segment 12 with 116 points - only 0.00% unknown mean border=80.6, 214 (214) missing vertices, mean dist 0.1 [1.0 (%40.6)->0.8 (%59.4))] %47 local maxima, %49 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host= TRON, 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 0.89 +- 0.27 (0.06-->4.22) (max @ vno 88688 --> 97969) face area 0.27 +- 0.14 (0.00-->2.69) mean absolute distance = 0.52 +- 0.82 5707 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5657199.5, rms=10.20 001: dt: 0.5000, sse=7319710.5, rms=7.106 (0.000%) 002: dt: 0.5000, sse=7879799.5, rms=5.347 (0.000%) 003: dt: 0.5000, sse=8480515.0, rms=4.406 (0.000%) 004: dt: 0.5000, sse=8786842.0, rms=3.967 (0.000%) 005: dt: 0.5000, sse=9091308.0, rms=3.738 (0.000%) 006: dt: 0.5000, sse=9131829.0, rms=3.639 (0.000%) 007: dt: 0.5000, sse=9280736.0, rms=3.568 (0.000%) rms = 3.55, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=9232253.0, rms=3.546 (0.000%) 009: dt: 0.2500, sse=6152849.0, rms=2.636 (0.000%) 010: dt: 0.2500, sse=5789411.5, rms=2.349 (0.000%) rms = 2.31, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=5536262.0, rms=2.306 (0.000%) 012: dt: 0.1250, sse=5382324.5, rms=2.210 (0.000%) rms = 2.20, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=5330881.5, rms=2.201 (0.000%) positioning took 2.4 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 18 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 4 with 28 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 5 with 3 points - only 0.00% unknown deleting segment 7 with 40 points - only 0.00% unknown deleting segment 9 with 9 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 10 with 2 points - only 0.00% unknown deleting segment 11 with 411 points - only 17.52% unknown mean border=83.2, 256 (97) missing vertices, mean dist -0.3 [0.7 (%62.4)->0.3 (%37.6))] %62 local maxima, %33 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host= TRON, 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 0.87 +- 0.27 (0.08-->4.15) (max @ vno 88688 --> 97969) face area 0.33 +- 0.17 (0.00-->3.41) mean absolute distance = 0.41 +- 0.54 5425 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5900574.0, rms=4.60 014: dt: 0.5000, sse=6481662.5, rms=3.331 (0.000%) rms = 3.37, time step reduction 1 of 3 to 0.250... 015: dt: 0.2500, sse=6006639.5, rms=2.748 (0.000%) 016: dt: 0.2500, sse=5849208.5, rms=2.339 (0.000%) 017: dt: 0.2500, sse=5706668.0, rms=2.139 (0.000%) 018: dt: 0.2500, sse=5687104.0, rms=2.044 (0.000%) rms = 2.00, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=5639619.5, rms=2.002 (0.000%) 020: dt: 0.1250, sse=5558685.5, rms=1.930 (0.000%) rms = 1.92, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=5520689.5, rms=1.917 (0.000%) positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 17 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 14 points - only 0.00% unknown deleting segment 4 with 7 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 5 with 2 points - only 0.00% unknown deleting segment 6 with 38 points - only 0.00% unknown deleting segment 8 with 11 points - only 0.00% unknown deleting segment 9 with 6 points - only 0.00% unknown deleting segment 10 with 429 points - only 16.78% unknown deleting segment 11 with 7 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 12 with 3 points - only 0.00% unknown mean border=85.8, 228 (68) missing vertices, mean dist -0.2 [0.5 (%66.5)->0.3 (%33.5))] %78 local maxima, %18 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host= TRON, 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 0.87 +- 0.26 (0.06-->4.09) (max @ vno 88688 --> 97969) face area 0.32 +- 0.17 (0.00-->3.03) mean absolute distance = 0.33 +- 0.42 4353 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5842030.0, rms=4.00 022: dt: 0.5000, sse=6275622.0, rms=2.958 (0.000%) rms = 3.20, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=5895654.0, rms=2.272 (0.000%) 024: dt: 0.2500, sse=5922738.0, rms=1.934 (0.000%) 025: dt: 0.2500, sse=5847743.5, rms=1.831 (0.000%) rms = 1.81, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=5818597.0, rms=1.811 (0.000%) 027: dt: 0.1250, sse=5703906.5, rms=1.738 (0.000%) rms = 1.74, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=5666104.5, rms=1.736 (0.000%) positioning took 1.4 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 17 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 3 with 43 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 4 with 4 points - only 0.00% unknown deleting segment 5 with 34 points - only 0.00% unknown deleting segment 6 with 11 points - only 0.00% unknown deleting segment 7 with 6 points - only 0.00% unknown deleting segment 8 with 371 points - only 16.71% unknown deleting segment 9 with 17 points - only 0.00% unknown mean border=86.9, 239 (51) missing vertices, mean dist -0.1 [0.4 (%57.0)->0.3 (%43.0))] %84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host= TRON, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=5723121.5, rms=2.33 029: dt: 0.5000, sse=7831189.0, rms=2.195 (0.000%) rms = 2.91, time step reduction 1 of 3 to 0.250... 030: dt: 0.2500, sse=6882179.5, rms=1.552 (0.000%) rms = 1.53, time step reduction 2 of 3 to 0.125... 031: dt: 0.2500, sse=6376636.5, rms=1.529 (0.000%) 032: dt: 0.1250, sse=6418019.0, rms=1.352 (0.000%) rms = 1.32, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=6434062.5, rms=1.316 (0.000%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... smoothing surface for 5 iterations... mean border=56.5, 280 (280) missing vertices, mean dist 1.8 [1.2 (%0.0)->2.3 (%100.0))] %31 local maxima, %44 large gradients and %21 min vals, 856 gradients ignored tol=1.0e-04, sigma=2.0, host= TRON, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=28311870.0, rms=30.45 001: dt: 0.5000, sse=22314374.0, rms=26.617 (0.000%) 002: dt: 0.5000, sse=17635522.0, rms=23.213 (0.000%) 003: dt: 0.5000, sse=14190244.0, rms=20.248 (0.000%) 004: dt: 0.5000, sse=11945697.0, rms=17.668 (0.000%) 005: dt: 0.5000, sse=10462017.0, rms=15.420 (0.000%) 006: dt: 0.5000, sse=9520101.0, rms=13.455 (0.000%) 007: dt: 0.5000, sse=8808010.0, rms=11.638 (0.000%) 008: dt: 0.5000, sse=8360015.0, rms=9.994 (0.000%) 009: dt: 0.5000, sse=8053129.5, rms=8.569 (0.000%) 010: dt: 0.5000, sse=8059567.0, rms=7.479 (0.000%) 011: dt: 0.5000, sse=8082994.5, rms=6.723 (0.000%) 012: dt: 0.5000, sse=8198979.0, rms=6.176 (0.000%) 013: dt: 0.5000, sse=8246884.5, rms=5.817 (0.000%) 014: dt: 0.5000, sse=8353751.0, rms=5.566 (0.000%) 015: dt: 0.5000, sse=8381996.0, rms=5.438 (0.000%) 016: dt: 0.5000, sse=8388303.0, rms=5.314 (0.000%) rms = 5.27, time step reduction 1 of 3 to 0.250... 017: dt: 0.5000, sse=8418591.0, rms=5.269 (0.000%) 018: dt: 0.2500, sse=5522423.0, rms=4.074 (0.000%) 019: dt: 0.2500, sse=5318373.5, rms=3.735 (0.000%) rms = 3.69, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=5072358.5, rms=3.693 (0.000%) 021: dt: 0.1250, sse=4565861.0, rms=3.238 (0.000%) 022: dt: 0.1250, sse=4503380.0, rms=3.159 (0.000%) rms = 3.15, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=4474071.5, rms=3.152 (0.000%) positioning took 4.0 minutes mean border=53.4, 866 (20) missing vertices, mean dist 0.2 [0.2 (%40.4)->0.5 (%59.6))] %49 local maxima, %31 large gradients and %15 min vals, 340 gradients ignored tol=1.0e-04, sigma=1.0, host= TRON, 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=5282233.5, rms=5.68 024: dt: 0.5000, sse=5762795.5, rms=5.250 (0.000%) rms = 5.35, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=5116575.5, rms=4.165 (0.000%) 026: dt: 0.2500, sse=5222529.0, rms=3.818 (0.000%) 027: dt: 0.2500, sse=5151951.5, rms=3.691 (0.000%) rms = 3.66, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=5270259.0, rms=3.664 (0.000%) 029: dt: 0.1250, sse=4832568.0, rms=3.234 (0.000%) 030: dt: 0.1250, sse=4797898.0, rms=3.142 (0.000%) rms = 3.12, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=4773724.0, rms=3.122 (0.000%) positioning took 1.5 minutes mean border=51.6, 1154 (15) missing vertices, mean dist 0.1 [0.2 (%42.7)->0.4 (%57.3))] %60 local maxima, %20 large gradients and %15 min vals, 335 gradients ignored tol=1.0e-04, sigma=0.5, host= TRON, 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=4997872.0, rms=4.18 rms = 5.05, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=4805448.5, rms=3.576 (0.000%) 033: dt: 0.2500, sse=4898941.0, rms=3.358 (0.000%) rms = 3.36, time step reduction 2 of 3 to 0.125... 034: dt: 0.2500, sse=5104938.5, rms=3.356 (0.000%) 035: dt: 0.1250, sse=4867270.5, rms=3.072 (0.000%) 036: dt: 0.1250, sse=4858097.0, rms=3.010 (0.000%) rms = 3.00, time step reduction 3 of 3 to 0.062... 037: dt: 0.1250, sse=4856861.0, rms=3.001 (0.000%) positioning took 1.1 minutes mean border=50.5, 2189 (12) missing vertices, mean dist 0.1 [0.2 (%47.9)->0.3 (%52.1))] %62 local maxima, %18 large gradients and %14 min vals, 282 gradients ignored tol=1.0e-04, sigma=0.2, host= TRON, 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 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=4922149.0, rms=3.39 rms = 4.49, time step reduction 1 of 3 to 0.250... 038: dt: 0.2500, sse=4813526.0, rms=3.095 (0.000%) 039: dt: 0.2500, sse=5046354.0, rms=3.040 (0.000%) rms = 3.09, time step reduction 2 of 3 to 0.125... 040: dt: 0.1250, sse=4976752.0, rms=2.980 (0.000%) 041: dt: 0.1250, sse=4918731.5, rms=2.904 (0.000%) rms = 2.87, time step reduction 3 of 3 to 0.062... 042: dt: 0.1250, sse=4916162.0, rms=2.868 (0.000%) positioning took 1.1 minutes writing curvature file /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.area.pial vertex spacing 0.94 +- 0.40 (0.05-->6.96) (max @ vno 110386 --> 109430) face area 0.36 +- 0.27 (0.00-->6.57) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 144029 vertices processed 25000 of 144029 vertices processed 50000 of 144029 vertices processed 75000 of 144029 vertices processed 100000 of 144029 vertices processed 125000 of 144029 vertices processed 0 of 144029 vertices processed 25000 of 144029 vertices processed 50000 of 144029 vertices processed 75000 of 144029 vertices processed 100000 of 144029 vertices processed 125000 of 144029 vertices processed thickness calculation complete, 119:215 truncations. 38014 vertices at 0 distance 101644 vertices at 1 distance 86512 vertices at 2 distance 35053 vertices at 3 distance 10416 vertices at 4 distance 2945 vertices at 5 distance 866 vertices at 6 distance 258 vertices at 7 distance 92 vertices at 8 distance 44 vertices at 9 distance 24 vertices at 10 distance 28 vertices at 11 distance 18 vertices at 12 distance 11 vertices at 13 distance 7 vertices at 14 distance 7 vertices at 15 distance 5 vertices at 16 distance 6 vertices at 17 distance 7 vertices at 18 distance 1 vertices at 19 distance 2 vertices at 20 distance writing curvature file /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.thickness positioning took 18.8 minutes #-------------------------------------------- #@# Surf Volume rh Tue Dec 13 11:07:18 EST 2016 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.volume rh.area.mid mul rh.thickness Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# Parcellation Stats lh Tue Dec 13 11:07:18 EST 2016 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/scripts mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab 1_S_5002 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/wm.mgz... reading input surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.white... reading input pial surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.pial... reading input white surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1582 1064 2395 2.152 0.429 0.162 0.085 50 5.3 bankssts 1254 790 1992 2.372 0.787 0.182 0.108 36 4.9 caudalanteriorcingulate 3972 2490 5729 2.198 0.420 0.183 0.496 849 22.5 caudalmiddlefrontal 2435 1548 2712 1.678 0.413 0.174 0.076 46 7.9 cuneus 743 470 1495 2.498 0.832 0.191 0.131 30 4.3 entorhinal 4600 2956 8627 2.463 0.573 0.180 0.125 164 27.9 fusiform 6494 4183 10387 2.236 0.406 0.165 0.085 174 23.7 inferiorparietal 4474 2857 8153 2.448 0.554 0.176 0.108 127 19.1 inferiortemporal 1621 1030 2394 2.258 0.787 0.176 0.137 55 6.9 isthmuscingulate 7838 4842 10864 2.036 0.522 0.175 0.099 210 30.6 lateraloccipital 3661 2404 5891 2.288 0.554 0.198 0.150 172 21.7 lateralorbitofrontal 5603 3378 6706 1.879 0.566 0.195 0.239 375 37.4 lingual 3017 2010 4968 2.284 0.670 0.208 0.163 148 20.2 medialorbitofrontal 4187 2758 7867 2.412 0.529 0.173 0.159 142 37.5 middletemporal 1033 641 1928 2.535 0.659 0.172 0.136 40 5.8 parahippocampal 2852 1725 3865 2.186 0.509 0.192 0.238 308 20.2 paracentral 2103 1369 3279 2.225 0.364 0.165 0.102 59 8.9 parsopercularis 785 500 1483 2.339 0.468 0.196 0.134 29 4.1 parsorbitalis 2017 1261 3057 2.177 0.398 0.178 0.224 289 19.5 parstriangularis 2366 1552 2066 1.460 0.392 0.178 0.084 47 8.1 pericalcarine 6991 4202 8846 1.919 0.503 0.171 0.128 297 42.0 postcentral 1769 1167 2907 2.244 0.639 0.172 0.116 57 6.3 posteriorcingulate 8401 5059 12233 2.374 0.541 0.203 0.313 1273 103.4 precentral 5177 3372 7604 2.097 0.466 0.160 0.083 130 18.2 precuneus 1382 925 2785 2.716 0.605 0.207 0.118 47 6.5 rostralanteriorcingulate 8980 6013 14482 2.137 0.445 0.188 0.119 397 39.6 rostralmiddlefrontal 11742 7435 19634 2.368 0.500 0.182 0.147 842 69.3 superiorfrontal 7960 5025 11200 2.058 0.394 0.160 0.099 226 28.9 superiorparietal 5547 3597 10090 2.458 0.498 0.155 0.084 148 18.3 superiortemporal 5401 3535 8932 2.339 0.362 0.169 0.090 121 20.1 supramarginal 324 206 682 2.451 0.440 0.242 0.207 22 2.6 frontalpole 700 465 1892 3.003 0.603 0.187 0.111 19 3.1 temporalpole 842 455 1207 2.259 0.370 0.158 0.223 34 8.7 transversetemporal 3852 2362 6085 2.705 0.723 0.181 0.184 178 27.9 insula #----------------------------------------- #@# Cortical Parc 2 lh Tue Dec 13 11:07:57 EST 2016 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 1_S_5002 lh ../surf/lh.sphere.reg /usr/local/freesurfer/average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/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... 24 labels changed using aseg relabeling using gibbs priors... 000: 9116 changed, 140473 examined... 001: 2127 changed, 35320 examined... 002: 646 changed, 10998 examined... 003: 335 changed, 3666 examined... 004: 162 changed, 1849 examined... 005: 74 changed, 900 examined... 006: 29 changed, 408 examined... 007: 15 changed, 162 examined... 008: 2 changed, 92 examined... 009: 0 changed, 14 examined... 2 labels changed using aseg 000: 279 total segments, 197 labels (2087 vertices) changed 001: 89 total segments, 7 labels (15 vertices) changed 002: 82 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 109 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 992 vertices marked for relabeling... 992 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 1 minutes and 51 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Tue Dec 13 11:09:48 EST 2016 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/scripts mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab 1_S_5002 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/wm.mgz... reading input surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.white... reading input pial surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.pial... reading input white surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1319 862 1887 2.007 0.404 0.167 0.075 33 4.3 G_and_S_frontomargin 1432 947 2554 2.265 0.562 0.178 0.098 38 5.6 G_and_S_occipital_inf 2099 1270 2859 2.005 0.516 0.216 0.189 327 16.0 G_and_S_paracentral 1657 1056 2795 2.359 0.422 0.182 0.315 448 7.2 G_and_S_subcentral 871 578 1739 2.330 0.473 0.210 0.150 40 5.0 G_and_S_transv_frontopol 2525 1689 4445 2.454 0.529 0.187 0.098 66 10.3 G_and_S_cingul-Ant 1473 974 2554 2.559 0.593 0.170 0.097 30 5.2 G_and_S_cingul-Mid-Ant 1311 867 2126 2.325 0.531 0.150 0.076 25 4.4 G_and_S_cingul-Mid-Post 430 277 967 2.596 0.611 0.203 0.115 18 1.9 G_cingul-Post-dorsal 477 278 742 2.248 0.932 0.162 0.104 11 2.0 G_cingul-Post-ventral 2199 1370 2433 1.580 0.409 0.190 0.086 51 8.4 G_cuneus 1108 712 2174 2.367 0.409 0.176 0.100 29 4.7 G_front_inf-Opercular 274 162 465 2.203 0.344 0.196 0.113 10 1.2 G_front_inf-Orbital 1305 796 2181 2.163 0.396 0.193 0.203 65 7.5 G_front_inf-Triangul 5023 3261 9267 2.265 0.440 0.213 0.441 967 31.2 G_front_middle 8511 5156 15014 2.415 0.524 0.204 0.220 921 67.7 G_front_sup 562 338 893 2.523 0.657 0.235 0.304 53 6.7 G_Ins_lg_and_S_cent_ins 851 487 1773 3.053 0.659 0.220 0.176 40 5.2 G_insular_short 1969 1222 3750 2.366 0.452 0.184 0.119 67 8.9 G_occipital_middle 1894 1143 2661 2.033 0.539 0.176 0.128 63 9.0 G_occipital_sup 1811 1076 3659 2.571 0.546 0.203 0.201 114 18.9 G_oc-temp_lat-fusifor 4222 2449 5002 1.837 0.587 0.204 0.270 210 30.3 G_oc-temp_med-Lingual 1317 804 2835 2.620 0.784 0.195 0.174 69 9.9 G_oc-temp_med-Parahip 2326 1470 4454 2.366 0.558 0.218 0.199 154 18.6 G_orbital 2560 1603 4661 2.340 0.376 0.188 0.111 113 12.2 G_pariet_inf-Angular 2895 1899 5445 2.393 0.390 0.187 0.108 86 12.6 G_pariet_inf-Supramar 2667 1681 4129 2.064 0.391 0.179 0.127 121 12.0 G_parietal_sup 2817 1443 3557 1.993 0.517 0.180 0.199 208 27.0 G_postcentral 3504 1722 5184 2.449 0.564 0.207 0.367 333 56.7 G_precentral 2261 1403 3688 2.100 0.510 0.173 0.114 78 10.6 G_precuneus 965 640 2173 2.510 0.495 0.223 0.149 57 5.3 G_rectus 508 337 778 2.471 1.057 0.225 0.245 26 3.8 G_subcallosal 696 344 1069 2.394 0.339 0.155 0.260 34 8.4 G_temp_sup-G_T_transv 2328 1433 5392 2.755 0.443 0.190 0.124 109 10.8 G_temp_sup-Lateral 458 318 965 2.697 0.591 0.149 0.073 7 1.2 G_temp_sup-Plan_polar 942 614 1508 2.307 0.307 0.129 0.059 12 2.1 G_temp_sup-Plan_tempo 2315 1436 5080 2.618 0.578 0.203 0.149 96 13.7 G_temporal_inf 2759 1769 6071 2.558 0.538 0.191 0.203 117 32.6 G_temporal_middle 348 219 524 2.316 0.413 0.194 0.496 227 12.2 Lat_Fis-ant-Horizont 306 210 393 2.096 0.254 0.132 0.051 3 0.7 Lat_Fis-ant-Vertical 1300 872 1623 2.215 0.311 0.149 0.071 18 4.0 Lat_Fis-post 2770 1637 3221 1.837 0.539 0.183 0.117 84 12.3 Pole_occipital 1931 1246 4578 2.710 0.713 0.185 0.124 66 9.6 Pole_temporal 3142 2075 3155 1.708 0.512 0.173 0.104 195 12.1 S_calcarine 3500 2563 4398 1.973 0.615 0.197 0.215 373 36.4 S_central 1227 850 1715 2.196 0.372 0.122 0.038 9 2.0 S_cingul-Marginalis 578 403 817 2.380 0.601 0.197 0.202 24 5.0 S_circular_insula_ant 1716 1088 2300 2.521 0.817 0.124 0.077 28 4.5 S_circular_insula_inf 1910 1236 2396 2.314 0.379 0.151 0.104 43 10.1 S_circular_insula_sup 1129 791 1876 2.310 0.436 0.156 0.062 18 3.0 S_collat_transv_ant 553 363 555 1.809 0.418 0.164 0.125 13 3.6 S_collat_transv_post 2317 1543 2843 1.968 0.398 0.150 0.088 68 6.6 S_front_inf 1983 1325 2684 2.066 0.392 0.172 0.142 119 8.8 S_front_middle 3177 2087 4474 2.199 0.386 0.156 0.080 51 10.8 S_front_sup 114 71 127 2.154 0.286 0.173 0.110 3 0.7 S_interm_prim-Jensen 3106 2024 4035 2.085 0.332 0.138 0.060 37 7.3 S_intrapariet_and_P_trans 1137 746 1329 1.990 0.336 0.134 0.053 12 2.7 S_oc_middle_and_Lunatus 1172 730 1435 2.023 0.389 0.148 0.055 16 2.9 S_oc_sup_and_transversal 781 528 996 2.181 0.330 0.150 0.073 11 2.4 S_occipital_ant 750 497 964 2.184 0.410 0.150 0.063 10 2.0 S_oc-temp_lat 1704 1166 2506 2.307 0.433 0.161 0.074 29 4.8 S_oc-temp_med_and_Lingual 381 242 463 2.133 0.355 0.160 0.076 8 1.2 S_orbital_lateral 820 593 1133 2.201 0.674 0.170 0.101 23 3.5 S_orbital_med-olfact 1251 835 1918 2.270 0.578 0.181 0.101 32 4.7 S_orbital-H_Shaped 2310 1514 2902 2.031 0.401 0.145 0.060 29 5.9 S_parieto_occipital 1467 928 1324 1.831 0.818 0.179 0.158 64 4.8 S_pericallosal 3186 2057 3980 2.022 0.391 0.154 0.072 48 9.8 S_postcentral 1214 800 1662 2.439 0.371 0.144 0.074 18 3.6 S_precentral-inf-part 1571 1003 1898 2.289 0.477 0.173 0.109 41 8.1 S_precentral-sup-part 674 443 922 2.170 0.467 0.210 0.196 37 6.9 S_suborbital 820 538 1294 2.266 0.460 0.169 0.078 29 2.5 S_subparietal 1287 848 1605 2.165 0.386 0.148 0.057 19 3.2 S_temporal_inf 5134 3484 7115 2.148 0.396 0.140 0.058 86 12.1 S_temporal_sup 298 203 349 1.893 0.376 0.166 0.100 4 1.4 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Tue Dec 13 11:10:28 EST 2016 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 1_S_5002 lh ../surf/lh.sphere.reg /usr/local/freesurfer/average/lh.DKTatlas40.gcs ../label/lh.aparc.DKTatlas40.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/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... 932 labels changed using aseg relabeling using gibbs priors... 000: 2706 changed, 140473 examined... 001: 586 changed, 11561 examined... 002: 133 changed, 3369 examined... 003: 56 changed, 791 examined... 004: 21 changed, 303 examined... 005: 13 changed, 127 examined... 006: 11 changed, 78 examined... 007: 8 changed, 65 examined... 008: 4 changed, 45 examined... 009: 1 changed, 27 examined... 010: 0 changed, 6 examined... 109 labels changed using aseg 000: 70 total segments, 37 labels (457 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, 30 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 725 vertices marked for relabeling... 725 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas40.annot... classification took 1 minutes and 40 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Tue Dec 13 11:12:08 EST 2016 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/scripts mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab 1_S_5002 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot. reading volume /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/wm.mgz... reading input surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.white... reading input pial surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.pial... reading input white surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /Applications/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas40.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1803 1150 3012 2.462 0.717 0.177 0.100 45 6.8 caudalanteriorcingulate 4023 2516 5786 2.196 0.422 0.183 0.492 851 22.9 caudalmiddlefrontal 3348 2150 3837 1.739 0.411 0.164 0.070 55 10.2 cuneus 705 451 1428 2.478 0.851 0.188 0.128 29 3.9 entorhinal 4069 2614 7447 2.445 0.558 0.181 0.129 151 25.8 fusiform 6124 3932 9639 2.223 0.398 0.164 0.086 175 22.4 inferiorparietal 4696 2992 8716 2.459 0.567 0.177 0.106 132 20.3 inferiortemporal 1592 1008 2365 2.265 0.785 0.174 0.138 54 6.8 isthmuscingulate 8161 5038 11345 2.036 0.521 0.173 0.097 209 31.4 lateraloccipital 4031 2627 6652 2.292 0.583 0.199 0.151 197 24.5 lateralorbitofrontal 5591 3374 6681 1.878 0.566 0.195 0.240 375 37.4 lingual 2424 1604 4258 2.308 0.654 0.210 0.166 125 16.2 medialorbitofrontal 5522 3667 10190 2.368 0.535 0.173 0.145 190 42.2 middletemporal 1081 675 2015 2.524 0.643 0.172 0.132 40 5.9 parahippocampal 3184 1914 4295 2.204 0.502 0.192 0.231 338 23.0 paracentral 1895 1215 2863 2.238 0.357 0.171 0.132 69 11.9 parsopercularis 943 628 1452 2.144 0.405 0.193 0.117 24 4.5 parsorbitalis 2499 1592 3791 2.140 0.430 0.173 0.193 296 20.8 parstriangularis 2362 1547 2065 1.463 0.392 0.177 0.083 47 8.0 pericalcarine 7688 4658 9717 1.926 0.503 0.170 0.126 315 44.5 postcentral 1928 1270 3087 2.256 0.651 0.170 0.112 60 6.8 posteriorcingulate 8393 5052 12192 2.378 0.537 0.202 0.312 1270 103.0 precentral 5080 3289 7581 2.097 0.475 0.163 0.085 133 18.4 precuneus 1804 1196 3316 2.646 0.609 0.202 0.115 56 8.5 rostralanteriorcingulate 5977 4011 9639 2.141 0.441 0.190 0.122 229 25.7 rostralmiddlefrontal 13385 8582 22641 2.319 0.494 0.187 0.150 985 79.2 superiorfrontal 6325 3993 9107 2.102 0.377 0.162 0.105 191 23.7 superiorparietal 7519 4873 13837 2.480 0.531 0.160 0.089 199 26.9 superiortemporal 5304 3470 8694 2.338 0.359 0.169 0.090 119 19.7 supramarginal 841 458 1210 2.254 0.374 0.157 0.221 34 8.5 transversetemporal 3408 2102 5579 2.748 0.736 0.176 0.170 147 21.2 insula #----------------------------------------- #@# WM/GM Contrast lh Tue Dec 13 11:12:45 EST 2016 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/scripts pctsurfcon --s 1_S_5002 --lh-only Log file is /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/scripts/pctsurfcon.log Tue Dec 13 11:12:45 EST 2016 setenv SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL cd /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/scripts /usr/local/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux TRON 3.8.0-44-generic #66~precise1-Ubuntu SMP Tue Jul 15 04:01:04 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_vol2surf --mov /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/tmp.pctsurfcon.12873/lh.wm.mgh --regheader 1_S_5002 --cortex srcvol = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/orig.mgz as target reference. Loading label /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/label/lh.cortex.label Reading surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 = 73676 Masking with /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/label/lh.cortex.label Writing to /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/tmp.pctsurfcon.12873/lh.wm.mgh Dim: 140473 1 1 mri_vol2surf --mov /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/tmp.pctsurfcon.12873/lh.gm.mgh --projfrac 0.3 --regheader 1_S_5002 --cortex srcvol = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/orig.mgz as target reference. Loading label /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/label/lh.cortex.label Reading surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.white Done reading source surface Reading thickness /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 = 89999 Masking with /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/label/lh.cortex.label Writing to /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/tmp.pctsurfcon.12873/lh.gm.mgh Dim: 140473 1 1 mri_concat /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/tmp.pctsurfcon.12873/lh.wm.mgh /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/tmp.pctsurfcon.12873/lh.gm.mgh --paired-diff-norm --mul 100 --o /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.w-g.pct.mgh mri_segstats --in /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.w-g.pct.mgh --annot 1_S_5002 lh aparc --sum /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/stats/lh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --in /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.w-g.pct.mgh --annot 1_S_5002 lh aparc --sum /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/stats/lh.w-g.pct.stats --snr sysname Linux hostname TRON machine x86_64 user sneha UseRobust 0 Constructing seg from annotation Reading annotation reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Seg base 1000 Loading /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.w-g.pct.mgh Vertex Area is 0.636303 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 1000 unknown 0 0.000 1 1001 bankssts 1582 1063.787 2 1002 caudalanteriorcingulate 1254 790.326 3 1003 caudalmiddlefrontal 3972 2489.578 4 1004 corpuscallosum 0 0.000 5 1005 cuneus 2435 1547.799 6 1006 entorhinal 743 470.246 7 1007 fusiform 4600 2956.252 8 1008 inferiorparietal 6494 4182.925 9 1009 inferiortemporal 4474 2856.905 10 1010 isthmuscingulate 1621 1030.133 11 1011 lateraloccipital 7838 4842.043 12 1012 lateralorbitofrontal 3661 2404.040 13 1013 lingual 5603 3377.881 14 1014 medialorbitofrontal 3017 2009.863 15 1015 middletemporal 4187 2757.766 16 1016 parahippocampal 1033 641.140 17 1017 paracentral 2852 1724.509 18 1018 parsopercularis 2103 1368.791 19 1019 parsorbitalis 785 499.783 20 1020 parstriangularis 2017 1260.908 21 1021 pericalcarine 2366 1551.706 22 1022 postcentral 6991 4201.572 23 1023 posteriorcingulate 1769 1167.363 24 1024 precentral 8401 5058.928 25 1025 precuneus 5177 3372.085 26 1026 rostralanteriorcingulate 1382 925.289 27 1027 rostralmiddlefrontal 8980 6012.660 28 1028 superiorfrontal 11742 7435.352 29 1029 superiorparietal 7960 5025.091 30 1030 superiortemporal 5547 3596.930 31 1031 supramarginal 5401 3535.240 32 1032 frontalpole 324 205.901 33 1033 temporalpole 700 465.035 34 1034 transversetemporal 842 455.316 35 1035 insula 3852 2362.110 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats rh Tue Dec 13 11:13:01 EST 2016 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/scripts mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab 1_S_5002 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/wm.mgz... reading input surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.white... reading input pial surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.pial... reading input white surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1078 724 1541 2.191 0.445 0.142 0.059 12 2.9 bankssts 1272 866 2135 2.115 0.912 0.177 0.130 106 9.3 caudalanteriorcingulate 3586 2191 4986 2.224 0.461 0.164 0.101 154 17.9 caudalmiddlefrontal 2805 1696 3390 1.775 0.467 0.175 0.103 74 13.0 cuneus 585 386 1669 2.969 1.033 0.241 0.225 32 6.3 entorhinal 4344 2767 8038 2.536 0.584 0.186 0.134 319 20.5 fusiform 7806 4981 11374 2.155 0.516 0.181 0.192 748 41.4 inferiorparietal 4257 2674 7643 2.568 0.647 0.188 0.135 174 26.2 inferiortemporal 1622 1048 2394 2.145 0.686 0.192 0.123 57 9.0 isthmuscingulate 8098 4840 10185 2.017 0.512 0.186 0.146 317 58.3 lateraloccipital 4216 2708 6265 2.230 0.689 0.212 0.492 448 31.2 lateralorbitofrontal 5446 3358 6968 1.911 0.597 0.192 0.181 261 56.7 lingual 3122 2071 5261 2.247 0.652 0.182 0.090 107 11.5 medialorbitofrontal 4975 3215 10191 2.606 0.662 0.177 0.128 161 25.3 middletemporal 1073 647 1726 2.301 0.780 0.171 0.130 35 6.3 parahippocampal 2816 1643 3461 2.147 0.507 0.210 0.193 1181 25.2 paracentral 2158 1332 3095 2.196 0.496 0.169 0.103 47 10.2 parsopercularis 1223 780 2067 2.276 0.503 0.206 0.534 467 6.6 parsorbitalis 2093 1354 3487 2.261 0.460 0.184 0.093 54 8.5 parstriangularis 2851 1858 2601 1.525 0.416 0.196 0.132 106 17.3 pericalcarine 7512 4651 8291 1.694 0.539 0.169 0.128 378 37.6 postcentral 1811 1204 2824 2.185 0.724 0.178 0.103 55 8.8 posteriorcingulate 8435 5229 10652 2.069 0.559 0.205 0.184 375 71.7 precentral 5823 3684 8689 2.233 0.577 0.165 0.102 273 23.6 precuneus 1217 796 2231 2.575 0.719 0.210 0.140 53 6.7 rostralanteriorcingulate 9234 6254 15663 2.208 0.482 0.192 0.138 302 41.0 rostralmiddlefrontal 11232 7121 18980 2.396 0.523 0.179 0.149 432 64.5 superiorfrontal 7663 4812 10238 1.990 0.420 0.163 0.090 187 30.1 superiorparietal 5352 3432 9753 2.460 0.616 0.150 0.103 790 16.6 superiortemporal 6410 4015 8807 2.124 0.598 0.174 0.100 151 28.5 supramarginal 381 257 759 2.303 0.362 0.229 0.129 16 2.0 frontalpole 643 453 1780 3.106 0.561 0.217 0.114 19 3.3 temporalpole 614 320 736 2.082 0.406 0.173 0.529 91 23.9 transversetemporal 3637 2254 5583 2.571 0.729 0.199 0.154 135 23.3 insula #----------------------------------------- #@# Cortical Parc 2 rh Tue Dec 13 11:13:44 EST 2016 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 1_S_5002 rh ../surf/rh.sphere.reg /usr/local/freesurfer/average/rh.destrieux.simple.2009-07-29.gcs ../label/rh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/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... 11 labels changed using aseg relabeling using gibbs priors... 000: 9994 changed, 144029 examined... 001: 2315 changed, 38286 examined... 002: 706 changed, 12007 examined... 003: 328 changed, 3979 examined... 004: 176 changed, 1826 examined... 005: 94 changed, 997 examined... 006: 57 changed, 549 examined... 007: 32 changed, 364 examined... 008: 13 changed, 179 examined... 009: 9 changed, 80 examined... 010: 5 changed, 45 examined... 011: 8 changed, 37 examined... 012: 5 changed, 38 examined... 013: 2 changed, 31 examined... 014: 2 changed, 17 examined... 015: 0 changed, 9 examined... 20 labels changed using aseg 000: 308 total segments, 224 labels (3137 vertices) changed 001: 96 total segments, 13 labels (30 vertices) changed 002: 83 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 117 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1190 vertices marked for relabeling... 1190 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 2 minutes and 5 seconds. #----------------------------------------- #@# Parcellation Stats 2 rh Tue Dec 13 11:15:48 EST 2016 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/scripts mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab 1_S_5002 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/wm.mgz... reading input surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.white... reading input pial surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.pial... reading input white surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1042 704 1817 2.279 0.447 0.202 0.338 52 5.3 G_and_S_frontomargin 1424 898 2345 2.297 0.502 0.178 0.111 35 7.0 G_and_S_occipital_inf 1616 923 2027 1.990 0.487 0.222 0.193 98 14.3 G_and_S_paracentral 1672 1012 2364 2.157 0.551 0.178 0.201 82 17.8 G_and_S_subcentral 988 671 1766 2.143 0.366 0.215 0.216 61 6.3 G_and_S_transv_frontopol 2758 1816 4631 2.397 0.601 0.160 0.082 57 8.2 G_and_S_cingul-Ant 1443 974 2748 2.592 0.579 0.166 0.128 105 10.3 G_and_S_cingul-Mid-Ant 1504 961 2346 2.425 0.529 0.181 0.126 66 9.6 G_and_S_cingul-Mid-Post 638 387 1273 2.566 0.530 0.196 0.120 17 3.4 G_cingul-Post-dorsal 423 250 815 2.488 0.723 0.197 0.175 19 3.7 G_cingul-Post-ventral 2529 1551 2980 1.693 0.496 0.193 0.127 84 14.6 G_cuneus 1281 753 2077 2.204 0.536 0.183 0.130 39 7.7 G_front_inf-Opercular 297 184 632 2.507 0.466 0.205 0.098 9 1.4 G_front_inf-Orbital 997 629 1814 2.274 0.464 0.190 0.098 28 4.3 G_front_inf-Triangul 5107 3300 9555 2.303 0.500 0.210 0.152 259 31.2 G_front_middle 8249 5037 14928 2.429 0.564 0.207 0.207 1485 65.5 G_front_sup 602 348 858 2.465 0.631 0.208 0.220 32 5.0 G_Ins_lg_and_S_cent_ins 908 553 1910 2.851 0.840 0.223 0.160 35 6.4 G_insular_short 2151 1286 3438 2.246 0.487 0.205 0.374 503 16.2 G_occipital_middle 2067 1165 2711 2.001 0.410 0.165 0.088 45 8.1 G_occipital_sup 1825 1146 3915 2.674 0.583 0.195 0.169 257 10.5 G_oc-temp_lat-fusifor 3868 2318 5312 1.977 0.643 0.206 0.236 239 54.0 G_oc-temp_med-Lingual 1441 908 3186 2.698 0.900 0.220 0.176 71 11.0 G_oc-temp_med-Parahip 2879 1791 5213 2.316 0.748 0.226 0.352 766 23.3 G_orbital 2585 1619 4516 2.362 0.525 0.201 0.211 214 18.5 G_pariet_inf-Angular 3755 2252 5971 2.254 0.604 0.186 0.123 118 20.5 G_pariet_inf-Supramar 2522 1545 4016 2.125 0.409 0.183 0.108 75 11.8 G_parietal_sup 2911 1557 3092 1.724 0.485 0.191 0.205 291 21.0 G_postcentral 3430 1918 4250 1.990 0.615 0.236 0.234 209 39.0 G_precentral 2068 1350 3729 2.221 0.576 0.164 0.085 171 8.5 G_precuneus 764 535 1638 2.379 0.544 0.208 0.109 31 3.2 G_rectus 565 357 1055 2.637 0.973 0.287 0.199 56 5.0 G_subcallosal 430 208 554 2.100 0.394 0.187 0.731 90 23.4 G_temp_sup-G_T_transv 1772 1082 4450 2.922 0.523 0.188 0.197 751 8.7 G_temp_sup-Lateral 636 429 1296 2.807 0.527 0.146 0.060 8 1.7 G_temp_sup-Plan_polar 866 570 1164 1.985 0.564 0.144 0.065 12 2.5 G_temp_sup-Plan_tempo 2150 1307 4448 2.655 0.770 0.218 0.200 144 19.9 G_temporal_inf 3079 1960 7237 2.752 0.650 0.200 0.168 138 19.8 G_temporal_middle 505 329 724 2.175 0.498 0.165 0.090 8 2.0 Lat_Fis-ant-Horizont 143 92 198 2.290 0.395 0.173 0.075 2 0.4 Lat_Fis-ant-Vertical 1376 898 1584 2.205 0.582 0.155 0.081 20 4.6 Lat_Fis-post 4025 2381 4340 1.740 0.526 0.198 0.179 206 37.6 Pole_occipital 1823 1203 4756 2.978 0.671 0.209 0.155 62 10.6 Pole_temporal 3443 2180 3400 1.799 0.588 0.181 0.121 112 18.6 S_calcarine 3367 2493 3636 1.645 0.569 0.172 0.079 52 12.6 S_central 1452 960 1916 2.160 0.405 0.137 0.063 17 3.8 S_cingul-Marginalis 757 496 985 2.411 0.626 0.223 0.299 46 5.8 S_circular_insula_ant 1572 1003 1838 2.140 0.544 0.132 0.071 19 5.1 S_circular_insula_inf 1301 856 1666 2.303 0.435 0.151 0.066 15 3.8 S_circular_insula_sup 1037 677 1438 2.463 0.420 0.141 0.056 11 2.6 S_collat_transv_ant 755 491 926 2.178 0.378 0.182 0.094 20 2.8 S_collat_transv_post 2180 1406 2798 2.128 0.435 0.159 0.076 63 7.4 S_front_inf 2183 1498 3124 2.152 0.449 0.167 0.076 36 6.8 S_front_middle 2870 1891 3936 2.248 0.370 0.149 0.068 36 8.7 S_front_sup 501 337 480 1.647 0.327 0.161 0.064 7 1.5 S_interm_prim-Jensen 3002 1956 3484 1.950 0.472 0.154 0.071 47 9.2 S_intrapariet_and_P_trans 1100 714 1198 1.834 0.398 0.172 0.093 27 5.0 S_oc_middle_and_Lunatus 1425 916 1531 1.845 0.358 0.148 0.068 19 4.0 S_oc_sup_and_transversal 585 368 735 2.230 0.489 0.158 0.071 9 1.7 S_occipital_ant 698 467 1053 2.417 0.546 0.174 0.090 13 2.9 S_oc-temp_lat 1422 947 1910 2.171 0.530 0.155 0.062 22 3.8 S_oc-temp_med_and_Lingual 491 308 638 2.075 0.477 0.176 0.110 17 2.6 S_orbital_lateral 952 636 1158 2.034 0.811 0.159 1.459 81 4.4 S_orbital_med-olfact 1441 984 2076 2.189 0.494 0.196 0.113 38 7.1 S_orbital-H_Shaped 2661 1668 3367 2.135 0.478 0.147 0.087 60 7.2 S_parieto_occipital 1866 1214 1550 1.631 0.672 0.178 0.096 65 7.4 S_pericallosal 3073 2048 3267 1.766 0.449 0.150 0.066 39 8.6 S_postcentral 1789 1174 2176 2.086 0.434 0.152 0.078 29 6.4 S_precentral-inf-part 1342 841 1456 2.126 0.489 0.150 0.068 20 4.1 S_precentral-sup-part 407 276 530 2.040 0.378 0.154 0.060 6 1.2 S_suborbital 1149 756 1651 2.143 0.476 0.178 0.091 23 4.7 S_subparietal 1346 856 1719 2.300 0.414 0.147 0.064 16 4.1 S_temporal_inf 5749 3803 7667 2.117 0.439 0.148 0.067 90 17.1 S_temporal_sup 360 246 473 2.275 0.354 0.152 0.057 4 1.0 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 rh Tue Dec 13 11:16:31 EST 2016 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 1_S_5002 rh ../surf/rh.sphere.reg /usr/local/freesurfer/average/rh.DKTatlas40.gcs ../label/rh.aparc.DKTatlas40.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/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... 1016 labels changed using aseg relabeling using gibbs priors... 000: 2797 changed, 144029 examined... 001: 677 changed, 11923 examined... 002: 196 changed, 3671 examined... 003: 74 changed, 1133 examined... 004: 20 changed, 427 examined... 005: 9 changed, 115 examined... 006: 6 changed, 51 examined... 007: 3 changed, 26 examined... 008: 4 changed, 17 examined... 009: 2 changed, 20 examined... 010: 3 changed, 14 examined... 011: 4 changed, 16 examined... 012: 2 changed, 24 examined... 013: 2 changed, 10 examined... 014: 1 changed, 10 examined... 015: 1 changed, 7 examined... 016: 1 changed, 7 examined... 017: 1 changed, 7 examined... 018: 0 changed, 8 examined... 124 labels changed using aseg 000: 68 total segments, 35 labels (220 vertices) changed 001: 35 total segments, 2 labels (2 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 49 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1040 vertices marked for relabeling... 1040 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas40.annot... classification took 1 minutes and 38 seconds. #----------------------------------------- #@# Parcellation Stats 3 rh Tue Dec 13 11:18:10 EST 2016 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/scripts mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas40.stats -b -a ../label/rh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab 1_S_5002 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot. reading volume /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/wm.mgz... reading input surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.white... reading input pial surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.pial... reading input white surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /Applications/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas40.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1290 879 2186 2.144 0.910 0.180 0.131 107 9.4 caudalanteriorcingulate 3675 2238 5091 2.228 0.460 0.163 0.101 156 18.1 caudalmiddlefrontal 3425 2099 4162 1.818 0.447 0.170 0.094 82 14.4 cuneus 646 425 1851 2.963 0.989 0.237 0.210 34 6.4 entorhinal 3701 2354 6600 2.513 0.585 0.179 0.118 292 16.0 fusiform 7362 4698 10761 2.162 0.518 0.183 0.200 740 40.0 inferiorparietal 4834 3049 8951 2.595 0.645 0.191 0.142 195 29.4 inferiortemporal 1622 1046 2395 2.143 0.685 0.192 0.123 57 9.0 isthmuscingulate 8437 5046 10591 2.005 0.516 0.186 0.147 328 60.6 lateraloccipital 4427 2889 7201 2.292 0.669 0.213 0.502 459 30.5 lateralorbitofrontal 5469 3386 7025 1.916 0.595 0.191 0.178 259 56.3 lingual 2498 1677 4404 2.259 0.711 0.203 0.110 111 11.3 medialorbitofrontal 5833 3786 11287 2.520 0.662 0.171 0.117 173 27.4 middletemporal 1044 624 1680 2.305 0.772 0.171 0.131 35 6.2 parahippocampal 2975 1722 3625 2.130 0.516 0.212 0.218 1217 29.8 paracentral 2223 1376 3210 2.201 0.499 0.167 0.100 46 10.2 parsopercularis 1438 906 2235 2.206 0.500 0.190 0.455 458 6.7 parsorbitalis 2091 1346 3429 2.252 0.463 0.186 0.099 58 8.9 parstriangularis 2836 1838 2593 1.531 0.414 0.200 0.136 109 17.9 pericalcarine 8048 4954 8884 1.705 0.531 0.169 0.132 423 42.4 postcentral 1946 1282 2988 2.194 0.715 0.177 0.103 57 9.4 posteriorcingulate 8202 5088 10359 2.057 0.557 0.205 0.175 356 70.3 precentral 5701 3635 8644 2.237 0.581 0.164 0.100 267 22.6 precuneus 1341 882 2331 2.559 0.686 0.193 0.117 41 6.3 rostralanteriorcingulate 6024 4045 9772 2.156 0.480 0.194 0.117 188 27.8 rostralmiddlefrontal 14750 9528 25183 2.366 0.512 0.179 0.139 522 76.0 superiorfrontal 6467 4063 8757 1.993 0.429 0.163 0.085 133 23.6 superiorparietal 7019 4534 12949 2.501 0.631 0.162 0.108 848 25.4 superiortemporal 6021 3769 8337 2.129 0.596 0.174 0.101 142 26.8 supramarginal 604 316 724 2.071 0.405 0.173 0.536 91 23.8 transversetemporal 3441 2141 5256 2.554 0.730 0.199 0.176 134 22.3 insula #----------------------------------------- #@# WM/GM Contrast rh Tue Dec 13 11:18:49 EST 2016 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/scripts pctsurfcon --s 1_S_5002 --rh-only Log file is /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/scripts/pctsurfcon.log Tue Dec 13 11:18:49 EST 2016 setenv SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL cd /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/scripts /usr/local/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux TRON 3.8.0-44-generic #66~precise1-Ubuntu SMP Tue Jul 15 04:01:04 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_vol2surf --mov /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/tmp.pctsurfcon.13033/rh.wm.mgh --regheader 1_S_5002 --cortex srcvol = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/orig.mgz as target reference. Loading label /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/label/rh.cortex.label Reading surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 = 75539 Masking with /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/label/rh.cortex.label Writing to /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/tmp.pctsurfcon.13033/rh.wm.mgh Dim: 144029 1 1 mri_vol2surf --mov /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/tmp.pctsurfcon.13033/rh.gm.mgh --projfrac 0.3 --regheader 1_S_5002 --cortex srcvol = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/orig.mgz as target reference. Loading label /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/label/rh.cortex.label Reading surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.white Done reading source surface Reading thickness /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 = 91316 Masking with /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/label/rh.cortex.label Writing to /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/tmp.pctsurfcon.13033/rh.gm.mgh Dim: 144029 1 1 mri_concat /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/tmp.pctsurfcon.13033/rh.wm.mgh /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/tmp.pctsurfcon.13033/rh.gm.mgh --paired-diff-norm --mul 100 --o /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.w-g.pct.mgh mri_segstats --in /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.w-g.pct.mgh --annot 1_S_5002 rh aparc --sum /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/stats/rh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --in /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.w-g.pct.mgh --annot 1_S_5002 rh aparc --sum /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/stats/rh.w-g.pct.stats --snr sysname Linux hostname TRON machine x86_64 user sneha UseRobust 0 Constructing seg from annotation Reading annotation reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Seg base 2000 Loading /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.w-g.pct.mgh Vertex Area is 0.632793 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 2000 unknown 0 0.000 1 2001 bankssts 1078 724.310 2 2002 caudalanteriorcingulate 1272 866.494 3 2003 caudalmiddlefrontal 3586 2190.647 4 2004 corpuscallosum 0 0.000 5 2005 cuneus 2805 1695.835 6 2006 entorhinal 585 386.032 7 2007 fusiform 4344 2767.261 8 2008 inferiorparietal 7806 4981.324 9 2009 inferiortemporal 4257 2674.207 10 2010 isthmuscingulate 1622 1047.651 11 2011 lateraloccipital 8098 4839.597 12 2012 lateralorbitofrontal 4216 2708.447 13 2013 lingual 5446 3358.085 14 2014 medialorbitofrontal 3122 2070.650 15 2015 middletemporal 4975 3214.692 16 2016 parahippocampal 1073 646.759 17 2017 paracentral 2816 1643.120 18 2018 parsopercularis 2158 1332.244 19 2019 parsorbitalis 1223 780.417 20 2020 parstriangularis 2093 1354.305 21 2021 pericalcarine 2851 1858.148 22 2022 postcentral 7512 4651.177 23 2023 posteriorcingulate 1811 1203.672 24 2024 precentral 8435 5228.706 25 2025 precuneus 5823 3683.588 26 2026 rostralanteriorcingulate 1217 796.362 27 2027 rostralmiddlefrontal 9234 6254.148 28 2028 superiorfrontal 11232 7120.868 29 2029 superiorparietal 7663 4811.560 30 2030 superiortemporal 5352 3432.181 31 2031 supramarginal 6410 4014.970 32 2032 frontalpole 381 256.938 33 2033 temporalpole 643 452.662 34 2034 transversetemporal 614 319.545 35 2035 insula 3637 2254.266 Reporting on 34 segmentations mri_segstats done Cleaning up #-------------------------------------------- #@# Cortical ribbon mask Tue Dec 13 11:19:04 EST 2016 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon 1_S_5002 SUBJECTS_DIR is /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL 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 = 45 writing volume /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/ribbon.mgz writing ribbon files #-------------------------------------------- #@# ASeg Stats Tue Dec 13 11:39:37 EST 2016 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/freesurfer/ASegStatsLUT.txt --subject 1_S_5002 $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/freesurfer/ASegStatsLUT.txt --subject 1_S_5002 sysname Linux hostname TRON machine x86_64 user sneha UseRobust 0 atlas_icv (eTIV) = 1428293 mm^3 (det: 1.363940 ) Computing euler number orig.nofix lheno = -188, rheno = -138 orig.nofix lhholes = 95, rhholes = 70 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 201675.585 201244.000 diff= 431.6 pctdiff= 0.214 rhCtxGM: 200966.618 200354.000 diff= 612.6 pctdiff= 0.305 lhCtxWM: 220473.107 220951.000 diff= -477.9 pctdiff=-0.217 rhCtxWM: 230504.814 231234.000 diff= -729.2 pctdiff=-0.316 SubCortGMVol 54162.000 SupraTentVol 944800.124 (943840.000) diff=960.124 pctdiff=0.102 SupraTentVolNotVent 909127.124 (908167.000) diff=960.124 pctdiff=0.106 BrainSegVol 1017205.000 (1012230.000) diff=4975.000 pctdiff=0.489 BrainSegVolNotVent 975336.000 (974840.124) diff=495.876 pctdiff=0.051 BrainSegVolNotVent 975336.000 CerebellumVol 66836.000 VentChorVol 35673.000 3rd4th5thCSF 6196.000 CSFVol 1303.000, OptChiasmVol 251.000 MaskVol 1514856.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation 3 4 Left-Lateral-Ventricle 15908 15907.985 4 5 Left-Inf-Lat-Vent 1078 1078.179 5 7 Left-Cerebellum-White-Matter 9387 9386.782 6 8 Left-Cerebellum-Cortex 24555 24555.211 7 10 Left-Thalamus-Proper 7507 7506.509 8 11 Left-Caudate 3343 3342.553 9 12 Left-Putamen 5451 5450.772 10 13 Left-Pallidum 1867 1867.219 11 14 3rd-Ventricle 2693 2693.160 12 15 4th-Ventricle 2258 2258.200 13 16 Brain-Stem 20992 20992.330 14 17 Left-Hippocampus 3346 3345.640 15 18 Left-Amygdala 1489 1488.733 16 24 CSF 1195 1194.624 17 26 Left-Accumbens-area 429 429.132 18 28 Left-VentralDC 3492 3492.313 19 30 Left-vessel 104 104.481 20 31 Left-choroid-plexus 1371 1371.404 23 43 Right-Lateral-Ventricle 13663 13662.890 24 44 Right-Inf-Lat-Vent 890 890.498 25 46 Right-Cerebellum-White-Matter 9779 9779.438 26 47 Right-Cerebellum-Cortex 25266 25265.570 27 49 Right-Thalamus-Proper 6658 6658.403 28 50 Right-Caudate 3827 3827.370 29 51 Right-Putamen 5231 5231.248 30 52 Right-Pallidum 1644 1643.794 31 53 Right-Hippocampus 3265 3264.508 32 54 Right-Amygdala 1143 1143.120 33 58 Right-Accumbens-area 480 479.553 34 60 Right-VentralDC 3594 3594.172 35 62 Right-vessel 123 123.349 36 63 Right-choroid-plexus 2545 2545.221 37 72 5th-Ventricle 11 10.790 38 77 WM-hypointensities 5765 5765.400 39 78 Left-WM-hypointensities 0 0.000 40 79 Right-WM-hypointensities 0 0.000 41 80 non-WM-hypointensities 88 87.601 42 81 Left-non-WM-hypointensities 0 0.000 43 82 Right-non-WM-hypointensities 0 0.000 44 85 Optic-Chiasm 243 243.119 45 251 CC_Posterior 941 941.290 46 252 CC_Mid_Posterior 323 322.564 47 253 CC_Central 377 376.623 48 254 CC_Mid_Anterior 356 356.344 49 255 CC_Anterior 744 743.504 Reporting on 45 segmentations mri_segstats done #----------------------------------------- #@# AParc-to-ASeg Tue Dec 13 11:43:08 EST 2016 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002 mri_aparc2aseg --s 1_S_5002 --volmask SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL subject 1_S_5002 outvol /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.white Reading lh pial surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.pial Loading lh annotations from /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.white Reading rh pial surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.pial Loading rh annotations from /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 400092 Used brute-force search on 0 voxels Writing output aseg to /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/aparc+aseg.mgz /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002 mri_aparc2aseg --s 1_S_5002 --volmask --a2009s SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL subject 1_S_5002 outvol /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.white Reading lh pial surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.pial Loading lh annotations from /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.white Reading rh pial surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.pial Loading rh annotations from /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 400092 Used brute-force search on 0 voxels Writing output aseg to /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# WMParc Tue Dec 13 11:47:42 EST 2016 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002 mri_aparc2aseg --s 1_S_5002 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL subject 1_S_5002 outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/aparc+aseg.mgz Reading lh white surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.white Reading lh pial surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.pial Loading lh annotations from /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.white Reading rh pial surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.pial Loading rh annotations from /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/ribbon.mgz Loading filled from /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/filled.mgz Ripping vertices labeled as unkown Ripped 8768 vertices from left hemi Ripped 8639 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 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/aseg.mgz Loading Ctx Seg File /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/aparc+aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 850992 Used brute-force search on 185 voxels Fixing Parahip LH WM Found 5 clusters 0 k 1.000000 1 k 1.000000 2 k 1.000000 3 k 1.000000 4 k 1428.000000 Fixing Parahip RH WM Found 11 clusters 0 k 1.000000 1 k 1.000000 2 k 1416.000000 3 k 1.000000 4 k 1.000000 5 k 1.000000 6 k 1.000000 7 k 1.000000 8 k 2.000000 9 k 10.000000 10 k 1.000000 Writing output aseg to mri/wmparc.mgz /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002 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 1_S_5002 --surf-wm-vol --ctab /usr/local/freesurfer/WMParcStatsLUT.txt --etiv $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject 1_S_5002 --surf-wm-vol --ctab /usr/local/freesurfer/WMParcStatsLUT.txt --etiv sysname Linux hostname TRON machine x86_64 user sneha UseRobust 0 atlas_icv (eTIV) = 1428293 mm^3 (det: 1.363940 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 201675.585 201244.000 diff= 431.6 pctdiff= 0.214 rhCtxGM: 200966.618 200354.000 diff= 612.6 pctdiff= 0.305 lhCtxWM: 220473.107 220951.000 diff= -477.9 pctdiff=-0.217 rhCtxWM: 230504.814 231234.000 diff= -729.2 pctdiff=-0.316 SubCortGMVol 54162.000 SupraTentVol 944800.124 (943840.000) diff=960.124 pctdiff=0.102 SupraTentVolNotVent 909127.124 (908167.000) diff=960.124 pctdiff=0.106 BrainSegVol 1017205.000 (1012230.000) diff=4975.000 pctdiff=0.489 BrainSegVolNotVent 975336.000 (974840.124) diff=495.876 pctdiff=0.051 BrainSegVolNotVent 975336.000 CerebellumVol 66836.000 VentChorVol 35673.000 3rd4th5thCSF 6196.000 CSFVol 1303.000, OptChiasmVol 251.000 MaskVol 1514856.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 390 segmentations Computing statistics for each segmentation 0 3000 wm-lh-unknown 0 0.000 1 3001 wm-lh-bankssts 2174 2174.049 2 3002 wm-lh-caudalanteriorcingulate 2990 2989.986 3 3003 wm-lh-caudalmiddlefrontal 7504 7504.089 4 3004 wm-lh-corpuscallosum 0 0.000 5 3005 wm-lh-cuneus 2794 2793.964 6 3006 wm-lh-entorhinal 941 941.135 7 3007 wm-lh-fusiform 5736 5736.035 8 3008 wm-lh-inferiorparietal 9129 9129.022 9 3009 wm-lh-inferiortemporal 5582 5582.294 10 3010 wm-lh-isthmuscingulate 3996 3996.125 11 3011 wm-lh-lateraloccipital 9378 9378.170 12 3012 wm-lh-lateralorbitofrontal 6197 6196.889 13 3013 wm-lh-lingual 5880 5879.894 14 3014 wm-lh-medialorbitofrontal 4401 4401.332 15 3015 wm-lh-middletemporal 4621 4621.402 16 3016 wm-lh-parahippocampal 1463 1462.723 17 3017 wm-lh-paracentral 4957 4956.821 18 3018 wm-lh-parsopercularis 2903 2903.422 19 3019 wm-lh-parsorbitalis 693 693.422 20 3020 wm-lh-parstriangularis 2665 2664.500 21 3021 wm-lh-pericalcarine 3852 3852.052 22 3022 wm-lh-postcentral 7012 7011.936 23 3023 wm-lh-posteriorcingulate 4661 4660.797 24 3024 wm-lh-precentral 13889 13889.240 25 3025 wm-lh-precuneus 7886 7885.694 26 3026 wm-lh-rostralanteriorcingulate 2688 2687.714 27 3027 wm-lh-rostralmiddlefrontal 13131 13130.599 28 3028 wm-lh-superiorfrontal 18563 18563.465 29 3029 wm-lh-superiorparietal 11256 11255.832 30 3030 wm-lh-superiortemporal 6963 6962.891 31 3031 wm-lh-supramarginal 7992 7991.644 32 3032 wm-lh-frontalpole 190 189.555 33 3033 wm-lh-temporalpole 631 630.759 34 3034 wm-lh-transversetemporal 744 743.969 35 3035 wm-lh-insula 9151 9151.390 36 3100 wm-lh-Unknown 0 0.000 37 3101 wm-lh-Corpus_callosum 0 0.000 38 3102 wm-lh-G_and_S_Insula_ONLY_AVERAGE 0 0.000 39 3103 wm-lh-G_cingulate-Isthmus 0 0.000 40 3104 wm-lh-G_cingulate-Main_part 0 0.000 41 3105 wm-lh-G_cuneus 0 0.000 42 3106 wm-lh-G_frontal_inf-Opercular_part 0 0.000 43 3107 wm-lh-G_frontal_inf-Orbital_part 0 0.000 44 3108 wm-lh-G_frontal_inf-Triangular_part 0 0.000 45 3109 wm-lh-G_frontal_middle 0 0.000 46 3110 wm-lh-G_frontal_superior 0 0.000 47 3111 wm-lh-G_frontomarginal 0 0.000 48 3112 wm-lh-G_insular_long 0 0.000 49 3113 wm-lh-G_insular_short 0 0.000 50 3114 wm-lh-G_and_S_occipital_inferior 0 0.000 51 3115 wm-lh-G_occipital_middle 0 0.000 52 3116 wm-lh-G_occipital_superior 0 0.000 53 3117 wm-lh-G_occipit-temp_lat-Or_fusiform 0 0.000 54 3118 wm-lh-G_occipit-temp_med-Lingual_part 0 0.000 55 3119 wm-lh-G_occipit-temp_med-Parahippocampal_part 0 0.000 56 3120 wm-lh-G_orbital 0 0.000 57 3121 wm-lh-G_paracentral 0 0.000 58 3122 wm-lh-G_parietal_inferior-Angular_part 0 0.000 59 3123 wm-lh-G_parietal_inferior-Supramarginal_part 0 0.000 60 3124 wm-lh-G_parietal_superior 0 0.000 61 3125 wm-lh-G_postcentral 0 0.000 62 3126 wm-lh-G_precentral 0 0.000 63 3127 wm-lh-G_precuneus 0 0.000 64 3128 wm-lh-G_rectus 0 0.000 65 3129 wm-lh-G_subcallosal 0 0.000 66 3130 wm-lh-G_subcentral 0 0.000 67 3131 wm-lh-G_temporal_inferior 0 0.000 68 3132 wm-lh-G_temporal_middle 0 0.000 69 3133 wm-lh-G_temp_sup-G_temp_transv_and_interm_S 0 0.000 70 3134 wm-lh-G_temp_sup-Lateral_aspect 0 0.000 71 3135 wm-lh-G_temp_sup-Planum_polare 0 0.000 72 3136 wm-lh-G_temp_sup-Planum_tempolare 0 0.000 73 3137 wm-lh-G_and_S_transverse_frontopolar 0 0.000 74 3138 wm-lh-Lat_Fissure-ant_sgt-ramus_horizontal 0 0.000 75 3139 wm-lh-Lat_Fissure-ant_sgt-ramus_vertical 0 0.000 76 3140 wm-lh-Lat_Fissure-post_sgt 0 0.000 77 3141 wm-lh-Medial_wall 0 0.000 78 3142 wm-lh-Pole_occipital 0 0.000 79 3143 wm-lh-Pole_temporal 0 0.000 80 3144 wm-lh-S_calcarine 0 0.000 81 3145 wm-lh-S_central 0 0.000 82 3146 wm-lh-S_central_insula 0 0.000 83 3147 wm-lh-S_cingulate-Main_part_and_Intracingulate 0 0.000 84 3148 wm-lh-S_cingulate-Marginalis_part 0 0.000 85 3149 wm-lh-S_circular_insula_anterior 0 0.000 86 3150 wm-lh-S_circular_insula_inferior 0 0.000 87 3151 wm-lh-S_circular_insula_superior 0 0.000 88 3152 wm-lh-S_collateral_transverse_ant 0 0.000 89 3153 wm-lh-S_collateral_transverse_post 0 0.000 90 3154 wm-lh-S_frontal_inferior 0 0.000 91 3155 wm-lh-S_frontal_middle 0 0.000 92 3156 wm-lh-S_frontal_superior 0 0.000 93 3157 wm-lh-S_frontomarginal 0 0.000 94 3158 wm-lh-S_intermedius_primus-Jensen 0 0.000 95 3159 wm-lh-S_intraparietal-and_Parietal_transverse 0 0.000 96 3160 wm-lh-S_occipital_anterior 0 0.000 97 3161 wm-lh-S_occipital_middle_and_Lunatus 0 0.000 98 3162 wm-lh-S_occipital_superior_and_transversalis 0 0.000 99 3163 wm-lh-S_occipito-temporal_lateral 0 0.000 100 3164 wm-lh-S_occipito-temporal_medial_and_S_Lingual 0 0.000 101 3165 wm-lh-S_orbital-H_shapped 0 0.000 102 3166 wm-lh-S_orbital_lateral 0 0.000 103 3167 wm-lh-S_orbital_medial-Or_olfactory 0 0.000 104 3168 wm-lh-S_paracentral 0 0.000 105 3169 wm-lh-S_parieto_occipital 0 0.000 106 3170 wm-lh-S_pericallosal 0 0.000 107 3171 wm-lh-S_postcentral 0 0.000 108 3172 wm-lh-S_precentral-Inferior-part 0 0.000 109 3173 wm-lh-S_precentral-Superior-part 0 0.000 110 3174 wm-lh-S_subcentral_ant 0 0.000 111 3175 wm-lh-S_subcentral_post 0 0.000 112 3176 wm-lh-S_suborbital 0 0.000 113 3177 wm-lh-S_subparietal 0 0.000 114 3178 wm-lh-S_supracingulate 0 0.000 115 3179 wm-lh-S_temporal_inferior 0 0.000 116 3180 wm-lh-S_temporal_superior 0 0.000 117 3181 wm-lh-S_temporal_transverse 0 0.000 118 4000 wm-rh-unknown 0 0.000 119 4001 wm-rh-bankssts 2189 2189.203 120 4002 wm-rh-caudalanteriorcingulate 3230 3230.430 121 4003 wm-rh-caudalmiddlefrontal 6614 6613.550 122 4004 wm-rh-corpuscallosum 0 0.000 123 4005 wm-rh-cuneus 2894 2894.065 124 4006 wm-rh-entorhinal 715 714.532 125 4007 wm-rh-fusiform 5775 5775.332 126 4008 wm-rh-inferiorparietal 11551 11551.176 127 4009 wm-rh-inferiortemporal 5513 5513.144 128 4010 wm-rh-isthmuscingulate 3723 3722.533 129 4011 wm-rh-lateraloccipital 9412 9412.125 130 4012 wm-rh-lateralorbitofrontal 7399 7398.501 131 4013 wm-rh-lingual 5847 5847.129 132 4014 wm-rh-medialorbitofrontal 3978 3978.496 133 4015 wm-rh-middletemporal 5395 5395.014 134 4016 wm-rh-parahippocampal 1434 1434.366 135 4017 wm-rh-paracentral 5106 5105.793 136 4018 wm-rh-parsopercularis 3729 3728.937 137 4019 wm-rh-parsorbitalis 1290 1290.384 138 4020 wm-rh-parstriangularis 2804 2803.526 139 4021 wm-rh-pericalcarine 4121 4120.585 140 4022 wm-rh-postcentral 9189 9188.513 141 4023 wm-rh-posteriorcingulate 4135 4135.359 142 4024 wm-rh-precentral 14496 14495.854 143 4025 wm-rh-precuneus 9366 9365.954 144 4026 wm-rh-rostralanteriorcingulate 2275 2275.179 145 4027 wm-rh-rostralmiddlefrontal 13542 13541.771 146 4028 wm-rh-superiorfrontal 18610 18610.281 147 4029 wm-rh-superiorparietal 10375 10374.893 148 4030 wm-rh-superiortemporal 5878 5877.572 149 4031 wm-rh-supramarginal 9979 9979.192 150 4032 wm-rh-frontalpole 239 239.144 151 4033 wm-rh-temporalpole 681 680.572 152 4034 wm-rh-transversetemporal 586 586.230 153 4035 wm-rh-insula 8613 8612.713 154 4100 wm-rh-Unknown 0 0.000 155 4101 wm-rh-Corpus_callosum 0 0.000 156 4102 wm-rh-G_and_S_Insula_ONLY_AVERAGE 0 0.000 157 4103 wm-rh-G_cingulate-Isthmus 0 0.000 158 4104 wm-rh-G_cingulate-Main_part 0 0.000 159 4105 wm-rh-G_cuneus 0 0.000 160 4106 wm-rh-G_frontal_inf-Opercular_part 0 0.000 161 4107 wm-rh-G_frontal_inf-Orbital_part 0 0.000 162 4108 wm-rh-G_frontal_inf-Triangular_part 0 0.000 163 4109 wm-rh-G_frontal_middle 0 0.000 164 4110 wm-rh-G_frontal_superior 0 0.000 165 4111 wm-rh-G_frontomarginal 0 0.000 166 4112 wm-rh-G_insular_long 0 0.000 167 4113 wm-rh-G_insular_short 0 0.000 168 4114 wm-rh-G_and_S_occipital_inferior 0 0.000 169 4115 wm-rh-G_occipital_middle 0 0.000 170 4116 wm-rh-G_occipital_superior 0 0.000 171 4117 wm-rh-G_occipit-temp_lat-Or_fusiform 0 0.000 172 4118 wm-rh-G_occipit-temp_med-Lingual_part 0 0.000 173 4119 wm-rh-G_occipit-temp_med-Parahippocampal_part 0 0.000 174 4120 wm-rh-G_orbital 0 0.000 175 4121 wm-rh-G_paracentral 0 0.000 176 4122 wm-rh-G_parietal_inferior-Angular_part 0 0.000 177 4123 wm-rh-G_parietal_inferior-Supramarginal_part 0 0.000 178 4124 wm-rh-G_parietal_superior 0 0.000 179 4125 wm-rh-G_postcentral 0 0.000 180 4126 wm-rh-G_precentral 0 0.000 181 4127 wm-rh-G_precuneus 0 0.000 182 4128 wm-rh-G_rectus 0 0.000 183 4129 wm-rh-G_subcallosal 0 0.000 184 4130 wm-rh-G_subcentral 0 0.000 185 4131 wm-rh-G_temporal_inferior 0 0.000 186 4132 wm-rh-G_temporal_middle 0 0.000 187 4133 wm-rh-G_temp_sup-G_temp_transv_and_interm_S 0 0.000 188 4134 wm-rh-G_temp_sup-Lateral_aspect 0 0.000 189 4135 wm-rh-G_temp_sup-Planum_polare 0 0.000 190 4136 wm-rh-G_temp_sup-Planum_tempolare 0 0.000 191 4137 wm-rh-G_and_S_transverse_frontopolar 0 0.000 192 4138 wm-rh-Lat_Fissure-ant_sgt-ramus_horizontal 0 0.000 193 4139 wm-rh-Lat_Fissure-ant_sgt-ramus_vertical 0 0.000 194 4140 wm-rh-Lat_Fissure-post_sgt 0 0.000 195 4141 wm-rh-Medial_wall 0 0.000 196 4142 wm-rh-Pole_occipital 0 0.000 197 4143 wm-rh-Pole_temporal 0 0.000 198 4144 wm-rh-S_calcarine 0 0.000 199 4145 wm-rh-S_central 0 0.000 200 4146 wm-rh-S_central_insula 0 0.000 201 4147 wm-rh-S_cingulate-Main_part_and_Intracingulate 0 0.000 202 4148 wm-rh-S_cingulate-Marginalis_part 0 0.000 203 4149 wm-rh-S_circular_insula_anterior 0 0.000 204 4150 wm-rh-S_circular_insula_inferior 0 0.000 205 4151 wm-rh-S_circular_insula_superior 0 0.000 206 4152 wm-rh-S_collateral_transverse_ant 0 0.000 207 4153 wm-rh-S_collateral_transverse_post 0 0.000 208 4154 wm-rh-S_frontal_inferior 0 0.000 209 4155 wm-rh-S_frontal_middle 0 0.000 210 4156 wm-rh-S_frontal_superior 0 0.000 211 4157 wm-rh-S_frontomarginal 0 0.000 212 4158 wm-rh-S_intermedius_primus-Jensen 0 0.000 213 4159 wm-rh-S_intraparietal-and_Parietal_transverse 0 0.000 214 4160 wm-rh-S_occipital_anterior 0 0.000 215 4161 wm-rh-S_occipital_middle_and_Lunatus 0 0.000 216 4162 wm-rh-S_occipital_superior_and_transversalis 0 0.000 217 4163 wm-rh-S_occipito-temporal_lateral 0 0.000 218 4164 wm-rh-S_occipito-temporal_medial_and_S_Lingual 0 0.000 219 4165 wm-rh-S_orbital-H_shapped 0 0.000 220 4166 wm-rh-S_orbital_lateral 0 0.000 221 4167 wm-rh-S_orbital_medial-Or_olfactory 0 0.000 222 4168 wm-rh-S_paracentral 0 0.000 223 4169 wm-rh-S_parieto_occipital 0 0.000 224 4170 wm-rh-S_pericallosal 0 0.000 225 4171 wm-rh-S_postcentral 0 0.000 226 4172 wm-rh-S_precentral-Inferior-part 0 0.000 227 4173 wm-rh-S_precentral-Superior-part 0 0.000 228 4174 wm-rh-S_subcentral_ant 0 0.000 229 4175 wm-rh-S_subcentral_post 0 0.000 230 4176 wm-rh-S_suborbital 0 0.000 231 4177 wm-rh-S_subparietal 0 0.000 232 4178 wm-rh-S_supracingulate 0 0.000 233 4179 wm-rh-S_temporal_inferior 0 0.000 234 4180 wm-rh-S_temporal_superior 0 0.000 235 4181 wm-rh-S_temporal_transverse 0 0.000 236 5001 Left-UnsegmentedWhiteMatter 29405 29405.045 237 5002 Right-UnsegmentedWhiteMatter 31674 31673.801 238 13100 wm_lh_Unknown 0 0.000 239 13101 wm_lh_G_and_S_frontomargin 0 0.000 240 13102 wm_lh_G_and_S_occipital_inf 0 0.000 241 13103 wm_lh_G_and_S_paracentral 0 0.000 242 13104 wm_lh_G_and_S_subcentral 0 0.000 243 13105 wm_lh_G_and_S_transv_frontopol 0 0.000 244 13106 wm_lh_G_and_S_cingul-Ant 0 0.000 245 13107 wm_lh_G_and_S_cingul-Mid-Ant 0 0.000 246 13108 wm_lh_G_and_S_cingul-Mid-Post 0 0.000 247 13109 wm_lh_G_cingul-Post-dorsal 0 0.000 248 13110 wm_lh_G_cingul-Post-ventral 0 0.000 249 13111 wm_lh_G_cuneus 0 0.000 250 13112 wm_lh_G_front_inf-Opercular 0 0.000 251 13113 wm_lh_G_front_inf-Orbital 0 0.000 252 13114 wm_lh_G_front_inf-Triangul 0 0.000 253 13115 wm_lh_G_front_middle 0 0.000 254 13116 wm_lh_G_front_sup 0 0.000 255 13117 wm_lh_G_Ins_lg_and_S_cent_ins 0 0.000 256 13118 wm_lh_G_insular_short 0 0.000 257 13119 wm_lh_G_occipital_middle 0 0.000 258 13120 wm_lh_G_occipital_sup 0 0.000 259 13121 wm_lh_G_oc-temp_lat-fusifor 0 0.000 260 13122 wm_lh_G_oc-temp_med-Lingual 0 0.000 261 13123 wm_lh_G_oc-temp_med-Parahip 0 0.000 262 13124 wm_lh_G_orbital 0 0.000 263 13125 wm_lh_G_pariet_inf-Angular 0 0.000 264 13126 wm_lh_G_pariet_inf-Supramar 0 0.000 265 13127 wm_lh_G_parietal_sup 0 0.000 266 13128 wm_lh_G_postcentral 0 0.000 267 13129 wm_lh_G_precentral 0 0.000 268 13130 wm_lh_G_precuneus 0 0.000 269 13131 wm_lh_G_rectus 0 0.000 270 13132 wm_lh_G_subcallosal 0 0.000 271 13133 wm_lh_G_temp_sup-G_T_transv 0 0.000 272 13134 wm_lh_G_temp_sup-Lateral 0 0.000 273 13135 wm_lh_G_temp_sup-Plan_polar 0 0.000 274 13136 wm_lh_G_temp_sup-Plan_tempo 0 0.000 275 13137 wm_lh_G_temporal_inf 0 0.000 276 13138 wm_lh_G_temporal_middle 0 0.000 277 13139 wm_lh_Lat_Fis-ant-Horizont 0 0.000 278 13140 wm_lh_Lat_Fis-ant-Vertical 0 0.000 279 13141 wm_lh_Lat_Fis-post 0 0.000 280 13142 wm_lh_Medial_wall 0 0.000 281 13143 wm_lh_Pole_occipital 0 0.000 282 13144 wm_lh_Pole_temporal 0 0.000 283 13145 wm_lh_S_calcarine 0 0.000 284 13146 wm_lh_S_central 0 0.000 285 13147 wm_lh_S_cingul-Marginalis 0 0.000 286 13148 wm_lh_S_circular_insula_ant 0 0.000 287 13149 wm_lh_S_circular_insula_inf 0 0.000 288 13150 wm_lh_S_circular_insula_sup 0 0.000 289 13151 wm_lh_S_collat_transv_ant 0 0.000 290 13152 wm_lh_S_collat_transv_post 0 0.000 291 13153 wm_lh_S_front_inf 0 0.000 292 13154 wm_lh_S_front_middle 0 0.000 293 13155 wm_lh_S_front_sup 0 0.000 294 13156 wm_lh_S_interm_prim-Jensen 0 0.000 295 13157 wm_lh_S_intrapariet_and_P_trans 0 0.000 296 13158 wm_lh_S_oc_middle_and_Lunatus 0 0.000 297 13159 wm_lh_S_oc_sup_and_transversal 0 0.000 298 13160 wm_lh_S_occipital_ant 0 0.000 299 13161 wm_lh_S_oc-temp_lat 0 0.000 300 13162 wm_lh_S_oc-temp_med_and_Lingual 0 0.000 301 13163 wm_lh_S_orbital_lateral 0 0.000 302 13164 wm_lh_S_orbital_med-olfact 0 0.000 303 13165 wm_lh_S_orbital-H_Shaped 0 0.000 304 13166 wm_lh_S_parieto_occipital 0 0.000 305 13167 wm_lh_S_pericallosal 0 0.000 306 13168 wm_lh_S_postcentral 0 0.000 307 13169 wm_lh_S_precentral-inf-part 0 0.000 308 13170 wm_lh_S_precentral-sup-part 0 0.000 309 13171 wm_lh_S_suborbital 0 0.000 310 13172 wm_lh_S_subparietal 0 0.000 311 13173 wm_lh_S_temporal_inf 0 0.000 312 13174 wm_lh_S_temporal_sup 0 0.000 313 13175 wm_lh_S_temporal_transverse 0 0.000 314 14100 wm_rh_Unknown 0 0.000 315 14101 wm_rh_G_and_S_frontomargin 0 0.000 316 14102 wm_rh_G_and_S_occipital_inf 0 0.000 317 14103 wm_rh_G_and_S_paracentral 0 0.000 318 14104 wm_rh_G_and_S_subcentral 0 0.000 319 14105 wm_rh_G_and_S_transv_frontopol 0 0.000 320 14106 wm_rh_G_and_S_cingul-Ant 0 0.000 321 14107 wm_rh_G_and_S_cingul-Mid-Ant 0 0.000 322 14108 wm_rh_G_and_S_cingul-Mid-Post 0 0.000 323 14109 wm_rh_G_cingul-Post-dorsal 0 0.000 324 14110 wm_rh_G_cingul-Post-ventral 0 0.000 325 14111 wm_rh_G_cuneus 0 0.000 326 14112 wm_rh_G_front_inf-Opercular 0 0.000 327 14113 wm_rh_G_front_inf-Orbital 0 0.000 328 14114 wm_rh_G_front_inf-Triangul 0 0.000 329 14115 wm_rh_G_front_middle 0 0.000 330 14116 wm_rh_G_front_sup 0 0.000 331 14117 wm_rh_G_Ins_lg_and_S_cent_ins 0 0.000 332 14118 wm_rh_G_insular_short 0 0.000 333 14119 wm_rh_G_occipital_middle 0 0.000 334 14120 wm_rh_G_occipital_sup 0 0.000 335 14121 wm_rh_G_oc-temp_lat-fusifor 0 0.000 336 14122 wm_rh_G_oc-temp_med-Lingual 0 0.000 337 14123 wm_rh_G_oc-temp_med-Parahip 0 0.000 338 14124 wm_rh_G_orbital 0 0.000 339 14125 wm_rh_G_pariet_inf-Angular 0 0.000 340 14126 wm_rh_G_pariet_inf-Supramar 0 0.000 341 14127 wm_rh_G_parietal_sup 0 0.000 342 14128 wm_rh_G_postcentral 0 0.000 343 14129 wm_rh_G_precentral 0 0.000 344 14130 wm_rh_G_precuneus 0 0.000 345 14131 wm_rh_G_rectus 0 0.000 346 14132 wm_rh_G_subcallosal 0 0.000 347 14133 wm_rh_G_temp_sup-G_T_transv 0 0.000 348 14134 wm_rh_G_temp_sup-Lateral 0 0.000 349 14135 wm_rh_G_temp_sup-Plan_polar 0 0.000 350 14136 wm_rh_G_temp_sup-Plan_tempo 0 0.000 351 14137 wm_rh_G_temporal_inf 0 0.000 352 14138 wm_rh_G_temporal_middle 0 0.000 353 14139 wm_rh_Lat_Fis-ant-Horizont 0 0.000 354 14140 wm_rh_Lat_Fis-ant-Vertical 0 0.000 355 14141 wm_rh_Lat_Fis-post 0 0.000 356 14142 wm_rh_Medial_wall 0 0.000 357 14143 wm_rh_Pole_occipital 0 0.000 358 14144 wm_rh_Pole_temporal 0 0.000 359 14145 wm_rh_S_calcarine 0 0.000 360 14146 wm_rh_S_central 0 0.000 361 14147 wm_rh_S_cingul-Marginalis 0 0.000 362 14148 wm_rh_S_circular_insula_ant 0 0.000 363 14149 wm_rh_S_circular_insula_inf 0 0.000 364 14150 wm_rh_S_circular_insula_sup 0 0.000 365 14151 wm_rh_S_collat_transv_ant 0 0.000 366 14152 wm_rh_S_collat_transv_post 0 0.000 367 14153 wm_rh_S_front_inf 0 0.000 368 14154 wm_rh_S_front_middle 0 0.000 369 14155 wm_rh_S_front_sup 0 0.000 370 14156 wm_rh_S_interm_prim-Jensen 0 0.000 371 14157 wm_rh_S_intrapariet_and_P_trans 0 0.000 372 14158 wm_rh_S_oc_middle_and_Lunatus 0 0.000 373 14159 wm_rh_S_oc_sup_and_transversal 0 0.000 374 14160 wm_rh_S_occipital_ant 0 0.000 375 14161 wm_rh_S_oc-temp_lat 0 0.000 376 14162 wm_rh_S_oc-temp_med_and_Lingual 0 0.000 377 14163 wm_rh_S_orbital_lateral 0 0.000 378 14164 wm_rh_S_orbital_med-olfact 0 0.000 379 14165 wm_rh_S_orbital-H_Shaped 0 0.000 380 14166 wm_rh_S_parieto_occipital 0 0.000 381 14167 wm_rh_S_pericallosal 0 0.000 382 14168 wm_rh_S_postcentral 0 0.000 383 14169 wm_rh_S_precentral-inf-part 0 0.000 384 14170 wm_rh_S_precentral-sup-part 0 0.000 385 14171 wm_rh_S_suborbital 0 0.000 386 14172 wm_rh_S_subparietal 0 0.000 387 14173 wm_rh_S_temporal_inf 0 0.000 388 14174 wm_rh_S_temporal_sup 0 0.000 389 14175 wm_rh_S_temporal_transverse 0 0.000 Reporting on 70 segmentations mri_segstats done /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf #-------------------------------------------- #@# Qdec Cache lh thickness fsaverage Tue Dec 13 11:59:35 EST 2016 mris_preproc --s 1_S_5002 --hemi lh --meas thickness --target fsaverage --out lh.thickness.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.13282 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf Log file is lh.thickness.fsaverage.mris_preproc.log Tue Dec 13 11:59:35 EST 2016 setenv SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL cd /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf /usr/local/freesurfer/bin/mris_preproc --s 1_S_5002 --hemi lh --meas thickness --target fsaverage --out lh.thickness.fsaverage.mgh Linux TRON 3.8.0-44-generic #66~precise1-Ubuntu SMP Tue Jul 15 04:01:04 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.4 2012/12/06 16:06:52 mreuter Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 tmpdir is ./tmp.mris_preproc.13282 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 1_S_5002 Tue Dec 13 11:59:36 EST 2016 -------------- ----------------------- mri_surf2surf --srcsubject 1_S_5002 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.13282/1_S_5002.1.mgh --sval /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.thickness --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = 1_S_5002 srcval = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.thickness srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.13282/1_S_5002.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.sphere.reg Loading source data Reading curvature file /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.thickness Reading target surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (140473) Reverse Loop had 27576 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 144254, nTrgMulti = 19588, MnTrgMultiHits = 2.4078 nSrc121 = 102295, nSrcLost = 0, nSrcMulti = 38178, MnSrcMultiHits = 2.33441 Saving target data Saving to ./tmp.mris_preproc.13282/1_S_5002.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.13282/1_S_5002.1.mgh --o lh.thickness.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to lh.thickness.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.13282 Tue Dec 13 11:59:47 EST 2016 mris_preproc done #-------------------------------------------- #@# Qdec Cache lh thickness fwhm0 fsaverage Tue Dec 13 11:59:47 EST 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 0 --sval lh.thickness.fsaverage.mgh --tval lh.thickness.fwhm0.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.thickness.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.thickness.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to lh.thickness.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh thickness fwhm5 fsaverage Tue Dec 13 11:59:52 EST 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 5 --sval lh.thickness.fsaverage.mgh --tval lh.thickness.fwhm5.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.thickness.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.thickness.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 18 Saving target data Saving to lh.thickness.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh thickness fwhm10 fsaverage Tue Dec 13 12:00:01 EST 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval lh.thickness.fsaverage.mgh --tval lh.thickness.fwhm10.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.thickness.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.thickness.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 74 Saving target data Saving to lh.thickness.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh thickness fwhm15 fsaverage Tue Dec 13 12:00:12 EST 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 15 --sval lh.thickness.fsaverage.mgh --tval lh.thickness.fwhm15.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.thickness.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.thickness.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 165 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 165 Saving target data Saving to lh.thickness.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh thickness fwhm20 fsaverage Tue Dec 13 12:00:23 EST 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 20 --sval lh.thickness.fsaverage.mgh --tval lh.thickness.fwhm20.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.thickness.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.thickness.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 294 Saving target data Saving to lh.thickness.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh thickness fwhm25 fsaverage Tue Dec 13 12:00:32 EST 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 25 --sval lh.thickness.fsaverage.mgh --tval lh.thickness.fwhm25.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.thickness.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.thickness.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 460 Saving target data Saving to lh.thickness.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh area fsaverage Tue Dec 13 12:00:45 EST 2016 mris_preproc --s 1_S_5002 --hemi lh --meas area --target fsaverage --out lh.area.fsaverage.mgh nsubjects = 1 INFO: turning on jacobican correction tmpdir is ./tmp.mris_preproc.13496 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf Log file is lh.area.fsaverage.mris_preproc.log Tue Dec 13 12:00:45 EST 2016 setenv SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL cd /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf /usr/local/freesurfer/bin/mris_preproc --s 1_S_5002 --hemi lh --meas area --target fsaverage --out lh.area.fsaverage.mgh Linux TRON 3.8.0-44-generic #66~precise1-Ubuntu SMP Tue Jul 15 04:01:04 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.4 2012/12/06 16:06:52 mreuter Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 tmpdir is ./tmp.mris_preproc.13496 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 1_S_5002 Tue Dec 13 12:00:45 EST 2016 -------------- ----------------------- mri_surf2surf --srcsubject 1_S_5002 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.13496/1_S_5002.1.mgh --sval /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.area --jac --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = 1_S_5002 srcval = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.area srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.13496/1_S_5002.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.sphere.reg Loading source data Reading curvature file /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.area Reading target surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Done Mapping Source Volume onto Source Subject Surface with Jacobian Correction surf2surf_nnfr_jac: building source hash (res=16). Surf2SurfJac: 1st Forward Loop (163842) Surf2SurfJac: 2nd Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2SurfJac: Reverse Loop (140473) Reverse Loop had 27576 hits INFO: nSrcLost = 0 surf2surf_nnfr_jac() done nTrg121 = 144254, nTrgMulti = 19588, MnTrgMultiHits = 2.4078 nSrc121 = 102295, nSrcLost = 0, nSrcMulti = 38178, MnSrcMultiHits = 2.33441 Saving target data Saving to ./tmp.mris_preproc.13496/1_S_5002.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.13496/1_S_5002.1.mgh --o lh.area.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to lh.area.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.13496 Tue Dec 13 12:01:00 EST 2016 mris_preproc done #-------------------------------------------- #@# Qdec Cache lh area fwhm0 fsaverage Tue Dec 13 12:01:00 EST 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 0 --sval lh.area.fsaverage.mgh --tval lh.area.fwhm0.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to lh.area.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh area fwhm5 fsaverage Tue Dec 13 12:01:03 EST 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 5 --sval lh.area.fsaverage.mgh --tval lh.area.fwhm5.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 18 Saving target data Saving to lh.area.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh area fwhm10 fsaverage Tue Dec 13 12:01:12 EST 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval lh.area.fsaverage.mgh --tval lh.area.fwhm10.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 74 Saving target data Saving to lh.area.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh area fwhm15 fsaverage Tue Dec 13 12:01:22 EST 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 15 --sval lh.area.fsaverage.mgh --tval lh.area.fwhm15.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 165 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 165 Saving target data Saving to lh.area.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh area fwhm20 fsaverage Tue Dec 13 12:01:32 EST 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 20 --sval lh.area.fsaverage.mgh --tval lh.area.fwhm20.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 294 Saving target data Saving to lh.area.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh area fwhm25 fsaverage Tue Dec 13 12:01:43 EST 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 25 --sval lh.area.fsaverage.mgh --tval lh.area.fwhm25.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 460 Saving target data Saving to lh.area.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh area.pial fsaverage Tue Dec 13 12:01:53 EST 2016 mris_preproc --s 1_S_5002 --hemi lh --meas area.pial --target fsaverage --out lh.area.pial.fsaverage.mgh nsubjects = 1 INFO: turning on jacobican correction tmpdir is ./tmp.mris_preproc.13708 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf Log file is lh.area.pial.fsaverage.mris_preproc.log Tue Dec 13 12:01:53 EST 2016 setenv SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL cd /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf /usr/local/freesurfer/bin/mris_preproc --s 1_S_5002 --hemi lh --meas area.pial --target fsaverage --out lh.area.pial.fsaverage.mgh Linux TRON 3.8.0-44-generic #66~precise1-Ubuntu SMP Tue Jul 15 04:01:04 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.4 2012/12/06 16:06:52 mreuter Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 tmpdir is ./tmp.mris_preproc.13708 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 1_S_5002 Tue Dec 13 12:01:53 EST 2016 -------------- ----------------------- mri_surf2surf --srcsubject 1_S_5002 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.13708/1_S_5002.1.mgh --sval /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.area.pial --jac --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = 1_S_5002 srcval = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.area.pial srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.13708/1_S_5002.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.sphere.reg Loading source data Reading curvature file /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.area.pial Reading target surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Done Mapping Source Volume onto Source Subject Surface with Jacobian Correction surf2surf_nnfr_jac: building source hash (res=16). Surf2SurfJac: 1st Forward Loop (163842) Surf2SurfJac: 2nd Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2SurfJac: Reverse Loop (140473) Reverse Loop had 27576 hits INFO: nSrcLost = 0 surf2surf_nnfr_jac() done nTrg121 = 144254, nTrgMulti = 19588, MnTrgMultiHits = 2.4078 nSrc121 = 102295, nSrcLost = 0, nSrcMulti = 38178, MnSrcMultiHits = 2.33441 Saving target data Saving to ./tmp.mris_preproc.13708/1_S_5002.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.13708/1_S_5002.1.mgh --o lh.area.pial.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to lh.area.pial.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.13708 Tue Dec 13 12:02:10 EST 2016 mris_preproc done #-------------------------------------------- #@# Qdec Cache lh area.pial fwhm0 fsaverage Tue Dec 13 12:02:10 EST 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 0 --sval lh.area.pial.fsaverage.mgh --tval lh.area.pial.fwhm0.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.pial.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.pial.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to lh.area.pial.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh area.pial fwhm5 fsaverage Tue Dec 13 12:02:14 EST 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 5 --sval lh.area.pial.fsaverage.mgh --tval lh.area.pial.fwhm5.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.pial.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.pial.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 18 Saving target data Saving to lh.area.pial.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh area.pial fwhm10 fsaverage Tue Dec 13 12:02:22 EST 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval lh.area.pial.fsaverage.mgh --tval lh.area.pial.fwhm10.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.pial.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.pial.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 74 Saving target data Saving to lh.area.pial.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh area.pial fwhm15 fsaverage Tue Dec 13 12:02:31 EST 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 15 --sval lh.area.pial.fsaverage.mgh --tval lh.area.pial.fwhm15.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.pial.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.pial.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 165 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 165 Saving target data Saving to lh.area.pial.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh area.pial fwhm20 fsaverage Tue Dec 13 12:02:42 EST 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 20 --sval lh.area.pial.fsaverage.mgh --tval lh.area.pial.fwhm20.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.pial.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.pial.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 294 Saving target data Saving to lh.area.pial.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh area.pial fwhm25 fsaverage Tue Dec 13 12:02:53 EST 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 25 --sval lh.area.pial.fsaverage.mgh --tval lh.area.pial.fwhm25.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.pial.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.pial.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 460 Saving target data Saving to lh.area.pial.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh volume fsaverage Tue Dec 13 12:03:08 EST 2016 mris_preproc --s 1_S_5002 --hemi lh --meas volume --target fsaverage --out lh.volume.fsaverage.mgh nsubjects = 1 INFO: turning on jacobican correction tmpdir is ./tmp.mris_preproc.13924 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf Log file is lh.volume.fsaverage.mris_preproc.log Tue Dec 13 12:03:08 EST 2016 setenv SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL cd /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf /usr/local/freesurfer/bin/mris_preproc --s 1_S_5002 --hemi lh --meas volume --target fsaverage --out lh.volume.fsaverage.mgh Linux TRON 3.8.0-44-generic #66~precise1-Ubuntu SMP Tue Jul 15 04:01:04 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.4 2012/12/06 16:06:52 mreuter Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 tmpdir is ./tmp.mris_preproc.13924 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 1_S_5002 Tue Dec 13 12:03:08 EST 2016 -------------- ----------------------- mri_surf2surf --srcsubject 1_S_5002 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.13924/1_S_5002.1.mgh --sval /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.volume --jac --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = 1_S_5002 srcval = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.volume srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.13924/1_S_5002.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.sphere.reg Loading source data Reading curvature file /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.volume Reading target surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Done Mapping Source Volume onto Source Subject Surface with Jacobian Correction surf2surf_nnfr_jac: building source hash (res=16). Surf2SurfJac: 1st Forward Loop (163842) Surf2SurfJac: 2nd Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2SurfJac: Reverse Loop (140473) Reverse Loop had 27576 hits INFO: nSrcLost = 0 surf2surf_nnfr_jac() done nTrg121 = 144254, nTrgMulti = 19588, MnTrgMultiHits = 2.4078 nSrc121 = 102295, nSrcLost = 0, nSrcMulti = 38178, MnSrcMultiHits = 2.33441 Saving target data Saving to ./tmp.mris_preproc.13924/1_S_5002.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.13924/1_S_5002.1.mgh --o lh.volume.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to lh.volume.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.13924 Tue Dec 13 12:03:24 EST 2016 mris_preproc done #-------------------------------------------- #@# Qdec Cache lh volume fwhm0 fsaverage Tue Dec 13 12:03:24 EST 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 0 --sval lh.volume.fsaverage.mgh --tval lh.volume.fwhm0.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.volume.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.volume.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to lh.volume.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh volume fwhm5 fsaverage Tue Dec 13 12:03:29 EST 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 5 --sval lh.volume.fsaverage.mgh --tval lh.volume.fwhm5.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.volume.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.volume.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 18 Saving target data Saving to lh.volume.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh volume fwhm10 fsaverage Tue Dec 13 12:03:38 EST 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval lh.volume.fsaverage.mgh --tval lh.volume.fwhm10.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.volume.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.volume.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 74 Saving target data Saving to lh.volume.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh volume fwhm15 fsaverage Tue Dec 13 12:03:48 EST 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 15 --sval lh.volume.fsaverage.mgh --tval lh.volume.fwhm15.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.volume.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.volume.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 165 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 165 Saving target data Saving to lh.volume.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh volume fwhm20 fsaverage Tue Dec 13 12:03:57 EST 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 20 --sval lh.volume.fsaverage.mgh --tval lh.volume.fwhm20.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.volume.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.volume.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 294 Saving target data Saving to lh.volume.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh volume fwhm25 fsaverage Tue Dec 13 12:04:08 EST 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 25 --sval lh.volume.fsaverage.mgh --tval lh.volume.fwhm25.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.volume.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.volume.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 460 Saving target data Saving to lh.volume.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh curv fsaverage Tue Dec 13 12:04:19 EST 2016 mris_preproc --s 1_S_5002 --hemi lh --meas curv --target fsaverage --out lh.curv.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.14139 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf Log file is lh.curv.fsaverage.mris_preproc.log Tue Dec 13 12:04:19 EST 2016 setenv SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL cd /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf /usr/local/freesurfer/bin/mris_preproc --s 1_S_5002 --hemi lh --meas curv --target fsaverage --out lh.curv.fsaverage.mgh Linux TRON 3.8.0-44-generic #66~precise1-Ubuntu SMP Tue Jul 15 04:01:04 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.4 2012/12/06 16:06:52 mreuter Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 tmpdir is ./tmp.mris_preproc.14139 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 1_S_5002 Tue Dec 13 12:04:19 EST 2016 -------------- ----------------------- mri_surf2surf --srcsubject 1_S_5002 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.14139/1_S_5002.1.mgh --sval /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.curv --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = 1_S_5002 srcval = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.curv srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.14139/1_S_5002.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.sphere.reg Loading source data Reading curvature file /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.curv Reading target surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (140473) Reverse Loop had 27576 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 144254, nTrgMulti = 19588, MnTrgMultiHits = 2.4078 nSrc121 = 102295, nSrcLost = 0, nSrcMulti = 38178, MnSrcMultiHits = 2.33441 Saving target data Saving to ./tmp.mris_preproc.14139/1_S_5002.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.14139/1_S_5002.1.mgh --o lh.curv.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to lh.curv.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.14139 Tue Dec 13 12:04:30 EST 2016 mris_preproc done #-------------------------------------------- #@# Qdec Cache lh curv fwhm0 fsaverage Tue Dec 13 12:04:30 EST 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 0 --sval lh.curv.fsaverage.mgh --tval lh.curv.fwhm0.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.curv.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.curv.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to lh.curv.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh curv fwhm5 fsaverage Tue Dec 13 12:04:33 EST 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 5 --sval lh.curv.fsaverage.mgh --tval lh.curv.fwhm5.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.curv.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.curv.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 18 Saving target data Saving to lh.curv.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh curv fwhm10 fsaverage Tue Dec 13 12:04:43 EST 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval lh.curv.fsaverage.mgh --tval lh.curv.fwhm10.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.curv.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.curv.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 74 Saving target data Saving to lh.curv.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh curv fwhm15 fsaverage Tue Dec 13 12:04:53 EST 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 15 --sval lh.curv.fsaverage.mgh --tval lh.curv.fwhm15.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.curv.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.curv.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 165 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 165 Saving target data Saving to lh.curv.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh curv fwhm20 fsaverage Tue Dec 13 12:05:04 EST 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 20 --sval lh.curv.fsaverage.mgh --tval lh.curv.fwhm20.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.curv.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.curv.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 294 Saving target data Saving to lh.curv.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh curv fwhm25 fsaverage Tue Dec 13 12:05:13 EST 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 25 --sval lh.curv.fsaverage.mgh --tval lh.curv.fwhm25.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.curv.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.curv.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 460 Saving target data Saving to lh.curv.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh sulc fsaverage Tue Dec 13 12:05:24 EST 2016 mris_preproc --s 1_S_5002 --hemi lh --meas sulc --target fsaverage --out lh.sulc.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.14350 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf Log file is lh.sulc.fsaverage.mris_preproc.log Tue Dec 13 12:05:24 EST 2016 setenv SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL cd /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf /usr/local/freesurfer/bin/mris_preproc --s 1_S_5002 --hemi lh --meas sulc --target fsaverage --out lh.sulc.fsaverage.mgh Linux TRON 3.8.0-44-generic #66~precise1-Ubuntu SMP Tue Jul 15 04:01:04 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.4 2012/12/06 16:06:52 mreuter Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 tmpdir is ./tmp.mris_preproc.14350 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 1_S_5002 Tue Dec 13 12:05:25 EST 2016 -------------- ----------------------- mri_surf2surf --srcsubject 1_S_5002 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.14350/1_S_5002.1.mgh --sval /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.sulc --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = 1_S_5002 srcval = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.sulc srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.14350/1_S_5002.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.sphere.reg Loading source data Reading curvature file /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.sulc Reading target surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (140473) Reverse Loop had 27576 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 144254, nTrgMulti = 19588, MnTrgMultiHits = 2.4078 nSrc121 = 102295, nSrcLost = 0, nSrcMulti = 38178, MnSrcMultiHits = 2.33441 Saving target data Saving to ./tmp.mris_preproc.14350/1_S_5002.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.14350/1_S_5002.1.mgh --o lh.sulc.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to lh.sulc.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.14350 Tue Dec 13 12:05:35 EST 2016 mris_preproc done #-------------------------------------------- #@# Qdec Cache lh sulc fwhm0 fsaverage Tue Dec 13 12:05:35 EST 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 0 --sval lh.sulc.fsaverage.mgh --tval lh.sulc.fwhm0.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.sulc.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.sulc.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to lh.sulc.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh sulc fwhm5 fsaverage Tue Dec 13 12:05:39 EST 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 5 --sval lh.sulc.fsaverage.mgh --tval lh.sulc.fwhm5.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.sulc.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.sulc.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 18 Saving target data Saving to lh.sulc.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh sulc fwhm10 fsaverage Tue Dec 13 12:05:49 EST 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval lh.sulc.fsaverage.mgh --tval lh.sulc.fwhm10.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.sulc.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.sulc.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 74 Saving target data Saving to lh.sulc.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh sulc fwhm15 fsaverage Tue Dec 13 12:05:58 EST 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 15 --sval lh.sulc.fsaverage.mgh --tval lh.sulc.fwhm15.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.sulc.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.sulc.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 165 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 165 Saving target data Saving to lh.sulc.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh sulc fwhm20 fsaverage Tue Dec 13 12:06:09 EST 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 20 --sval lh.sulc.fsaverage.mgh --tval lh.sulc.fwhm20.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.sulc.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.sulc.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 294 Saving target data Saving to lh.sulc.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh sulc fwhm25 fsaverage Tue Dec 13 12:06:21 EST 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 25 --sval lh.sulc.fsaverage.mgh --tval lh.sulc.fwhm25.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.sulc.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.sulc.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 460 Saving target data Saving to lh.sulc.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh white.K fsaverage Tue Dec 13 12:06:33 EST 2016 INFO: File lh.white.K does not exist! Skipping creation of smoothed data for lh.white.K #-------------------------------------------- #@# Qdec Cache lh white.H fsaverage Tue Dec 13 12:06:33 EST 2016 INFO: File lh.white.H does not exist! Skipping creation of smoothed data for lh.white.H #-------------------------------------------- #@# Qdec Cache lh jacobian_white fsaverage Tue Dec 13 12:06:33 EST 2016 mris_preproc --s 1_S_5002 --hemi lh --meas jacobian_white --target fsaverage --out lh.jacobian_white.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.14590 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf Log file is lh.jacobian_white.fsaverage.mris_preproc.log Tue Dec 13 12:06:33 EST 2016 setenv SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL cd /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf /usr/local/freesurfer/bin/mris_preproc --s 1_S_5002 --hemi lh --meas jacobian_white --target fsaverage --out lh.jacobian_white.fsaverage.mgh Linux TRON 3.8.0-44-generic #66~precise1-Ubuntu SMP Tue Jul 15 04:01:04 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.4 2012/12/06 16:06:52 mreuter Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 tmpdir is ./tmp.mris_preproc.14590 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 1_S_5002 Tue Dec 13 12:06:33 EST 2016 -------------- ----------------------- mri_surf2surf --srcsubject 1_S_5002 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.14590/1_S_5002.1.mgh --sval /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.jacobian_white --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = 1_S_5002 srcval = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.jacobian_white srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.14590/1_S_5002.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.sphere.reg Loading source data Reading curvature file /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.jacobian_white Reading target surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (140473) Reverse Loop had 27576 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 144254, nTrgMulti = 19588, MnTrgMultiHits = 2.4078 nSrc121 = 102295, nSrcLost = 0, nSrcMulti = 38178, MnSrcMultiHits = 2.33441 Saving target data Saving to ./tmp.mris_preproc.14590/1_S_5002.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.14590/1_S_5002.1.mgh --o lh.jacobian_white.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to lh.jacobian_white.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.14590 Tue Dec 13 12:06:44 EST 2016 mris_preproc done #-------------------------------------------- #@# Qdec Cache lh jacobian_white fwhm0 fsaverage Tue Dec 13 12:06:44 EST 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 0 --sval lh.jacobian_white.fsaverage.mgh --tval lh.jacobian_white.fwhm0.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.jacobian_white.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.jacobian_white.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to lh.jacobian_white.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh jacobian_white fwhm5 fsaverage Tue Dec 13 12:06:47 EST 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 5 --sval lh.jacobian_white.fsaverage.mgh --tval lh.jacobian_white.fwhm5.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.jacobian_white.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.jacobian_white.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 18 Saving target data Saving to lh.jacobian_white.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh jacobian_white fwhm10 fsaverage Tue Dec 13 12:06:55 EST 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval lh.jacobian_white.fsaverage.mgh --tval lh.jacobian_white.fwhm10.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.jacobian_white.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.jacobian_white.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 74 Saving target data Saving to lh.jacobian_white.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh jacobian_white fwhm15 fsaverage Tue Dec 13 12:07:04 EST 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 15 --sval lh.jacobian_white.fsaverage.mgh --tval lh.jacobian_white.fwhm15.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.jacobian_white.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.jacobian_white.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 165 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 165 Saving target data Saving to lh.jacobian_white.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh jacobian_white fwhm20 fsaverage Tue Dec 13 12:07:13 EST 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 20 --sval lh.jacobian_white.fsaverage.mgh --tval lh.jacobian_white.fwhm20.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.jacobian_white.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.jacobian_white.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 294 Saving target data Saving to lh.jacobian_white.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh jacobian_white fwhm25 fsaverage Tue Dec 13 12:07:24 EST 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 25 --sval lh.jacobian_white.fsaverage.mgh --tval lh.jacobian_white.fwhm25.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.jacobian_white.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.jacobian_white.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 460 Saving target data Saving to lh.jacobian_white.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh w-g.pct.mgh fsaverage Tue Dec 13 12:07:34 EST 2016 mris_preproc --s 1_S_5002 --hemi lh --meas w-g.pct.mgh --target fsaverage --out lh.w-g.pct.mgh.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.14799 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf Log file is lh.w-g.pct.mgh.fsaverage.mris_preproc.log Tue Dec 13 12:07:34 EST 2016 setenv SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL cd /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf /usr/local/freesurfer/bin/mris_preproc --s 1_S_5002 --hemi lh --meas w-g.pct.mgh --target fsaverage --out lh.w-g.pct.mgh.fsaverage.mgh Linux TRON 3.8.0-44-generic #66~precise1-Ubuntu SMP Tue Jul 15 04:01:04 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.4 2012/12/06 16:06:52 mreuter Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 tmpdir is ./tmp.mris_preproc.14799 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 1_S_5002 Tue Dec 13 12:07:34 EST 2016 -------------- ----------------------- mri_surf2surf --srcsubject 1_S_5002 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.14799/1_S_5002.1.mgh --sval /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.w-g.pct.mgh --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = 1_S_5002 srcval = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.w-g.pct.mgh srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.14799/1_S_5002.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.sphere.reg Loading source data Reading curvature file /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.w-g.pct.mgh Reading target surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (140473) Reverse Loop had 27576 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 144254, nTrgMulti = 19588, MnTrgMultiHits = 2.4078 nSrc121 = 102295, nSrcLost = 0, nSrcMulti = 38178, MnSrcMultiHits = 2.33441 Saving target data Saving to ./tmp.mris_preproc.14799/1_S_5002.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.14799/1_S_5002.1.mgh --o lh.w-g.pct.mgh.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to lh.w-g.pct.mgh.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.14799 Tue Dec 13 12:07:45 EST 2016 mris_preproc done #-------------------------------------------- #@# Qdec Cache lh w-g.pct.mgh fwhm0 fsaverage Tue Dec 13 12:07:45 EST 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 0 --sval lh.w-g.pct.mgh.fsaverage.mgh --tval lh.w-g.pct.mgh.fwhm0.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.w-g.pct.mgh.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to lh.w-g.pct.mgh.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh w-g.pct.mgh fwhm5 fsaverage Tue Dec 13 12:07:50 EST 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 5 --sval lh.w-g.pct.mgh.fsaverage.mgh --tval lh.w-g.pct.mgh.fwhm5.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.w-g.pct.mgh.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 18 Saving target data Saving to lh.w-g.pct.mgh.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh w-g.pct.mgh fwhm10 fsaverage Tue Dec 13 12:08:00 EST 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval lh.w-g.pct.mgh.fsaverage.mgh --tval lh.w-g.pct.mgh.fwhm10.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.w-g.pct.mgh.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 74 Saving target data Saving to lh.w-g.pct.mgh.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh w-g.pct.mgh fwhm15 fsaverage Tue Dec 13 12:08:10 EST 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 15 --sval lh.w-g.pct.mgh.fsaverage.mgh --tval lh.w-g.pct.mgh.fwhm15.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.w-g.pct.mgh.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 165 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 165 Saving target data Saving to lh.w-g.pct.mgh.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh w-g.pct.mgh fwhm20 fsaverage Tue Dec 13 12:08:19 EST 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 20 --sval lh.w-g.pct.mgh.fsaverage.mgh --tval lh.w-g.pct.mgh.fwhm20.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.w-g.pct.mgh.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 294 Saving target data Saving to lh.w-g.pct.mgh.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh w-g.pct.mgh fwhm25 fsaverage Tue Dec 13 12:08:31 EST 2016 mri_surf2surf --s fsaverage --hemi lh --fwhm 25 --sval lh.w-g.pct.mgh.fsaverage.mgh --tval lh.w-g.pct.mgh.fwhm25.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.w-g.pct.mgh.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 460 Saving target data Saving to lh.w-g.pct.mgh.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache rh thickness fsaverage Tue Dec 13 12:08:43 EST 2016 mris_preproc --s 1_S_5002 --hemi rh --meas thickness --target fsaverage --out rh.thickness.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.15008 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf Log file is rh.thickness.fsaverage.mris_preproc.log Tue Dec 13 12:08:44 EST 2016 setenv SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL cd /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf /usr/local/freesurfer/bin/mris_preproc --s 1_S_5002 --hemi rh --meas thickness --target fsaverage --out rh.thickness.fsaverage.mgh Linux TRON 3.8.0-44-generic #66~precise1-Ubuntu SMP Tue Jul 15 04:01:04 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.4 2012/12/06 16:06:52 mreuter Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 tmpdir is ./tmp.mris_preproc.15008 Src rh sphere.reg Trg rh sphere.reg --------------------------------------------------- #@# 1/1 1_S_5002 Tue Dec 13 12:08:44 EST 2016 -------------- ----------------------- mri_surf2surf --srcsubject 1_S_5002 --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.15008/1_S_5002.1.mgh --sval /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.thickness --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = 1_S_5002 srcval = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.thickness srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.15008/1_S_5002.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.sphere.reg Loading source data Reading curvature file /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.thickness Reading target surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (144029) Reverse Loop had 30046 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 142407, nTrgMulti = 21435, MnTrgMultiHits = 2.40173 nSrc121 = 107012, nSrcLost = 0, nSrcMulti = 37017, MnSrcMultiHits = 2.34692 Saving target data Saving to ./tmp.mris_preproc.15008/1_S_5002.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.15008/1_S_5002.1.mgh --o rh.thickness.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to rh.thickness.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.15008 Tue Dec 13 12:08:56 EST 2016 mris_preproc done #-------------------------------------------- #@# Qdec Cache rh thickness fwhm0 fsaverage Tue Dec 13 12:08:56 EST 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 0 --sval rh.thickness.fsaverage.mgh --tval rh.thickness.fwhm0.fsaverage.mgh --cortex srcsubject = fsaverage srcval = rh.thickness.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.thickness.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to rh.thickness.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache rh thickness fwhm5 fsaverage Tue Dec 13 12:09:00 EST 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 5 --sval rh.thickness.fsaverage.mgh --tval rh.thickness.fwhm5.fsaverage.mgh --cortex srcsubject = fsaverage srcval = rh.thickness.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.thickness.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 18 Saving target data Saving to rh.thickness.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache rh thickness fwhm10 fsaverage Tue Dec 13 12:09:10 EST 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 10 --sval rh.thickness.fsaverage.mgh --tval rh.thickness.fwhm10.fsaverage.mgh --cortex srcsubject = fsaverage srcval = rh.thickness.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.thickness.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 74 Saving target data Saving to rh.thickness.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache rh thickness fwhm15 fsaverage Tue Dec 13 12:09:20 EST 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 15 --sval rh.thickness.fsaverage.mgh --tval rh.thickness.fwhm15.fsaverage.mgh --cortex srcsubject = fsaverage srcval = rh.thickness.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.thickness.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 166 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 166 Saving target data Saving to rh.thickness.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache rh thickness fwhm20 fsaverage Tue Dec 13 12:09:31 EST 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 20 --sval rh.thickness.fsaverage.mgh --tval rh.thickness.fwhm20.fsaverage.mgh --cortex srcsubject = fsaverage srcval = rh.thickness.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.thickness.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 294 Saving target data Saving to rh.thickness.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache rh thickness fwhm25 fsaverage Tue Dec 13 12:09:42 EST 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 25 --sval rh.thickness.fsaverage.mgh --tval rh.thickness.fwhm25.fsaverage.mgh --cortex srcsubject = fsaverage srcval = rh.thickness.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.thickness.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 460 Saving target data Saving to rh.thickness.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache rh area fsaverage Tue Dec 13 12:09:54 EST 2016 mris_preproc --s 1_S_5002 --hemi rh --meas area --target fsaverage --out rh.area.fsaverage.mgh nsubjects = 1 INFO: turning on jacobican correction tmpdir is ./tmp.mris_preproc.15217 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf Log file is rh.area.fsaverage.mris_preproc.log Tue Dec 13 12:09:54 EST 2016 setenv SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL cd /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf /usr/local/freesurfer/bin/mris_preproc --s 1_S_5002 --hemi rh --meas area --target fsaverage --out rh.area.fsaverage.mgh Linux TRON 3.8.0-44-generic #66~precise1-Ubuntu SMP Tue Jul 15 04:01:04 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.4 2012/12/06 16:06:52 mreuter Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 tmpdir is ./tmp.mris_preproc.15217 Src rh sphere.reg Trg rh sphere.reg --------------------------------------------------- #@# 1/1 1_S_5002 Tue Dec 13 12:09:54 EST 2016 -------------- ----------------------- mri_surf2surf --srcsubject 1_S_5002 --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.15217/1_S_5002.1.mgh --sval /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.area --jac --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = 1_S_5002 srcval = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.area srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.15217/1_S_5002.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.sphere.reg Loading source data Reading curvature file /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.area Reading target surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Done Mapping Source Volume onto Source Subject Surface with Jacobian Correction surf2surf_nnfr_jac: building source hash (res=16). Surf2SurfJac: 1st Forward Loop (163842) Surf2SurfJac: 2nd Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2SurfJac: Reverse Loop (144029) Reverse Loop had 30046 hits INFO: nSrcLost = 0 surf2surf_nnfr_jac() done nTrg121 = 142407, nTrgMulti = 21435, MnTrgMultiHits = 2.40173 nSrc121 = 107012, nSrcLost = 0, nSrcMulti = 37017, MnSrcMultiHits = 2.34692 Saving target data Saving to ./tmp.mris_preproc.15217/1_S_5002.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.15217/1_S_5002.1.mgh --o rh.area.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to rh.area.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.15217 Tue Dec 13 12:10:11 EST 2016 mris_preproc done #-------------------------------------------- #@# Qdec Cache rh area fwhm0 fsaverage Tue Dec 13 12:10:11 EST 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 0 --sval rh.area.fsaverage.mgh --tval rh.area.fwhm0.fsaverage.mgh --cortex srcsubject = fsaverage srcval = rh.area.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.area.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to rh.area.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache rh area fwhm5 fsaverage Tue Dec 13 12:10:15 EST 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 5 --sval rh.area.fsaverage.mgh --tval rh.area.fwhm5.fsaverage.mgh --cortex srcsubject = fsaverage srcval = rh.area.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.area.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 18 Saving target data Saving to rh.area.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache rh area fwhm10 fsaverage Tue Dec 13 12:10:24 EST 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 10 --sval rh.area.fsaverage.mgh --tval rh.area.fwhm10.fsaverage.mgh --cortex srcsubject = fsaverage srcval = rh.area.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.area.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 74 Saving target data Saving to rh.area.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache rh area fwhm15 fsaverage Tue Dec 13 12:10:33 EST 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 15 --sval rh.area.fsaverage.mgh --tval rh.area.fwhm15.fsaverage.mgh --cortex srcsubject = fsaverage srcval = rh.area.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.area.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 166 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 166 Saving target data Saving to rh.area.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache rh area fwhm20 fsaverage Tue Dec 13 12:10:41 EST 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 20 --sval rh.area.fsaverage.mgh --tval rh.area.fwhm20.fsaverage.mgh --cortex srcsubject = fsaverage srcval = rh.area.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.area.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 294 Saving target data Saving to rh.area.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache rh area fwhm25 fsaverage Tue Dec 13 12:10:51 EST 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 25 --sval rh.area.fsaverage.mgh --tval rh.area.fwhm25.fsaverage.mgh --cortex srcsubject = fsaverage srcval = rh.area.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.area.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 460 Saving target data Saving to rh.area.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache rh area.pial fsaverage Tue Dec 13 12:11:04 EST 2016 mris_preproc --s 1_S_5002 --hemi rh --meas area.pial --target fsaverage --out rh.area.pial.fsaverage.mgh nsubjects = 1 INFO: turning on jacobican correction tmpdir is ./tmp.mris_preproc.15427 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf Log file is rh.area.pial.fsaverage.mris_preproc.log Tue Dec 13 12:11:04 EST 2016 setenv SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL cd /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf /usr/local/freesurfer/bin/mris_preproc --s 1_S_5002 --hemi rh --meas area.pial --target fsaverage --out rh.area.pial.fsaverage.mgh Linux TRON 3.8.0-44-generic #66~precise1-Ubuntu SMP Tue Jul 15 04:01:04 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.4 2012/12/06 16:06:52 mreuter Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 tmpdir is ./tmp.mris_preproc.15427 Src rh sphere.reg Trg rh sphere.reg --------------------------------------------------- #@# 1/1 1_S_5002 Tue Dec 13 12:11:04 EST 2016 -------------- ----------------------- mri_surf2surf --srcsubject 1_S_5002 --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.15427/1_S_5002.1.mgh --sval /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.area.pial --jac --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = 1_S_5002 srcval = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.area.pial srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.15427/1_S_5002.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.sphere.reg Loading source data Reading curvature file /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.area.pial Reading target surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Done Mapping Source Volume onto Source Subject Surface with Jacobian Correction surf2surf_nnfr_jac: building source hash (res=16). Surf2SurfJac: 1st Forward Loop (163842) Surf2SurfJac: 2nd Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2SurfJac: Reverse Loop (144029) Reverse Loop had 30046 hits INFO: nSrcLost = 0 surf2surf_nnfr_jac() done nTrg121 = 142407, nTrgMulti = 21435, MnTrgMultiHits = 2.40173 nSrc121 = 107012, nSrcLost = 0, nSrcMulti = 37017, MnSrcMultiHits = 2.34692 Saving target data Saving to ./tmp.mris_preproc.15427/1_S_5002.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.15427/1_S_5002.1.mgh --o rh.area.pial.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to rh.area.pial.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.15427 Tue Dec 13 12:11:19 EST 2016 mris_preproc done #-------------------------------------------- #@# Qdec Cache rh area.pial fwhm0 fsaverage Tue Dec 13 12:11:19 EST 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 0 --sval rh.area.pial.fsaverage.mgh --tval rh.area.pial.fwhm0.fsaverage.mgh --cortex srcsubject = fsaverage srcval = rh.area.pial.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.area.pial.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to rh.area.pial.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache rh area.pial fwhm5 fsaverage Tue Dec 13 12:11:22 EST 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 5 --sval rh.area.pial.fsaverage.mgh --tval rh.area.pial.fwhm5.fsaverage.mgh --cortex srcsubject = fsaverage srcval = rh.area.pial.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.area.pial.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 18 Saving target data Saving to rh.area.pial.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache rh area.pial fwhm10 fsaverage Tue Dec 13 12:11:32 EST 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 10 --sval rh.area.pial.fsaverage.mgh --tval rh.area.pial.fwhm10.fsaverage.mgh --cortex srcsubject = fsaverage srcval = rh.area.pial.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.area.pial.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 74 Saving target data Saving to rh.area.pial.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache rh area.pial fwhm15 fsaverage Tue Dec 13 12:11:41 EST 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 15 --sval rh.area.pial.fsaverage.mgh --tval rh.area.pial.fwhm15.fsaverage.mgh --cortex srcsubject = fsaverage srcval = rh.area.pial.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.area.pial.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 166 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 166 Saving target data Saving to rh.area.pial.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache rh area.pial fwhm20 fsaverage Tue Dec 13 12:11:51 EST 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 20 --sval rh.area.pial.fsaverage.mgh --tval rh.area.pial.fwhm20.fsaverage.mgh --cortex srcsubject = fsaverage srcval = rh.area.pial.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.area.pial.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 294 Saving target data Saving to rh.area.pial.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache rh area.pial fwhm25 fsaverage Tue Dec 13 12:12:02 EST 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 25 --sval rh.area.pial.fsaverage.mgh --tval rh.area.pial.fwhm25.fsaverage.mgh --cortex srcsubject = fsaverage srcval = rh.area.pial.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.area.pial.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 460 Saving target data Saving to rh.area.pial.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache rh volume fsaverage Tue Dec 13 12:12:14 EST 2016 mris_preproc --s 1_S_5002 --hemi rh --meas volume --target fsaverage --out rh.volume.fsaverage.mgh nsubjects = 1 INFO: turning on jacobican correction tmpdir is ./tmp.mris_preproc.15637 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf Log file is rh.volume.fsaverage.mris_preproc.log Tue Dec 13 12:12:14 EST 2016 setenv SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL cd /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf /usr/local/freesurfer/bin/mris_preproc --s 1_S_5002 --hemi rh --meas volume --target fsaverage --out rh.volume.fsaverage.mgh Linux TRON 3.8.0-44-generic #66~precise1-Ubuntu SMP Tue Jul 15 04:01:04 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.4 2012/12/06 16:06:52 mreuter Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 tmpdir is ./tmp.mris_preproc.15637 Src rh sphere.reg Trg rh sphere.reg --------------------------------------------------- #@# 1/1 1_S_5002 Tue Dec 13 12:12:14 EST 2016 -------------- ----------------------- mri_surf2surf --srcsubject 1_S_5002 --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.15637/1_S_5002.1.mgh --sval /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.volume --jac --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = 1_S_5002 srcval = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.volume srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.15637/1_S_5002.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.sphere.reg Loading source data Reading curvature file /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.volume Reading target surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Done Mapping Source Volume onto Source Subject Surface with Jacobian Correction surf2surf_nnfr_jac: building source hash (res=16). Surf2SurfJac: 1st Forward Loop (163842) Surf2SurfJac: 2nd Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2SurfJac: Reverse Loop (144029) Reverse Loop had 30046 hits INFO: nSrcLost = 0 surf2surf_nnfr_jac() done nTrg121 = 142407, nTrgMulti = 21435, MnTrgMultiHits = 2.40173 nSrc121 = 107012, nSrcLost = 0, nSrcMulti = 37017, MnSrcMultiHits = 2.34692 Saving target data Saving to ./tmp.mris_preproc.15637/1_S_5002.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.15637/1_S_5002.1.mgh --o rh.volume.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to rh.volume.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.15637 Tue Dec 13 12:12:30 EST 2016 mris_preproc done #-------------------------------------------- #@# Qdec Cache rh volume fwhm0 fsaverage Tue Dec 13 12:12:30 EST 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 0 --sval rh.volume.fsaverage.mgh --tval rh.volume.fwhm0.fsaverage.mgh --cortex srcsubject = fsaverage srcval = rh.volume.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.volume.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to rh.volume.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache rh volume fwhm5 fsaverage Tue Dec 13 12:12:36 EST 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 5 --sval rh.volume.fsaverage.mgh --tval rh.volume.fwhm5.fsaverage.mgh --cortex srcsubject = fsaverage srcval = rh.volume.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.volume.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 18 Saving target data Saving to rh.volume.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache rh volume fwhm10 fsaverage Tue Dec 13 12:12:45 EST 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 10 --sval rh.volume.fsaverage.mgh --tval rh.volume.fwhm10.fsaverage.mgh --cortex srcsubject = fsaverage srcval = rh.volume.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.volume.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 74 Saving target data Saving to rh.volume.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache rh volume fwhm15 fsaverage Tue Dec 13 12:12:56 EST 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 15 --sval rh.volume.fsaverage.mgh --tval rh.volume.fwhm15.fsaverage.mgh --cortex srcsubject = fsaverage srcval = rh.volume.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.volume.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 166 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 166 Saving target data Saving to rh.volume.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache rh volume fwhm20 fsaverage Tue Dec 13 12:13:05 EST 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 20 --sval rh.volume.fsaverage.mgh --tval rh.volume.fwhm20.fsaverage.mgh --cortex srcsubject = fsaverage srcval = rh.volume.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.volume.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 294 Saving target data Saving to rh.volume.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache rh volume fwhm25 fsaverage Tue Dec 13 12:13:16 EST 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 25 --sval rh.volume.fsaverage.mgh --tval rh.volume.fwhm25.fsaverage.mgh --cortex srcsubject = fsaverage srcval = rh.volume.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.volume.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 460 Saving target data Saving to rh.volume.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache rh curv fsaverage Tue Dec 13 12:13:29 EST 2016 mris_preproc --s 1_S_5002 --hemi rh --meas curv --target fsaverage --out rh.curv.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.15843 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf Log file is rh.curv.fsaverage.mris_preproc.log Tue Dec 13 12:13:29 EST 2016 setenv SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL cd /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf /usr/local/freesurfer/bin/mris_preproc --s 1_S_5002 --hemi rh --meas curv --target fsaverage --out rh.curv.fsaverage.mgh Linux TRON 3.8.0-44-generic #66~precise1-Ubuntu SMP Tue Jul 15 04:01:04 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.4 2012/12/06 16:06:52 mreuter Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 tmpdir is ./tmp.mris_preproc.15843 Src rh sphere.reg Trg rh sphere.reg --------------------------------------------------- #@# 1/1 1_S_5002 Tue Dec 13 12:13:29 EST 2016 -------------- ----------------------- mri_surf2surf --srcsubject 1_S_5002 --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.15843/1_S_5002.1.mgh --sval /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.curv --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = 1_S_5002 srcval = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.curv srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.15843/1_S_5002.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.sphere.reg Loading source data Reading curvature file /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.curv Reading target surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (144029) Reverse Loop had 30046 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 142407, nTrgMulti = 21435, MnTrgMultiHits = 2.40173 nSrc121 = 107012, nSrcLost = 0, nSrcMulti = 37017, MnSrcMultiHits = 2.34692 Saving target data Saving to ./tmp.mris_preproc.15843/1_S_5002.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.15843/1_S_5002.1.mgh --o rh.curv.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to rh.curv.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.15843 Tue Dec 13 12:13:41 EST 2016 mris_preproc done #-------------------------------------------- #@# Qdec Cache rh curv fwhm0 fsaverage Tue Dec 13 12:13:41 EST 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 0 --sval rh.curv.fsaverage.mgh --tval rh.curv.fwhm0.fsaverage.mgh --cortex srcsubject = fsaverage srcval = rh.curv.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.curv.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to rh.curv.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache rh curv fwhm5 fsaverage Tue Dec 13 12:13:45 EST 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 5 --sval rh.curv.fsaverage.mgh --tval rh.curv.fwhm5.fsaverage.mgh --cortex srcsubject = fsaverage srcval = rh.curv.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.curv.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 18 Saving target data Saving to rh.curv.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache rh curv fwhm10 fsaverage Tue Dec 13 12:13:55 EST 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 10 --sval rh.curv.fsaverage.mgh --tval rh.curv.fwhm10.fsaverage.mgh --cortex srcsubject = fsaverage srcval = rh.curv.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.curv.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 74 Saving target data Saving to rh.curv.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache rh curv fwhm15 fsaverage Tue Dec 13 12:14:06 EST 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 15 --sval rh.curv.fsaverage.mgh --tval rh.curv.fwhm15.fsaverage.mgh --cortex srcsubject = fsaverage srcval = rh.curv.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.curv.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 166 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 166 Saving target data Saving to rh.curv.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache rh curv fwhm20 fsaverage Tue Dec 13 12:14:15 EST 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 20 --sval rh.curv.fsaverage.mgh --tval rh.curv.fwhm20.fsaverage.mgh --cortex srcsubject = fsaverage srcval = rh.curv.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.curv.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 294 Saving target data Saving to rh.curv.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache rh curv fwhm25 fsaverage Tue Dec 13 12:14:25 EST 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 25 --sval rh.curv.fsaverage.mgh --tval rh.curv.fwhm25.fsaverage.mgh --cortex srcsubject = fsaverage srcval = rh.curv.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.curv.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 460 Saving target data Saving to rh.curv.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache rh sulc fsaverage Tue Dec 13 12:14:38 EST 2016 mris_preproc --s 1_S_5002 --hemi rh --meas sulc --target fsaverage --out rh.sulc.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.16052 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf Log file is rh.sulc.fsaverage.mris_preproc.log Tue Dec 13 12:14:38 EST 2016 setenv SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL cd /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf /usr/local/freesurfer/bin/mris_preproc --s 1_S_5002 --hemi rh --meas sulc --target fsaverage --out rh.sulc.fsaverage.mgh Linux TRON 3.8.0-44-generic #66~precise1-Ubuntu SMP Tue Jul 15 04:01:04 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.4 2012/12/06 16:06:52 mreuter Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 tmpdir is ./tmp.mris_preproc.16052 Src rh sphere.reg Trg rh sphere.reg --------------------------------------------------- #@# 1/1 1_S_5002 Tue Dec 13 12:14:38 EST 2016 -------------- ----------------------- mri_surf2surf --srcsubject 1_S_5002 --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.16052/1_S_5002.1.mgh --sval /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.sulc --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = 1_S_5002 srcval = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.sulc srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.16052/1_S_5002.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.sphere.reg Loading source data Reading curvature file /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.sulc Reading target surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (144029) Reverse Loop had 30046 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 142407, nTrgMulti = 21435, MnTrgMultiHits = 2.40173 nSrc121 = 107012, nSrcLost = 0, nSrcMulti = 37017, MnSrcMultiHits = 2.34692 Saving target data Saving to ./tmp.mris_preproc.16052/1_S_5002.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.16052/1_S_5002.1.mgh --o rh.sulc.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to rh.sulc.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.16052 Tue Dec 13 12:14:49 EST 2016 mris_preproc done #-------------------------------------------- #@# Qdec Cache rh sulc fwhm0 fsaverage Tue Dec 13 12:14:49 EST 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 0 --sval rh.sulc.fsaverage.mgh --tval rh.sulc.fwhm0.fsaverage.mgh --cortex srcsubject = fsaverage srcval = rh.sulc.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.sulc.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to rh.sulc.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache rh sulc fwhm5 fsaverage Tue Dec 13 12:14:53 EST 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 5 --sval rh.sulc.fsaverage.mgh --tval rh.sulc.fwhm5.fsaverage.mgh --cortex srcsubject = fsaverage srcval = rh.sulc.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.sulc.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 18 Saving target data Saving to rh.sulc.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache rh sulc fwhm10 fsaverage Tue Dec 13 12:15:00 EST 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 10 --sval rh.sulc.fsaverage.mgh --tval rh.sulc.fwhm10.fsaverage.mgh --cortex srcsubject = fsaverage srcval = rh.sulc.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.sulc.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 74 Saving target data Saving to rh.sulc.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache rh sulc fwhm15 fsaverage Tue Dec 13 12:15:09 EST 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 15 --sval rh.sulc.fsaverage.mgh --tval rh.sulc.fwhm15.fsaverage.mgh --cortex srcsubject = fsaverage srcval = rh.sulc.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.sulc.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 166 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 166 Saving target data Saving to rh.sulc.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache rh sulc fwhm20 fsaverage Tue Dec 13 12:15:17 EST 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 20 --sval rh.sulc.fsaverage.mgh --tval rh.sulc.fwhm20.fsaverage.mgh --cortex srcsubject = fsaverage srcval = rh.sulc.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.sulc.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 294 Saving target data Saving to rh.sulc.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache rh sulc fwhm25 fsaverage Tue Dec 13 12:15:27 EST 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 25 --sval rh.sulc.fsaverage.mgh --tval rh.sulc.fwhm25.fsaverage.mgh --cortex srcsubject = fsaverage srcval = rh.sulc.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.sulc.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 460 Saving target data Saving to rh.sulc.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache rh white.K fsaverage Tue Dec 13 12:15:39 EST 2016 INFO: File rh.white.K does not exist! Skipping creation of smoothed data for rh.white.K #-------------------------------------------- #@# Qdec Cache rh white.H fsaverage Tue Dec 13 12:15:39 EST 2016 INFO: File rh.white.H does not exist! Skipping creation of smoothed data for rh.white.H #-------------------------------------------- #@# Qdec Cache rh jacobian_white fsaverage Tue Dec 13 12:15:39 EST 2016 mris_preproc --s 1_S_5002 --hemi rh --meas jacobian_white --target fsaverage --out rh.jacobian_white.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.16293 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf Log file is rh.jacobian_white.fsaverage.mris_preproc.log Tue Dec 13 12:15:40 EST 2016 setenv SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL cd /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf /usr/local/freesurfer/bin/mris_preproc --s 1_S_5002 --hemi rh --meas jacobian_white --target fsaverage --out rh.jacobian_white.fsaverage.mgh Linux TRON 3.8.0-44-generic #66~precise1-Ubuntu SMP Tue Jul 15 04:01:04 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.4 2012/12/06 16:06:52 mreuter Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 tmpdir is ./tmp.mris_preproc.16293 Src rh sphere.reg Trg rh sphere.reg --------------------------------------------------- #@# 1/1 1_S_5002 Tue Dec 13 12:15:40 EST 2016 -------------- ----------------------- mri_surf2surf --srcsubject 1_S_5002 --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.16293/1_S_5002.1.mgh --sval /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.jacobian_white --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = 1_S_5002 srcval = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.jacobian_white srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.16293/1_S_5002.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.sphere.reg Loading source data Reading curvature file /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.jacobian_white Reading target surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (144029) Reverse Loop had 30046 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 142407, nTrgMulti = 21435, MnTrgMultiHits = 2.40173 nSrc121 = 107012, nSrcLost = 0, nSrcMulti = 37017, MnSrcMultiHits = 2.34692 Saving target data Saving to ./tmp.mris_preproc.16293/1_S_5002.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.16293/1_S_5002.1.mgh --o rh.jacobian_white.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to rh.jacobian_white.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.16293 Tue Dec 13 12:15:51 EST 2016 mris_preproc done #-------------------------------------------- #@# Qdec Cache rh jacobian_white fwhm0 fsaverage Tue Dec 13 12:15:51 EST 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 0 --sval rh.jacobian_white.fsaverage.mgh --tval rh.jacobian_white.fwhm0.fsaverage.mgh --cortex srcsubject = fsaverage srcval = rh.jacobian_white.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.jacobian_white.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to rh.jacobian_white.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache rh jacobian_white fwhm5 fsaverage Tue Dec 13 12:15:54 EST 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 5 --sval rh.jacobian_white.fsaverage.mgh --tval rh.jacobian_white.fwhm5.fsaverage.mgh --cortex srcsubject = fsaverage srcval = rh.jacobian_white.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.jacobian_white.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 18 Saving target data Saving to rh.jacobian_white.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache rh jacobian_white fwhm10 fsaverage Tue Dec 13 12:16:02 EST 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 10 --sval rh.jacobian_white.fsaverage.mgh --tval rh.jacobian_white.fwhm10.fsaverage.mgh --cortex srcsubject = fsaverage srcval = rh.jacobian_white.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.jacobian_white.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 74 Saving target data Saving to rh.jacobian_white.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache rh jacobian_white fwhm15 fsaverage Tue Dec 13 12:16:12 EST 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 15 --sval rh.jacobian_white.fsaverage.mgh --tval rh.jacobian_white.fwhm15.fsaverage.mgh --cortex srcsubject = fsaverage srcval = rh.jacobian_white.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.jacobian_white.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 166 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 166 Saving target data Saving to rh.jacobian_white.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache rh jacobian_white fwhm20 fsaverage Tue Dec 13 12:16:22 EST 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 20 --sval rh.jacobian_white.fsaverage.mgh --tval rh.jacobian_white.fwhm20.fsaverage.mgh --cortex srcsubject = fsaverage srcval = rh.jacobian_white.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.jacobian_white.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 294 Saving target data Saving to rh.jacobian_white.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache rh jacobian_white fwhm25 fsaverage Tue Dec 13 12:16:34 EST 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 25 --sval rh.jacobian_white.fsaverage.mgh --tval rh.jacobian_white.fwhm25.fsaverage.mgh --cortex srcsubject = fsaverage srcval = rh.jacobian_white.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.jacobian_white.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 460 Saving target data Saving to rh.jacobian_white.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache rh w-g.pct.mgh fsaverage Tue Dec 13 12:16:46 EST 2016 mris_preproc --s 1_S_5002 --hemi rh --meas w-g.pct.mgh --target fsaverage --out rh.w-g.pct.mgh.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.16503 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf Log file is rh.w-g.pct.mgh.fsaverage.mris_preproc.log Tue Dec 13 12:16:46 EST 2016 setenv SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL cd /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf /usr/local/freesurfer/bin/mris_preproc --s 1_S_5002 --hemi rh --meas w-g.pct.mgh --target fsaverage --out rh.w-g.pct.mgh.fsaverage.mgh Linux TRON 3.8.0-44-generic #66~precise1-Ubuntu SMP Tue Jul 15 04:01:04 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.4 2012/12/06 16:06:52 mreuter Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 tmpdir is ./tmp.mris_preproc.16503 Src rh sphere.reg Trg rh sphere.reg --------------------------------------------------- #@# 1/1 1_S_5002 Tue Dec 13 12:16:46 EST 2016 -------------- ----------------------- mri_surf2surf --srcsubject 1_S_5002 --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.16503/1_S_5002.1.mgh --sval /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.w-g.pct.mgh --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = 1_S_5002 srcval = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.w-g.pct.mgh srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.16503/1_S_5002.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.sphere.reg Loading source data Reading curvature file /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.w-g.pct.mgh Reading target surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (144029) Reverse Loop had 30046 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 142407, nTrgMulti = 21435, MnTrgMultiHits = 2.40173 nSrc121 = 107012, nSrcLost = 0, nSrcMulti = 37017, MnSrcMultiHits = 2.34692 Saving target data Saving to ./tmp.mris_preproc.16503/1_S_5002.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.16503/1_S_5002.1.mgh --o rh.w-g.pct.mgh.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to rh.w-g.pct.mgh.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.16503 Tue Dec 13 12:16:58 EST 2016 mris_preproc done #-------------------------------------------- #@# Qdec Cache rh w-g.pct.mgh fwhm0 fsaverage Tue Dec 13 12:16:58 EST 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 0 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.w-g.pct.mgh.fwhm0.fsaverage.mgh --cortex srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.w-g.pct.mgh.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to rh.w-g.pct.mgh.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache rh w-g.pct.mgh fwhm5 fsaverage Tue Dec 13 12:17:02 EST 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 5 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.w-g.pct.mgh.fwhm5.fsaverage.mgh --cortex srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.w-g.pct.mgh.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 18 Saving target data Saving to rh.w-g.pct.mgh.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache rh w-g.pct.mgh fwhm10 fsaverage Tue Dec 13 12:17:10 EST 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 10 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.w-g.pct.mgh.fwhm10.fsaverage.mgh --cortex srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.w-g.pct.mgh.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 74 Saving target data Saving to rh.w-g.pct.mgh.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache rh w-g.pct.mgh fwhm15 fsaverage Tue Dec 13 12:17:21 EST 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 15 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.w-g.pct.mgh.fwhm15.fsaverage.mgh --cortex srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.w-g.pct.mgh.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 166 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 166 Saving target data Saving to rh.w-g.pct.mgh.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache rh w-g.pct.mgh fwhm20 fsaverage Tue Dec 13 12:17:31 EST 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 20 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.w-g.pct.mgh.fwhm20.fsaverage.mgh --cortex srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.w-g.pct.mgh.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 294 Saving target data Saving to rh.w-g.pct.mgh.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache rh w-g.pct.mgh fwhm25 fsaverage Tue Dec 13 12:17:43 EST 2016 mri_surf2surf --s fsaverage --hemi rh --fwhm 25 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.w-g.pct.mgh.fwhm25.fsaverage.mgh --cortex srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.w-g.pct.mgh.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = rh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label rh.cortex.label NN smoothing output with n = 460 Saving target data Saving to rh.w-g.pct.mgh.fwhm25.fsaverage.mgh /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/label #-------------------------------------------- #@# BA Labels lh Tue Dec 13 12:17:53 EST 2016 mri_label2label --srcsubject fsaverage --srclabel /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/lh.BA1.label --trgsubject 1_S_5002 --trglabel ./lh.BA1.label --hemi lh --regmethod surface srclabel = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = 1_S_5002 trglabel = ./lh.BA1.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.white Reading target registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 140473 Number of reverse mapping hits = 520 Checking for and removing duplicates Writing label file ./lh.BA1.label 4649 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/lh.BA2.label --trgsubject 1_S_5002 --trglabel ./lh.BA2.label --hemi lh --regmethod surface srclabel = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/lh.BA2.label srcsubject = fsaverage trgsubject = 1_S_5002 trglabel = ./lh.BA2.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.white Reading target registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 140473 Number of reverse mapping hits = 774 Checking for and removing duplicates Writing label file ./lh.BA2.label 8683 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/lh.BA3a.label --trgsubject 1_S_5002 --trglabel ./lh.BA3a.label --hemi lh --regmethod surface srclabel = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/lh.BA3a.label srcsubject = fsaverage trgsubject = 1_S_5002 trglabel = ./lh.BA3a.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.white Reading target registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 140473 Number of reverse mapping hits = 248 Checking for and removing duplicates Writing label file ./lh.BA3a.label 4325 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/lh.BA3b.label --trgsubject 1_S_5002 --trglabel ./lh.BA3b.label --hemi lh --regmethod surface srclabel = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/lh.BA3b.label srcsubject = fsaverage trgsubject = 1_S_5002 trglabel = ./lh.BA3b.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.white Reading target registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 140473 Number of reverse mapping hits = 525 Checking for and removing duplicates Writing label file ./lh.BA3b.label 6508 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/lh.BA4a.label --trgsubject 1_S_5002 --trglabel ./lh.BA4a.label --hemi lh --regmethod surface srclabel = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/lh.BA4a.label srcsubject = fsaverage trgsubject = 1_S_5002 trglabel = ./lh.BA4a.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.white Reading target registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 140473 Number of reverse mapping hits = 1156 Checking for and removing duplicates Writing label file ./lh.BA4a.label 6940 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/lh.BA4p.label --trgsubject 1_S_5002 --trglabel ./lh.BA4p.label --hemi lh --regmethod surface srclabel = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/lh.BA4p.label srcsubject = fsaverage trgsubject = 1_S_5002 trglabel = ./lh.BA4p.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.white Reading target registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 140473 Number of reverse mapping hits = 588 Checking for and removing duplicates Writing label file ./lh.BA4p.label 4658 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/lh.BA6.label --trgsubject 1_S_5002 --trglabel ./lh.BA6.label --hemi lh --regmethod surface srclabel = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/lh.BA6.label srcsubject = fsaverage trgsubject = 1_S_5002 trglabel = ./lh.BA6.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.white Reading target registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 140473 Number of reverse mapping hits = 2738 Checking for and removing duplicates Writing label file ./lh.BA6.label 16327 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/lh.BA44.label --trgsubject 1_S_5002 --trglabel ./lh.BA44.label --hemi lh --regmethod surface srclabel = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/lh.BA44.label srcsubject = fsaverage trgsubject = 1_S_5002 trglabel = ./lh.BA44.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.white Reading target registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 140473 Number of reverse mapping hits = 372 Checking for and removing duplicates Writing label file ./lh.BA44.label 4553 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/lh.BA45.label --trgsubject 1_S_5002 --trglabel ./lh.BA45.label --hemi lh --regmethod surface srclabel = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/lh.BA45.label srcsubject = fsaverage trgsubject = 1_S_5002 trglabel = ./lh.BA45.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.white Reading target registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 140473 Number of reverse mapping hits = 797 Checking for and removing duplicates Writing label file ./lh.BA45.label 4219 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/lh.V1.label --trgsubject 1_S_5002 --trglabel ./lh.V1.label --hemi lh --regmethod surface srclabel = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/lh.V1.label srcsubject = fsaverage trgsubject = 1_S_5002 trglabel = ./lh.V1.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.white Reading target registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 140473 Number of reverse mapping hits = 2165 Checking for and removing duplicates Writing label file ./lh.V1.label 6806 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/lh.V2.label --trgsubject 1_S_5002 --trglabel ./lh.V2.label --hemi lh --regmethod surface srclabel = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/lh.V2.label srcsubject = fsaverage trgsubject = 1_S_5002 trglabel = ./lh.V2.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.white Reading target registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 140473 Number of reverse mapping hits = 4410 Checking for and removing duplicates Writing label file ./lh.V2.label 12524 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/lh.MT.label --trgsubject 1_S_5002 --trglabel ./lh.MT.label --hemi lh --regmethod surface srclabel = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/lh.MT.label srcsubject = fsaverage trgsubject = 1_S_5002 trglabel = ./lh.MT.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.white Reading target registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 140473 Number of reverse mapping hits = 312 Checking for and removing duplicates Writing label file ./lh.MT.label 2330 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/lh.perirhinal.label --trgsubject 1_S_5002 --trglabel ./lh.perirhinal.label --hemi lh --regmethod surface srclabel = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/lh.perirhinal.label srcsubject = fsaverage trgsubject = 1_S_5002 trglabel = ./lh.perirhinal.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.white Reading target registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 140473 Number of reverse mapping hits = 245 Checking for and removing duplicates Writing label file ./lh.perirhinal.label 1444 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/lh.BA1.thresh.label --trgsubject 1_S_5002 --trglabel ./lh.BA1.thresh.label --hemi lh --regmethod surface srclabel = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/lh.BA1.thresh.label srcsubject = fsaverage trgsubject = 1_S_5002 trglabel = ./lh.BA1.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.white Reading target registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 140473 Number of reverse mapping hits = 107 Checking for and removing duplicates Writing label file ./lh.BA1.thresh.label 1121 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/lh.BA2.thresh.label --trgsubject 1_S_5002 --trglabel ./lh.BA2.thresh.label --hemi lh --regmethod surface srclabel = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/lh.BA2.thresh.label srcsubject = fsaverage trgsubject = 1_S_5002 trglabel = ./lh.BA2.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.white Reading target registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 140473 Number of reverse mapping hits = 330 Checking for and removing duplicates Writing label file ./lh.BA2.thresh.label 2422 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/lh.BA3a.thresh.label --trgsubject 1_S_5002 --trglabel ./lh.BA3a.thresh.label --hemi lh --regmethod surface srclabel = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/lh.BA3a.thresh.label srcsubject = fsaverage trgsubject = 1_S_5002 trglabel = ./lh.BA3a.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.white Reading target registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 140473 Number of reverse mapping hits = 66 Checking for and removing duplicates Writing label file ./lh.BA3a.thresh.label 1570 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/lh.BA3b.thresh.label --trgsubject 1_S_5002 --trglabel ./lh.BA3b.thresh.label --hemi lh --regmethod surface srclabel = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/lh.BA3b.thresh.label srcsubject = fsaverage trgsubject = 1_S_5002 trglabel = ./lh.BA3b.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.white Reading target registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 140473 Number of reverse mapping hits = 176 Checking for and removing duplicates Writing label file ./lh.BA3b.thresh.label 2172 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/lh.BA4a.thresh.label --trgsubject 1_S_5002 --trglabel ./lh.BA4a.thresh.label --hemi lh --regmethod surface srclabel = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/lh.BA4a.thresh.label srcsubject = fsaverage trgsubject = 1_S_5002 trglabel = ./lh.BA4a.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.white Reading target registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 140473 Number of reverse mapping hits = 459 Checking for and removing duplicates Writing label file ./lh.BA4a.thresh.label 2778 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/lh.BA4p.thresh.label --trgsubject 1_S_5002 --trglabel ./lh.BA4p.thresh.label --hemi lh --regmethod surface srclabel = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/lh.BA4p.thresh.label srcsubject = fsaverage trgsubject = 1_S_5002 trglabel = ./lh.BA4p.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.white Reading target registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 140473 Number of reverse mapping hits = 243 Checking for and removing duplicates Writing label file ./lh.BA4p.thresh.label 1792 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/lh.BA6.thresh.label --trgsubject 1_S_5002 --trglabel ./lh.BA6.thresh.label --hemi lh --regmethod surface srclabel = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/lh.BA6.thresh.label srcsubject = fsaverage trgsubject = 1_S_5002 trglabel = ./lh.BA6.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.white Reading target registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 140473 Number of reverse mapping hits = 1464 Checking for and removing duplicates Writing label file ./lh.BA6.thresh.label 8499 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/lh.BA44.thresh.label --trgsubject 1_S_5002 --trglabel ./lh.BA44.thresh.label --hemi lh --regmethod surface srclabel = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/lh.BA44.thresh.label srcsubject = fsaverage trgsubject = 1_S_5002 trglabel = ./lh.BA44.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.white Reading target registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 140473 Number of reverse mapping hits = 91 Checking for and removing duplicates Writing label file ./lh.BA44.thresh.label 2003 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/lh.BA45.thresh.label --trgsubject 1_S_5002 --trglabel ./lh.BA45.thresh.label --hemi lh --regmethod surface srclabel = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/lh.BA45.thresh.label srcsubject = fsaverage trgsubject = 1_S_5002 trglabel = ./lh.BA45.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.white Reading target registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 140473 Number of reverse mapping hits = 355 Checking for and removing duplicates Writing label file ./lh.BA45.thresh.label 1506 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/lh.V1.thresh.label --trgsubject 1_S_5002 --trglabel ./lh.V1.thresh.label --hemi lh --regmethod surface srclabel = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/lh.V1.thresh.label srcsubject = fsaverage trgsubject = 1_S_5002 trglabel = ./lh.V1.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.white Reading target registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 140473 Number of reverse mapping hits = 1530 Checking for and removing duplicates Writing label file ./lh.V1.thresh.label 4935 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/lh.V2.thresh.label --trgsubject 1_S_5002 --trglabel ./lh.V2.thresh.label --hemi lh --regmethod surface srclabel = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/lh.V2.thresh.label srcsubject = fsaverage trgsubject = 1_S_5002 trglabel = ./lh.V2.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.white Reading target registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 140473 Number of reverse mapping hits = 2032 Checking for and removing duplicates Writing label file ./lh.V2.thresh.label 5366 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/lh.MT.thresh.label --trgsubject 1_S_5002 --trglabel ./lh.MT.thresh.label --hemi lh --regmethod surface srclabel = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/lh.MT.thresh.label srcsubject = fsaverage trgsubject = 1_S_5002 trglabel = ./lh.MT.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.white Reading target registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 140473 Number of reverse mapping hits = 52 Checking for and removing duplicates Writing label file ./lh.MT.thresh.label 565 mri_label2label: Done mris_label2annot --s 1_S_5002 --hemi lh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --l lh.perirhinal.label --a BA --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/average/colortable_BA.txt Number of ctab entries 14 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/label cmdline mris_label2annot --s 1_S_5002 --hemi lh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --l lh.perirhinal.label --a BA --maxstatwinner --noverbose sysname Linux hostname TRON machine x86_64 user sneha subject 1_S_5002 hemi lh SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL ColorTable /usr/local/freesurfer/average/colortable_BA.txt AnnotName BA nlables 13 LabelThresh 0 0.000000 Loading /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.orig 1 1530880 BA1 2 16749699 BA2 3 16711680 BA3a 4 3368703 BA3b 5 1376196 BA4a 6 13382655 BA4p 7 10036737 BA6 8 2490521 BA44 9 39283 BA45 10 3993 V1 11 8508928 V2 12 10027163 MT 13 16422433 perirhinal Mapping unhit to unknown Found 93902 unhit vertices Writing annot to /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/label/lh.BA.annot mris_label2annot --s 1_S_5002 --hemi lh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l lh.BA1.thresh.label --l lh.BA2.thresh.label --l lh.BA3a.thresh.label --l lh.BA3b.thresh.label --l lh.BA4a.thresh.label --l lh.BA4p.thresh.label --l lh.BA6.thresh.label --l lh.BA44.thresh.label --l lh.BA45.thresh.label --l lh.V1.thresh.label --l lh.V2.thresh.label --l lh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/average/colortable_BA.txt Number of ctab entries 14 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/label cmdline mris_label2annot --s 1_S_5002 --hemi lh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l lh.BA1.thresh.label --l lh.BA2.thresh.label --l lh.BA3a.thresh.label --l lh.BA3b.thresh.label --l lh.BA4a.thresh.label --l lh.BA4p.thresh.label --l lh.BA6.thresh.label --l lh.BA44.thresh.label --l lh.BA45.thresh.label --l lh.V1.thresh.label --l lh.V2.thresh.label --l lh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose sysname Linux hostname TRON machine x86_64 user sneha subject 1_S_5002 hemi lh SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL ColorTable /usr/local/freesurfer/average/colortable_BA.txt AnnotName BA.thresh nlables 12 LabelThresh 0 0.000000 Loading /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.orig 1 1530880 BA1 2 16749699 BA2 3 16711680 BA3a 4 3368703 BA3b 5 1376196 BA4a 6 13382655 BA4p 7 10036737 BA6 8 2490521 BA44 9 39283 BA45 10 3993 V1 11 8508928 V2 12 10027163 MT Mapping unhit to unknown Found 112751 unhit vertices Writing annot to /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/label/lh.BA.thresh.annot mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab 1_S_5002 lh white computing statistics for each annotation in ./lh.BA.annot. reading volume /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/wm.mgz... reading input surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.white... reading input pial surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.pial... reading input white surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /usr/local/freesurfer/average/colortable_BA.txt) Saving annotation colortable ./BA.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1185 574 1418 1.928 0.422 0.200 0.278 154 15.1 BA1 4196 2556 5600 2.097 0.430 0.162 0.101 95 20.1 BA2 1070 827 1175 1.844 0.421 0.184 0.082 17 4.0 BA3a 2617 1695 3169 1.748 0.518 0.160 0.075 48 8.7 BA3b 2286 1323 3119 2.295 0.570 0.234 0.422 397 39.4 BA4a 1621 1073 2581 2.565 0.608 0.249 0.473 381 39.6 BA4p 11138 6463 17101 2.364 0.513 0.191 0.195 1041 80.5 BA6 2224 1417 3548 2.339 0.384 0.162 0.254 447 8.9 BA44 3128 2060 4812 2.071 0.434 0.180 0.186 350 23.7 BA45 4235 2708 4100 1.515 0.440 0.184 0.104 112 17.4 V1 10040 6042 11973 1.855 0.500 0.185 0.121 430 51.1 V2 1697 1138 2831 2.304 0.421 0.170 0.090 40 6.3 MT 1134 701 2103 2.418 0.728 0.179 0.148 54 7.1 perirhinal mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab 1_S_5002 lh white computing statistics for each annotation in ./lh.BA.thresh.annot. reading volume /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/wm.mgz... reading input surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.white... reading input pial surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.pial... reading input white surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /usr/local/freesurfer/average/colortable_BA.txt) Saving annotation colortable ./BA.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 804 351 906 1.930 0.403 0.197 0.311 119 11.3 BA1 1803 1033 2244 2.059 0.426 0.167 0.142 56 13.0 BA2 894 702 945 1.777 0.403 0.191 0.088 16 3.4 BA3a 1587 1078 1681 1.527 0.296 0.154 0.070 21 5.3 BA3b 2154 1287 3030 2.367 0.593 0.233 0.464 331 45.1 BA4a 1326 910 2125 2.532 0.603 0.266 0.436 404 27.0 BA4p 6569 3607 9445 2.362 0.516 0.194 0.237 476 53.3 BA6 1229 815 2072 2.326 0.386 0.162 0.078 26 4.3 BA44 1292 830 2107 2.076 0.450 0.188 0.203 65 6.6 BA45 4566 2885 4487 1.538 0.444 0.185 0.125 265 21.7 V1 5050 3089 5538 1.729 0.489 0.191 0.113 152 25.3 V2 448 301 598 2.123 0.280 0.136 0.043 5 0.8 MT #-------------------------------------------- #@# BA Labels rh Tue Dec 13 12:24:33 EST 2016 mri_label2label --srcsubject fsaverage --srclabel /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/rh.BA1.label --trgsubject 1_S_5002 --trglabel ./rh.BA1.label --hemi rh --regmethod surface srclabel = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/rh.BA1.label srcsubject = fsaverage trgsubject = 1_S_5002 trglabel = ./rh.BA1.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.white Reading target registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 144029 Number of reverse mapping hits = 838 Checking for and removing duplicates Writing label file ./rh.BA1.label 4800 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/rh.BA2.label --trgsubject 1_S_5002 --trglabel ./rh.BA2.label --hemi rh --regmethod surface srclabel = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/rh.BA2.label srcsubject = fsaverage trgsubject = 1_S_5002 trglabel = ./rh.BA2.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.white Reading target registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 144029 Number of reverse mapping hits = 1041 Checking for and removing duplicates Writing label file ./rh.BA2.label 7728 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/rh.BA3a.label --trgsubject 1_S_5002 --trglabel ./rh.BA3a.label --hemi rh --regmethod surface srclabel = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/rh.BA3a.label srcsubject = fsaverage trgsubject = 1_S_5002 trglabel = ./rh.BA3a.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.white Reading target registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 144029 Number of reverse mapping hits = 240 Checking for and removing duplicates Writing label file ./rh.BA3a.label 4220 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/rh.BA3b.label --trgsubject 1_S_5002 --trglabel ./rh.BA3b.label --hemi rh --regmethod surface srclabel = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/rh.BA3b.label srcsubject = fsaverage trgsubject = 1_S_5002 trglabel = ./rh.BA3b.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.white Reading target registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 144029 Number of reverse mapping hits = 440 Checking for and removing duplicates Writing label file ./rh.BA3b.label 4962 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/rh.BA4a.label --trgsubject 1_S_5002 --trglabel ./rh.BA4a.label --hemi rh --regmethod surface srclabel = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/rh.BA4a.label srcsubject = fsaverage trgsubject = 1_S_5002 trglabel = ./rh.BA4a.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.white Reading target registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 144029 Number of reverse mapping hits = 771 Checking for and removing duplicates Writing label file ./rh.BA4a.label 6518 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/rh.BA4p.label --trgsubject 1_S_5002 --trglabel ./rh.BA4p.label --hemi rh --regmethod surface srclabel = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/rh.BA4p.label srcsubject = fsaverage trgsubject = 1_S_5002 trglabel = ./rh.BA4p.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.white Reading target registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 144029 Number of reverse mapping hits = 296 Checking for and removing duplicates Writing label file ./rh.BA4p.label 4769 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/rh.BA6.label --trgsubject 1_S_5002 --trglabel ./rh.BA6.label --hemi rh --regmethod surface srclabel = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/rh.BA6.label srcsubject = fsaverage trgsubject = 1_S_5002 trglabel = ./rh.BA6.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.white Reading target registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 144029 Number of reverse mapping hits = 2003 Checking for and removing duplicates Writing label file ./rh.BA6.label 14259 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/rh.BA44.label --trgsubject 1_S_5002 --trglabel ./rh.BA44.label --hemi rh --regmethod surface srclabel = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/rh.BA44.label srcsubject = fsaverage trgsubject = 1_S_5002 trglabel = ./rh.BA44.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.white Reading target registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 144029 Number of reverse mapping hits = 1232 Checking for and removing duplicates Writing label file ./rh.BA44.label 8144 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/rh.BA45.label --trgsubject 1_S_5002 --trglabel ./rh.BA45.label --hemi rh --regmethod surface srclabel = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/rh.BA45.label srcsubject = fsaverage trgsubject = 1_S_5002 trglabel = ./rh.BA45.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.white Reading target registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 144029 Number of reverse mapping hits = 1273 Checking for and removing duplicates Writing label file ./rh.BA45.label 6628 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/rh.V1.label --trgsubject 1_S_5002 --trglabel ./rh.V1.label --hemi rh --regmethod surface srclabel = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/rh.V1.label srcsubject = fsaverage trgsubject = 1_S_5002 trglabel = ./rh.V1.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.white Reading target registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 144029 Number of reverse mapping hits = 2884 Checking for and removing duplicates Writing label file ./rh.V1.label 7611 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/rh.V2.label --trgsubject 1_S_5002 --trglabel ./rh.V2.label --hemi rh --regmethod surface srclabel = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/rh.V2.label srcsubject = fsaverage trgsubject = 1_S_5002 trglabel = ./rh.V2.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.white Reading target registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 144029 Number of reverse mapping hits = 4844 Checking for and removing duplicates Writing label file ./rh.V2.label 12860 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/rh.MT.label --trgsubject 1_S_5002 --trglabel ./rh.MT.label --hemi rh --regmethod surface srclabel = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/rh.MT.label srcsubject = fsaverage trgsubject = 1_S_5002 trglabel = ./rh.MT.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.white Reading target registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 144029 Number of reverse mapping hits = 387 Checking for and removing duplicates Writing label file ./rh.MT.label 2319 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/rh.perirhinal.label --trgsubject 1_S_5002 --trglabel ./rh.perirhinal.label --hemi rh --regmethod surface srclabel = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/rh.perirhinal.label srcsubject = fsaverage trgsubject = 1_S_5002 trglabel = ./rh.perirhinal.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.white Reading target registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 144029 Number of reverse mapping hits = 101 Checking for and removing duplicates Writing label file ./rh.perirhinal.label 853 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/rh.BA1.thresh.label --trgsubject 1_S_5002 --trglabel ./rh.BA1.thresh.label --hemi rh --regmethod surface srclabel = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/rh.BA1.thresh.label srcsubject = fsaverage trgsubject = 1_S_5002 trglabel = ./rh.BA1.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.white Reading target registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 144029 Number of reverse mapping hits = 113 Checking for and removing duplicates Writing label file ./rh.BA1.thresh.label 989 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/rh.BA2.thresh.label --trgsubject 1_S_5002 --trglabel ./rh.BA2.thresh.label --hemi rh --regmethod surface srclabel = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/rh.BA2.thresh.label srcsubject = fsaverage trgsubject = 1_S_5002 trglabel = ./rh.BA2.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.white Reading target registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 144029 Number of reverse mapping hits = 575 Checking for and removing duplicates Writing label file ./rh.BA2.thresh.label 3263 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/rh.BA3a.thresh.label --trgsubject 1_S_5002 --trglabel ./rh.BA3a.thresh.label --hemi rh --regmethod surface srclabel = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/rh.BA3a.thresh.label srcsubject = fsaverage trgsubject = 1_S_5002 trglabel = ./rh.BA3a.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.white Reading target registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 144029 Number of reverse mapping hits = 66 Checking for and removing duplicates Writing label file ./rh.BA3a.thresh.label 1764 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/rh.BA3b.thresh.label --trgsubject 1_S_5002 --trglabel ./rh.BA3b.thresh.label --hemi rh --regmethod surface srclabel = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/rh.BA3b.thresh.label srcsubject = fsaverage trgsubject = 1_S_5002 trglabel = ./rh.BA3b.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.white Reading target registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 144029 Number of reverse mapping hits = 234 Checking for and removing duplicates Writing label file ./rh.BA3b.thresh.label 2417 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/rh.BA4a.thresh.label --trgsubject 1_S_5002 --trglabel ./rh.BA4a.thresh.label --hemi rh --regmethod surface srclabel = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/rh.BA4a.thresh.label srcsubject = fsaverage trgsubject = 1_S_5002 trglabel = ./rh.BA4a.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.white Reading target registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 144029 Number of reverse mapping hits = 148 Checking for and removing duplicates Writing label file ./rh.BA4a.thresh.label 1536 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/rh.BA4p.thresh.label --trgsubject 1_S_5002 --trglabel ./rh.BA4p.thresh.label --hemi rh --regmethod surface srclabel = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/rh.BA4p.thresh.label srcsubject = fsaverage trgsubject = 1_S_5002 trglabel = ./rh.BA4p.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.white Reading target registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 144029 Number of reverse mapping hits = 92 Checking for and removing duplicates Writing label file ./rh.BA4p.thresh.label 1581 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/rh.BA6.thresh.label --trgsubject 1_S_5002 --trglabel ./rh.BA6.thresh.label --hemi rh --regmethod surface srclabel = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/rh.BA6.thresh.label srcsubject = fsaverage trgsubject = 1_S_5002 trglabel = ./rh.BA6.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.white Reading target registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 144029 Number of reverse mapping hits = 1105 Checking for and removing duplicates Writing label file ./rh.BA6.thresh.label 8064 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/rh.BA44.thresh.label --trgsubject 1_S_5002 --trglabel ./rh.BA44.thresh.label --hemi rh --regmethod surface srclabel = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/rh.BA44.thresh.label srcsubject = fsaverage trgsubject = 1_S_5002 trglabel = ./rh.BA44.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.white Reading target registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 144029 Number of reverse mapping hits = 265 Checking for and removing duplicates Writing label file ./rh.BA44.thresh.label 1277 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/rh.BA45.thresh.label --trgsubject 1_S_5002 --trglabel ./rh.BA45.thresh.label --hemi rh --regmethod surface srclabel = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/rh.BA45.thresh.label srcsubject = fsaverage trgsubject = 1_S_5002 trglabel = ./rh.BA45.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.white Reading target registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 144029 Number of reverse mapping hits = 204 Checking for and removing duplicates Writing label file ./rh.BA45.thresh.label 1382 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/rh.V1.thresh.label --trgsubject 1_S_5002 --trglabel ./rh.V1.thresh.label --hemi rh --regmethod surface srclabel = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/rh.V1.thresh.label srcsubject = fsaverage trgsubject = 1_S_5002 trglabel = ./rh.V1.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.white Reading target registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 144029 Number of reverse mapping hits = 1969 Checking for and removing duplicates Writing label file ./rh.V1.thresh.label 5201 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/rh.V2.thresh.label --trgsubject 1_S_5002 --trglabel ./rh.V2.thresh.label --hemi rh --regmethod surface srclabel = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/rh.V2.thresh.label srcsubject = fsaverage trgsubject = 1_S_5002 trglabel = ./rh.V2.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.white Reading target registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 144029 Number of reverse mapping hits = 2355 Checking for and removing duplicates Writing label file ./rh.V2.thresh.label 5792 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/rh.MT.thresh.label --trgsubject 1_S_5002 --trglabel ./rh.MT.thresh.label --hemi rh --regmethod surface srclabel = /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/label/rh.MT.thresh.label srcsubject = fsaverage trgsubject = 1_S_5002 trglabel = ./rh.MT.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.white Reading target registration /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/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 144029 Number of reverse mapping hits = 35 Checking for and removing duplicates Writing label file ./rh.MT.thresh.label 303 mri_label2label: Done mris_label2annot --s 1_S_5002 --hemi rh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l rh.BA1.label --l rh.BA2.label --l rh.BA3a.label --l rh.BA3b.label --l rh.BA4a.label --l rh.BA4p.label --l rh.BA6.label --l rh.BA44.label --l rh.BA45.label --l rh.V1.label --l rh.V2.label --l rh.MT.label --l rh.perirhinal.label --a BA --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/average/colortable_BA.txt Number of ctab entries 14 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/label cmdline mris_label2annot --s 1_S_5002 --hemi rh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l rh.BA1.label --l rh.BA2.label --l rh.BA3a.label --l rh.BA3b.label --l rh.BA4a.label --l rh.BA4p.label --l rh.BA6.label --l rh.BA44.label --l rh.BA45.label --l rh.V1.label --l rh.V2.label --l rh.MT.label --l rh.perirhinal.label --a BA --maxstatwinner --noverbose sysname Linux hostname TRON machine x86_64 user sneha subject 1_S_5002 hemi rh SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL ColorTable /usr/local/freesurfer/average/colortable_BA.txt AnnotName BA nlables 13 LabelThresh 0 0.000000 Loading /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.orig 1 1530880 BA1 2 16749699 BA2 3 16711680 BA3a 4 3368703 BA3b 5 1376196 BA4a 6 13382655 BA4p 7 10036737 BA6 8 2490521 BA44 9 39283 BA45 10 3993 V1 11 8508928 V2 12 10027163 MT 13 16422433 perirhinal Mapping unhit to unknown Found 96460 unhit vertices Writing annot to /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/label/rh.BA.annot mris_label2annot --s 1_S_5002 --hemi rh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l rh.BA1.thresh.label --l rh.BA2.thresh.label --l rh.BA3a.thresh.label --l rh.BA3b.thresh.label --l rh.BA4a.thresh.label --l rh.BA4p.thresh.label --l rh.BA6.thresh.label --l rh.BA44.thresh.label --l rh.BA45.thresh.label --l rh.V1.thresh.label --l rh.V2.thresh.label --l rh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/average/colortable_BA.txt Number of ctab entries 14 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/label cmdline mris_label2annot --s 1_S_5002 --hemi rh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l rh.BA1.thresh.label --l rh.BA2.thresh.label --l rh.BA3a.thresh.label --l rh.BA3b.thresh.label --l rh.BA4a.thresh.label --l rh.BA4p.thresh.label --l rh.BA6.thresh.label --l rh.BA44.thresh.label --l rh.BA45.thresh.label --l rh.V1.thresh.label --l rh.V2.thresh.label --l rh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose sysname Linux hostname TRON machine x86_64 user sneha subject 1_S_5002 hemi rh SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL ColorTable /usr/local/freesurfer/average/colortable_BA.txt AnnotName BA.thresh nlables 12 LabelThresh 0 0.000000 Loading /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.orig 1 1530880 BA1 2 16749699 BA2 3 16711680 BA3a 4 3368703 BA3b 5 1376196 BA4a 6 13382655 BA4p 7 10036737 BA6 8 2490521 BA44 9 39283 BA45 10 3993 V1 11 8508928 V2 12 10027163 MT Mapping unhit to unknown Found 116991 unhit vertices Writing annot to /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/label/rh.BA.thresh.annot mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab 1_S_5002 rh white computing statistics for each annotation in ./rh.BA.annot. reading volume /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/wm.mgz... reading input surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.white... reading input pial surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.pial... reading input white surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /usr/local/freesurfer/average/colortable_BA.txt) Saving annotation colortable ./BA.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1122 623 1264 1.699 0.490 0.219 0.191 59 8.0 BA1 4184 2539 4637 1.816 0.464 0.166 0.143 274 22.2 BA2 1083 821 1023 1.578 0.401 0.182 0.091 28 4.9 BA3a 2279 1489 2223 1.376 0.378 0.150 0.067 40 7.0 BA3b 1930 1167 2337 2.013 0.529 0.269 0.252 1169 22.4 BA4a 1315 964 1820 2.018 0.665 0.216 0.161 41 8.2 BA4p 9295 5486 13580 2.280 0.595 0.196 0.201 526 78.4 BA6 4089 2538 5658 2.193 0.476 0.168 0.132 116 27.0 BA44 4268 2743 6773 2.206 0.493 0.186 0.216 529 17.9 BA45 5226 3273 5284 1.567 0.446 0.196 0.166 246 46.5 V1 10325 6192 12495 1.937 0.556 0.188 0.115 302 50.2 V2 1826 1158 2362 2.094 0.495 0.171 0.111 54 8.7 MT 627 411 1705 2.964 0.891 0.212 0.161 24 4.6 perirhinal mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab 1_S_5002 rh white computing statistics for each annotation in ./rh.BA.thresh.annot. reading volume /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/wm.mgz... reading input surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.white... reading input pial surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.pial... reading input white surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /usr/local/freesurfer/average/colortable_BA.txt) Saving annotation colortable ./BA.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 710 377 651 1.496 0.387 0.209 0.194 34 4.5 BA1 2594 1539 2795 1.769 0.458 0.171 0.174 242 16.0 BA2 948 726 870 1.609 0.380 0.188 0.073 15 3.0 BA3a 1848 1261 1616 1.249 0.200 0.133 0.046 21 3.8 BA3b 1071 599 1281 2.031 0.516 0.284 0.290 86 14.1 BA4a 1058 825 1528 2.005 0.699 0.227 0.171 34 7.1 BA4p 5886 3385 8224 2.228 0.580 0.204 0.223 349 56.4 BA6 1071 625 1498 2.099 0.491 0.182 0.132 30 6.9 BA44 1086 688 1856 2.196 0.515 0.191 0.101 30 4.7 BA45 4985 3136 4970 1.558 0.444 0.194 0.124 169 28.4 V1 5563 3361 6267 1.793 0.524 0.199 0.163 249 44.9 V2 218 132 295 2.249 0.391 0.159 0.116 4 1.2 MT /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label lh Tue Dec 13 12:31:19 EST 2016 mris_spherical_average -erode 1 -orig white -t 0.4 -o 1_S_5002 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label painting output onto subject 1_S_5002. processing subject lh.EC_average... reading output surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.sphere.reg... eroding label 1 times before writing thresholding label stat at 0.400 before writing only 1 subject - copying statistics... writing label with 1107 points to lh.entorhinal_exvivo.label... mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label 1_S_5002 lh white limiting computations to label ./lh.entorhinal_exvivo.label. reading volume /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/wm.mgz... reading input surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.white... reading input pial surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.pial... reading input white surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/lh.white... INFO: assuming MGZ format for volumes. table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 439 239 1028 2.800 0.788 0.201 0.236 34 4.7 ./lh.entorhinal_exvivo.label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label rh Tue Dec 13 12:31:45 EST 2016 mris_spherical_average -erode 1 -orig white -t 0.4 -o 1_S_5002 label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label painting output onto subject 1_S_5002. processing subject rh.EC_average... reading output surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.sphere.reg... eroding label 1 times before writing thresholding label stat at 0.400 before writing only 1 subject - copying statistics... writing label with 812 points to rh.entorhinal_exvivo.label... mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label 1_S_5002 rh white limiting computations to label ./rh.entorhinal_exvivo.label. reading volume /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/mri/wm.mgz... reading input surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.white... reading input pial surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.pial... reading input white surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002/surf/rh.white... INFO: assuming MGZ format for volumes. table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 305 187 760 2.620 0.991 0.208 0.201 16 3.1 ./rh.entorhinal_exvivo.label #------------------------------------------ Started at Sat Dec 10 12:30:45 EST 2016 Ended at Tue Dec 13 12:32:09 EST 2016 #@#%# recon-all-run-time-hours 72.023 recon-all -s 1_S_5002 finished without error at Tue Dec 13 12:32:09 EST 2016 New invocation of recon-all Tue Jan 17 12:49:28 EST 2017 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header /usr/local/freesurfer/bin/recon-all -autorecon3 -s 1_S_5002_snp_bbr-init-header -bbr-init-header -FLAIRpial -bigventricles -openmp 12 -qcache -mail snp2003@med.cornell.edu subjid 1_S_5002_snp_bbr-init-header setenv SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux TRON 3.8.0-44-generic #66~precise1-Ubuntu SMP Tue Jul 15 04:01:04 UTC 2014 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 1804890 maxlocks unlimited maxsignal 1804890 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 231111108 225538752 5572356 0 1548880 219051068 -/+ buffers/cache: 4938804 226172304 Swap: 31255548 0 31255548 ######################################## program versions used $Id: recon-all,v 1.482 2014/08/26 20:36:16 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/17-17:49:28-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/17-17:49:29-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/17-17:49:29-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/17-17:49:29-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/17-17:49:29-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/17-17:49:29-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/17-17:49:29-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/17-17:49:29-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 12 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/17-17:49:29-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/17-17:49:29-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/17-17:49:29-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/17-17:49:29-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/17-17:49:30-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/17-17:49:30-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/17-17:49:30-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/17-17:49:30-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/17-17:49:30-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/17-17:49:30-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/17-17:49:30-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/17-17:49:30-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/17-17:49:30-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/17-17:49:30-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/17-17:49:30-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/17-17:49:31-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/17-17:49:31-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/17-17:49:31-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/17-17:49:31-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/17-17:49:31-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/17-17:49:31-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/17-17:49:31-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/17-17:49:31-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/17-17:49:31-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/17-17:49:31-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/17-17:49:31-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/17-17:49:32-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/17-17:49:32-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/17-17:49:32-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/17-17:49:32-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: sneha Machine: TRON Platform: Linux PlatformVersion: 3.8.0-44-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #----------------------------------------- #@# Curvature Stats lh Tue Jan 17 12:49:32 EST 2017 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 1_S_5002_snp_bbr-init-header 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 [ 1_S_5002_snp_bbr-init-header/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 [ 246 ] Gb_filter = 0 #-------------------------------------------- #@# Sphere lh Tue Jan 17 12:49:37 EST 2017 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... scaling brain by 0.298... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host= TRON, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.03 pass 1: epoch 2 of 3 starting distance error %18.96 unfolding complete - removing small folds... starting distance error %18.89 removing remaining folds... final distance error %18.91 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/lh.sphere spherical transformation took 0.82 hours #-------------------------------------------- #@# Surf Reg lh Tue Jan 17 13:38:48 EST 2017 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/scripts mris_register -curv ../surf/lh.sphere /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /usr/local/freesurfer/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= TRON, 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= TRON, 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 = 0.584 curvature mean = 0.030, std = 0.938 curvature mean = 0.026, std = 0.863 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 0.00) sse = 273573.0, tmin=0.9255 d=32.00 min @ (8.00, 8.00, 0.00) sse = 232717.2, tmin=1.8508 d=16.00 min @ (-4.00, -4.00, 4.00) sse = 206768.8, tmin=2.7827 d=8.00 min @ (0.00, 2.00, 0.00) sse = 195752.3, tmin=3.7849 d=4.00 min @ (0.00, 0.00, -1.00) sse = 195020.7, tmin=4.8044 d=2.00 min @ (0.00, 0.00, 0.50) sse = 194768.6, tmin=5.8312 d=1.00 min @ (0.25, 0.00, -0.25) sse = 194671.4, tmin=6.8334 d=0.50 min @ (-0.12, 0.00, 0.12) sse = 194660.7, tmin=7.8142 tol=1.0e+00, sigma=0.5, host= TRON, 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 7.81 min curvature mean = 0.005, std = 0.963 curvature mean = 0.010, std = 0.943 curvature mean = 0.001, std = 0.974 curvature mean = 0.004, std = 0.975 curvature mean = 0.000, std = 0.977 curvature mean = 0.001, std = 0.989 2 Reading smoothwm curvature mean = -0.028, std = 0.395 curvature mean = 0.003, std = 0.067 curvature mean = 0.049, std = 0.246 curvature mean = 0.003, std = 0.079 curvature mean = 0.022, std = 0.391 curvature mean = 0.003, std = 0.085 curvature mean = 0.013, std = 0.502 curvature mean = 0.003, std = 0.087 curvature mean = 0.006, std = 0.623 MRISregister() return, current seed 0 writing registered surface to ../surf/lh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white lh Tue Jan 17 14:03:35 EST 2017 mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white... writing curvature file ../surf/lh.jacobian_white #-------------------------------------------- #@# AvgCurv lh Tue Jan 17 14:03:38 EST 2017 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/scripts mrisp_paint -a 5 /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Tue Jan 17 14:03:40 EST 2017 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 1_S_5002_snp_bbr-init-header lh ../surf/lh.sphere.reg /usr/local/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/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... 1258 labels changed using aseg relabeling using gibbs priors... 000: 2912 changed, 140473 examined... 001: 688 changed, 12570 examined... 002: 183 changed, 3741 examined... 003: 66 changed, 1056 examined... 004: 31 changed, 397 examined... 005: 13 changed, 169 examined... 006: 3 changed, 72 examined... 007: 2 changed, 15 examined... 008: 3 changed, 15 examined... 009: 2 changed, 16 examined... 010: 0 changed, 10 examined... 253 labels changed using aseg 000: 126 total segments, 82 labels (395 vertices) changed 001: 47 total segments, 7 labels (17 vertices) changed 002: 40 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 38 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1597 vertices marked for relabeling... 1597 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 1 minutes and 12 seconds. #-------------------------------------------- #@# Make Pial Surf lh Tue Jan 17 14:04:52 EST 2017 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs 1_S_5002_snp_bbr-init-header lh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/filled.mgz... reading volume /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/brain.finalsurfs.mgz... reading volume /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/wm.mgz... 33253 bright wm thresholded. 849 bright non-wm voxels segmented. reading original surface position from /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/surf/lh.orig... computing class statistics... border white: 294157 voxels (1.75%) border gray 303787 voxels (1.81%) WM (93.0): 93.7 +- 9.1 [70.0 --> 110.0] GM (79.0) : 76.6 +- 12.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 56.4 (was 70) setting MAX_BORDER_WHITE to 110.1 (was 105) setting MIN_BORDER_WHITE to 69.0 (was 85) setting MAX_CSF to 43.8 (was 40) setting MAX_GRAY to 91.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 62.7 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 31.3 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=101, GM=69 mean inside = 92.8, mean outside = 73.7 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.80 +- 0.24 (0.02-->4.18) (max @ vno 56457 --> 139233) face area 0.27 +- 0.13 (0.00-->2.77) mean absolute distance = 0.92 +- 1.20 5293 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 2 with 111 points - only 0.00% unknown deleting segment 4 with 143 points - only 0.00% unknown deleting segment 5 with 15 points - only 0.00% unknown deleting segment 6 with 115 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 7 with 4 points - only 0.00% unknown mean border=80.3, 176 (176) missing vertices, mean dist 0.1 [1.2 (%36.4)->0.8 (%63.6))] %43 local maxima, %53 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host= TRON, 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 0.89 +- 0.27 (0.07-->5.08) (max @ vno 64259 --> 139402) face area 0.27 +- 0.14 (0.00-->2.62) mean absolute distance = 0.51 +- 0.80 5732 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5650097.0, rms=10.51 001: dt: 0.5000, sse=7235515.5, rms=7.427 (0.000%) 002: dt: 0.5000, sse=7794925.5, rms=5.597 (0.000%) 003: dt: 0.5000, sse=8363542.0, rms=4.547 (0.000%) 004: dt: 0.5000, sse=8717979.0, rms=4.026 (0.000%) 005: dt: 0.5000, sse=8927691.0, rms=3.782 (0.000%) 006: dt: 0.5000, sse=9038821.0, rms=3.660 (0.000%) 007: dt: 0.5000, sse=9088563.0, rms=3.584 (0.000%) rms = 3.53, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=9121331.0, rms=3.534 (0.000%) 009: dt: 0.2500, sse=6093093.5, rms=2.681 (0.000%) 010: dt: 0.2500, sse=5773956.0, rms=2.407 (0.000%) rms = 2.36, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=5514434.5, rms=2.364 (0.000%) 012: dt: 0.1250, sse=5367246.5, rms=2.275 (0.000%) rms = 2.26, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=5314476.0, rms=2.264 (0.000%) positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 17 points - only 0.00% unknown deleting segment 1 with 219 points - only 0.00% unknown deleting segment 4 with 27 points - only 0.00% unknown deleting segment 6 with 35 points - only 0.00% unknown deleting segment 7 with 73 points - only 0.00% unknown deleting segment 9 with 16 points - only 43.75% unknown removing 4 vertex label from ripped group deleting segment 10 with 4 points - only 0.00% unknown deleting segment 12 with 26 points - only 0.00% unknown deleting segment 13 with 12 points - only 0.00% unknown deleting segment 14 with 9 points - only 0.00% unknown mean border=83.4, 272 (85) missing vertices, mean dist -0.3 [0.6 (%65.6)->0.3 (%34.4))] %63 local maxima, %32 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host= TRON, 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 0.88 +- 0.27 (0.06-->5.37) (max @ vno 64259 --> 139402) face area 0.33 +- 0.17 (0.00-->3.38) mean absolute distance = 0.35 +- 0.47 4507 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5929978.5, rms=4.89 014: dt: 0.5000, sse=6412781.0, rms=3.364 (0.000%) rms = 3.42, time step reduction 1 of 3 to 0.250... 015: dt: 0.2500, sse=5934003.5, rms=2.758 (0.000%) 016: dt: 0.2500, sse=5760456.0, rms=2.343 (0.000%) 017: dt: 0.2500, sse=5626523.0, rms=2.156 (0.000%) 018: dt: 0.2500, sse=5593730.5, rms=2.074 (0.000%) rms = 2.03, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=5544575.0, rms=2.027 (0.000%) 020: dt: 0.1250, sse=5462362.0, rms=1.957 (0.000%) rms = 1.95, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=5423400.0, rms=1.947 (0.000%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 30 points - only 16.67% unknown deleting segment 1 with 307 points - only 0.00% unknown deleting segment 2 with 7 points - only 0.00% unknown deleting segment 3 with 11 points - only 0.00% unknown deleting segment 5 with 119 points - only 0.00% unknown deleting segment 7 with 18 points - only 50.00% unknown deleting segment 8 with 5 points - only 0.00% unknown deleting segment 10 with 26 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 11 with 3 points - only 0.00% unknown deleting segment 12 with 9 points - only 0.00% unknown mean border=86.1, 240 (59) missing vertices, mean dist -0.2 [0.4 (%70.2)->0.2 (%29.8))] %81 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host= TRON, 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 0.87 +- 0.27 (0.05-->5.47) (max @ vno 64259 --> 139402) face area 0.32 +- 0.17 (0.00-->3.46) mean absolute distance = 0.27 +- 0.37 3987 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5734971.5, rms=4.00 022: dt: 0.5000, sse=6094793.5, rms=3.016 (0.000%) rms = 3.29, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=5706364.0, rms=2.246 (0.000%) 024: dt: 0.2500, sse=5737659.5, rms=1.928 (0.000%) 025: dt: 0.2500, sse=5678309.0, rms=1.825 (0.000%) rms = 1.82, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=5643273.0, rms=1.821 (0.000%) 027: dt: 0.1250, sse=5531329.5, rms=1.743 (0.000%) rms = 1.74, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=5531329.5, rms=1.743 (0.000%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 15 points - only 0.00% unknown deleting segment 1 with 324 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 3 with 11 points - only 0.00% unknown deleting segment 4 with 11 points - only 0.00% unknown deleting segment 6 with 135 points - only 0.00% unknown deleting segment 7 with 42 points - only 21.43% unknown deleting segment 8 with 5 points - only 0.00% unknown deleting segment 9 with 26 points - only 0.00% unknown deleting segment 10 with 15 points - only 0.00% unknown mean border=87.1, 270 (53) missing vertices, mean dist -0.1 [0.3 (%57.2)->0.2 (%42.8))] %86 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host= TRON, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=5564584.0, rms=2.15 rms = 2.26, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=5737244.5, rms=1.613 (0.000%) 030: dt: 0.2500, sse=6085182.5, rms=1.329 (0.000%) rms = 1.34, time step reduction 2 of 3 to 0.125... rms = 1.32, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=6072862.0, rms=1.319 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 4 with 14 points - only 57.14% unknown smoothing surface for 5 iterations... mean border=57.6, 240 (240) missing vertices, mean dist 1.9 [0.3 (%0.1)->2.2 (%99.9))] %36 local maxima, %46 large gradients and %14 min vals, 483 gradients ignored tol=1.0e-04, sigma=2.0, host= TRON, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=25909456.0, rms=29.43 001: dt: 0.5000, sse=20097376.0, rms=25.440 (0.000%) 002: dt: 0.5000, sse=15771473.0, rms=22.005 (0.000%) 003: dt: 0.5000, sse=12734259.0, rms=19.132 (0.000%) 004: dt: 0.5000, sse=10905046.0, rms=16.739 (0.000%) 005: dt: 0.5000, sse=9724475.0, rms=14.694 (0.000%) 006: dt: 0.5000, sse=9041309.0, rms=12.919 (0.000%) 007: dt: 0.5000, sse=8407859.0, rms=11.263 (0.000%) 008: dt: 0.5000, sse=8088251.5, rms=9.708 (0.000%) 009: dt: 0.5000, sse=7863700.5, rms=8.300 (0.000%) 010: dt: 0.5000, sse=7872647.0, rms=7.226 (0.000%) 011: dt: 0.5000, sse=7933416.5, rms=6.490 (0.000%) 012: dt: 0.5000, sse=8084107.0, rms=6.052 (0.000%) 013: dt: 0.5000, sse=8188761.0, rms=5.758 (0.000%) 014: dt: 0.5000, sse=8272993.5, rms=5.602 (0.000%) 015: dt: 0.5000, sse=8277897.0, rms=5.464 (0.000%) 016: dt: 0.5000, sse=8363155.0, rms=5.410 (0.000%) 017: dt: 0.5000, sse=8321890.0, rms=5.336 (0.000%) rms = 5.31, time step reduction 1 of 3 to 0.250... 018: dt: 0.5000, sse=8364816.5, rms=5.314 (0.000%) 019: dt: 0.2500, sse=5508314.5, rms=4.100 (0.000%) 020: dt: 0.2500, sse=5306697.5, rms=3.746 (0.000%) rms = 3.74, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=5065076.0, rms=3.739 (0.000%) 022: dt: 0.1250, sse=4573290.5, rms=3.261 (0.000%) 023: dt: 0.1250, sse=4505347.5, rms=3.186 (0.000%) rms = 3.18, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=4457851.0, rms=3.181 (0.000%) positioning took 2.6 minutes mean border=53.5, 650 (26) missing vertices, mean dist 0.2 [0.2 (%35.1)->0.5 (%64.9))] %55 local maxima, %30 large gradients and %10 min vals, 167 gradients ignored tol=1.0e-04, sigma=1.0, host= TRON, 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=5531527.0, rms=6.54 025: dt: 0.5000, sse=5782432.5, rms=5.573 (0.000%) 026: dt: 0.5000, sse=7366781.5, rms=5.495 (0.000%) rms = 5.66, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=5835053.5, rms=4.179 (0.000%) 028: dt: 0.2500, sse=5325648.5, rms=3.804 (0.000%) rms = 3.78, time step reduction 2 of 3 to 0.125... 029: dt: 0.2500, sse=5361512.5, rms=3.782 (0.000%) 030: dt: 0.1250, sse=4872415.0, rms=3.242 (0.000%) 031: dt: 0.1250, sse=4817570.0, rms=3.138 (0.000%) rms = 3.12, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=4777443.5, rms=3.121 (0.000%) positioning took 0.9 minutes mean border=51.1, 901 (16) missing vertices, mean dist 0.1 [0.2 (%35.2)->0.3 (%64.8))] %66 local maxima, %19 large gradients and %10 min vals, 181 gradients ignored tol=1.0e-04, sigma=0.5, host= TRON, 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=5074881.0, rms=4.50 rms = 5.47, time step reduction 1 of 3 to 0.250... 033: dt: 0.2500, sse=4822188.0, rms=3.681 (0.000%) 034: dt: 0.2500, sse=4831473.5, rms=3.416 (0.000%) rms = 3.40, time step reduction 2 of 3 to 0.125... 035: dt: 0.2500, sse=5057901.0, rms=3.405 (0.000%) 036: dt: 0.1250, sse=4799932.0, rms=3.051 (0.000%) 037: dt: 0.1250, sse=4774328.5, rms=2.971 (0.000%) rms = 2.96, time step reduction 3 of 3 to 0.062... 038: dt: 0.1250, sse=4758231.5, rms=2.960 (0.000%) positioning took 0.7 minutes mean border=50.1, 1639 (14) missing vertices, mean dist 0.1 [0.2 (%44.6)->0.2 (%55.4))] %67 local maxima, %18 large gradients and % 9 min vals, 140 gradients ignored tol=1.0e-04, sigma=0.2, host= TRON, 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 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=4800812.0, rms=3.25 rms = 4.61, time step reduction 1 of 3 to 0.250... 039: dt: 0.2500, sse=4710727.5, rms=2.972 (0.000%) rms = 2.95, time step reduction 2 of 3 to 0.125... 040: dt: 0.2500, sse=4939472.0, rms=2.953 (0.000%) 041: dt: 0.1250, sse=4798532.0, rms=2.826 (0.000%) 042: dt: 0.1250, sse=4807828.5, rms=2.775 (0.000%) rms = 2.76, time step reduction 3 of 3 to 0.062... 043: dt: 0.1250, sse=4814807.5, rms=2.764 (0.000%) positioning took 0.6 minutes writing curvature file /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/surf/lh.area.pial vertex spacing 0.95 +- 0.40 (0.04-->6.65) (max @ vno 109954 --> 110725) face area 0.37 +- 0.28 (0.00-->6.54) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 140473 vertices processed 25000 of 140473 vertices processed 50000 of 140473 vertices processed 75000 of 140473 vertices processed 100000 of 140473 vertices processed 125000 of 140473 vertices processed 0 of 140473 vertices processed 25000 of 140473 vertices processed 50000 of 140473 vertices processed 75000 of 140473 vertices processed 100000 of 140473 vertices processed 125000 of 140473 vertices processed thickness calculation complete, 132:157 truncations. 37394 vertices at 0 distance 102966 vertices at 1 distance 85209 vertices at 2 distance 31469 vertices at 3 distance 8141 vertices at 4 distance 2166 vertices at 5 distance 692 vertices at 6 distance 261 vertices at 7 distance 140 vertices at 8 distance 62 vertices at 9 distance 36 vertices at 10 distance 37 vertices at 11 distance 18 vertices at 12 distance 22 vertices at 13 distance 10 vertices at 14 distance 8 vertices at 15 distance 1 vertices at 16 distance 1 vertices at 17 distance 1 vertices at 18 distance 4 vertices at 19 distance 0 vertices at 20 distance writing curvature file /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/surf/lh.thickness positioning took 11.9 minutes #-------------------------------------------- #@# Surf Volume lh Tue Jan 17 14:16:48 EST 2017 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.volume lh.area.mid mul lh.thickness Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# Curvature Stats rh Tue Jan 17 14:16:49 EST 2017 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 1_S_5002_snp_bbr-init-header 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 [ 1_S_5002_snp_bbr-init-header/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 [ 257 ] Gb_filter = 0 WARN: S lookup min: -0.340586 WARN: S explicit min: 0.000000 vertex = 141 #-------------------------------------------- #@# Sphere rh Tue Jan 17 14:16:54 EST 2017 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... scaling brain by 0.294... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host= TRON, 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 %19.09 pass 1: epoch 2 of 3 starting distance error %19.05 unfolding complete - removing small folds... starting distance error %18.99 removing remaining folds... final distance error %19.01 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/rh.sphere spherical transformation took 0.69 hours #-------------------------------------------- #@# Surf Reg rh Tue Jan 17 14:58:08 EST 2017 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/scripts mris_register -curv ../surf/rh.sphere /usr/local/freesurfer/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /usr/local/freesurfer/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= TRON, 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= TRON, 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 = 0.578 curvature mean = 0.033, std = 0.924 curvature mean = 0.026, std = 0.861 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 0.00, 16.00) sse = 426601.0, tmin=0.9268 d=32.00 min @ (-8.00, -8.00, -8.00) sse = 269980.0, tmin=1.8603 d=16.00 min @ (-4.00, 0.00, 4.00) sse = 255971.6, tmin=2.8058 d=8.00 min @ (2.00, 2.00, -2.00) sse = 237410.4, tmin=3.7635 d=4.00 min @ (1.00, 0.00, 1.00) sse = 233936.8, tmin=4.7423 d=2.00 min @ (-0.50, -0.50, -0.50) sse = 233145.8, tmin=5.7307 d=1.00 min @ (0.00, 0.00, 0.25) sse = 232937.2, tmin=6.7087 d=0.50 min @ (0.00, 0.12, 0.00) sse = 232918.0, tmin=7.6918 tol=1.0e+00, sigma=0.5, host= TRON, 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 7.69 min curvature mean = 0.005, std = 0.949 curvature mean = 0.010, std = 0.942 curvature mean = -0.000, std = 0.959 curvature mean = 0.004, std = 0.974 curvature mean = -0.003, std = 0.960 curvature mean = 0.001, std = 0.989 2 Reading smoothwm curvature mean = -0.028, std = 0.324 curvature mean = 0.005, std = 0.070 curvature mean = 0.061, std = 0.302 curvature mean = 0.005, std = 0.083 curvature mean = 0.027, std = 0.475 curvature mean = 0.005, std = 0.089 curvature mean = 0.015, std = 0.611 curvature mean = 0.005, std = 0.092 curvature mean = 0.005, std = 0.727 MRISregister() return, current seed 0 writing registered surface to ../surf/rh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white rh Tue Jan 17 15:23:10 EST 2017 mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white... writing curvature file ../surf/rh.jacobian_white #-------------------------------------------- #@# AvgCurv rh Tue Jan 17 15:23:12 EST 2017 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/scripts mrisp_paint -a 5 /usr/local/freesurfer/average/rh.average.curvature.filled.buckner40.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /usr/local/freesurfer/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc rh Tue Jan 17 15:23:15 EST 2017 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 1_S_5002_snp_bbr-init-header rh ../surf/rh.sphere.reg /usr/local/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/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... 1226 labels changed using aseg relabeling using gibbs priors... 000: 2960 changed, 144029 examined... 001: 759 changed, 12782 examined... 002: 155 changed, 4187 examined... 003: 53 changed, 960 examined... 004: 23 changed, 326 examined... 005: 11 changed, 143 examined... 006: 5 changed, 65 examined... 007: 1 changed, 31 examined... 008: 0 changed, 8 examined... 131 labels changed using aseg 000: 105 total segments, 67 labels (429 vertices) changed 001: 38 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 32 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1822 vertices marked for relabeling... 1822 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 1 minutes and 15 seconds. #-------------------------------------------- #@# Make Pial Surf rh Tue Jan 17 15:24:30 EST 2017 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs 1_S_5002_snp_bbr-init-header rh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/filled.mgz... reading volume /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/brain.finalsurfs.mgz... reading volume /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/wm.mgz... 34342 bright wm thresholded. 849 bright non-wm voxels segmented. reading original surface position from /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/surf/rh.orig... computing class statistics... border white: 294157 voxels (1.75%) border gray 303787 voxels (1.81%) WM (93.0): 93.7 +- 8.8 [70.0 --> 110.0] GM (79.0) : 76.2 +- 13.5 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 54.5 (was 70) setting MAX_BORDER_WHITE to 108.8 (was 105) setting MIN_BORDER_WHITE to 68.0 (was 85) setting MAX_CSF to 40.9 (was 40) setting MAX_GRAY to 91.2 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 61.2 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 27.4 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=100, GM=68 mean inside = 91.8, mean outside = 72.8 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.80 +- 0.23 (0.01-->3.97) (max @ vno 88688 --> 97969) face area 0.27 +- 0.13 (0.00-->2.96) mean absolute distance = 0.89 +- 1.18 5376 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 23 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 13 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 5 with 2 points - only 0.00% unknown deleting segment 6 with 42 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 10 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 11 with 3 points - only 0.00% unknown deleting segment 12 with 116 points - only 0.00% unknown mean border=80.6, 214 (214) missing vertices, mean dist 0.1 [1.0 (%40.6)->0.8 (%59.4))] %47 local maxima, %49 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host= TRON, 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 0.89 +- 0.27 (0.06-->4.22) (max @ vno 88688 --> 97969) face area 0.27 +- 0.14 (0.00-->2.69) mean absolute distance = 0.52 +- 0.82 5707 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5657199.5, rms=10.20 001: dt: 0.5000, sse=7319710.5, rms=7.106 (0.000%) 002: dt: 0.5000, sse=7879799.5, rms=5.347 (0.000%) 003: dt: 0.5000, sse=8480515.0, rms=4.406 (0.000%) 004: dt: 0.5000, sse=8786842.0, rms=3.967 (0.000%) 005: dt: 0.5000, sse=9091308.0, rms=3.738 (0.000%) 006: dt: 0.5000, sse=9131829.0, rms=3.639 (0.000%) 007: dt: 0.5000, sse=9280736.0, rms=3.568 (0.000%) rms = 3.55, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=9232253.0, rms=3.546 (0.000%) 009: dt: 0.2500, sse=6152849.0, rms=2.636 (0.000%) 010: dt: 0.2500, sse=5789411.5, rms=2.349 (0.000%) rms = 2.31, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=5536262.0, rms=2.306 (0.000%) 012: dt: 0.1250, sse=5382324.5, rms=2.210 (0.000%) rms = 2.20, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=5330881.5, rms=2.201 (0.000%) positioning took 1.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 18 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 4 with 28 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 5 with 3 points - only 0.00% unknown deleting segment 7 with 40 points - only 0.00% unknown deleting segment 9 with 9 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 10 with 2 points - only 0.00% unknown deleting segment 11 with 411 points - only 17.52% unknown mean border=83.2, 256 (97) missing vertices, mean dist -0.3 [0.7 (%62.4)->0.3 (%37.6))] %62 local maxima, %33 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host= TRON, 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 0.87 +- 0.27 (0.08-->4.15) (max @ vno 88688 --> 97969) face area 0.33 +- 0.17 (0.00-->3.41) mean absolute distance = 0.41 +- 0.54 5425 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5900574.0, rms=4.60 014: dt: 0.5000, sse=6481662.5, rms=3.331 (0.000%) rms = 3.37, time step reduction 1 of 3 to 0.250... 015: dt: 0.2500, sse=6006639.5, rms=2.748 (0.000%) 016: dt: 0.2500, sse=5849208.5, rms=2.339 (0.000%) 017: dt: 0.2500, sse=5706668.0, rms=2.139 (0.000%) 018: dt: 0.2500, sse=5687104.0, rms=2.044 (0.000%) rms = 2.00, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=5639619.5, rms=2.002 (0.000%) 020: dt: 0.1250, sse=5558685.5, rms=1.930 (0.000%) rms = 1.92, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=5520689.5, rms=1.917 (0.000%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 17 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 14 points - only 0.00% unknown deleting segment 4 with 7 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 5 with 2 points - only 0.00% unknown deleting segment 6 with 38 points - only 0.00% unknown deleting segment 8 with 11 points - only 0.00% unknown deleting segment 9 with 6 points - only 0.00% unknown deleting segment 10 with 429 points - only 16.78% unknown deleting segment 11 with 7 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 12 with 3 points - only 0.00% unknown mean border=85.8, 228 (68) missing vertices, mean dist -0.2 [0.5 (%66.5)->0.3 (%33.5))] %78 local maxima, %18 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host= TRON, 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 0.87 +- 0.26 (0.06-->4.09) (max @ vno 88688 --> 97969) face area 0.32 +- 0.17 (0.00-->3.03) mean absolute distance = 0.33 +- 0.42 4353 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5842030.0, rms=4.00 022: dt: 0.5000, sse=6275622.0, rms=2.958 (0.000%) rms = 3.20, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=5895654.0, rms=2.272 (0.000%) 024: dt: 0.2500, sse=5922738.0, rms=1.934 (0.000%) 025: dt: 0.2500, sse=5847743.5, rms=1.831 (0.000%) rms = 1.81, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=5818597.0, rms=1.811 (0.000%) 027: dt: 0.1250, sse=5703906.5, rms=1.738 (0.000%) rms = 1.74, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=5666104.5, rms=1.736 (0.000%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 17 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 3 with 43 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 4 with 4 points - only 0.00% unknown deleting segment 5 with 34 points - only 0.00% unknown deleting segment 6 with 11 points - only 0.00% unknown deleting segment 7 with 6 points - only 0.00% unknown deleting segment 8 with 371 points - only 16.71% unknown deleting segment 9 with 17 points - only 0.00% unknown mean border=86.9, 239 (51) missing vertices, mean dist -0.1 [0.4 (%57.0)->0.3 (%43.0))] %84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host= TRON, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=5723121.5, rms=2.33 029: dt: 0.5000, sse=7831189.0, rms=2.195 (0.000%) rms = 2.91, time step reduction 1 of 3 to 0.250... 030: dt: 0.2500, sse=6882179.5, rms=1.552 (0.000%) rms = 1.53, time step reduction 2 of 3 to 0.125... 031: dt: 0.2500, sse=6376636.5, rms=1.529 (0.000%) 032: dt: 0.1250, sse=6418019.0, rms=1.352 (0.000%) rms = 1.32, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=6434062.5, rms=1.316 (0.000%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... smoothing surface for 5 iterations... mean border=56.5, 280 (280) missing vertices, mean dist 1.8 [1.2 (%0.0)->2.3 (%100.0))] %31 local maxima, %44 large gradients and %21 min vals, 856 gradients ignored tol=1.0e-04, sigma=2.0, host= TRON, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=28311870.0, rms=30.45 001: dt: 0.5000, sse=22314374.0, rms=26.617 (0.000%) 002: dt: 0.5000, sse=17635522.0, rms=23.213 (0.000%) 003: dt: 0.5000, sse=14190244.0, rms=20.248 (0.000%) 004: dt: 0.5000, sse=11945697.0, rms=17.668 (0.000%) 005: dt: 0.5000, sse=10462017.0, rms=15.420 (0.000%) 006: dt: 0.5000, sse=9520101.0, rms=13.455 (0.000%) 007: dt: 0.5000, sse=8808010.0, rms=11.638 (0.000%) 008: dt: 0.5000, sse=8360015.0, rms=9.994 (0.000%) 009: dt: 0.5000, sse=8053129.5, rms=8.569 (0.000%) 010: dt: 0.5000, sse=8059567.0, rms=7.479 (0.000%) 011: dt: 0.5000, sse=8082994.5, rms=6.723 (0.000%) 012: dt: 0.5000, sse=8198979.0, rms=6.176 (0.000%) 013: dt: 0.5000, sse=8246884.5, rms=5.817 (0.000%) 014: dt: 0.5000, sse=8353751.0, rms=5.566 (0.000%) 015: dt: 0.5000, sse=8381996.0, rms=5.438 (0.000%) 016: dt: 0.5000, sse=8388303.0, rms=5.314 (0.000%) rms = 5.27, time step reduction 1 of 3 to 0.250... 017: dt: 0.5000, sse=8418591.0, rms=5.269 (0.000%) 018: dt: 0.2500, sse=5522423.0, rms=4.074 (0.000%) 019: dt: 0.2500, sse=5318373.5, rms=3.735 (0.000%) rms = 3.69, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=5072358.5, rms=3.693 (0.000%) 021: dt: 0.1250, sse=4565861.0, rms=3.238 (0.000%) 022: dt: 0.1250, sse=4503380.0, rms=3.159 (0.000%) rms = 3.15, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=4474071.5, rms=3.152 (0.000%) positioning took 2.6 minutes mean border=53.4, 866 (20) missing vertices, mean dist 0.2 [0.2 (%40.4)->0.5 (%59.6))] %49 local maxima, %31 large gradients and %15 min vals, 340 gradients ignored tol=1.0e-04, sigma=1.0, host= TRON, 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=5282233.5, rms=5.68 024: dt: 0.5000, sse=5762795.5, rms=5.250 (0.000%) rms = 5.35, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=5116575.5, rms=4.165 (0.000%) 026: dt: 0.2500, sse=5222529.0, rms=3.818 (0.000%) 027: dt: 0.2500, sse=5151951.5, rms=3.691 (0.000%) rms = 3.66, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=5270259.0, rms=3.664 (0.000%) 029: dt: 0.1250, sse=4832568.0, rms=3.234 (0.000%) 030: dt: 0.1250, sse=4797898.0, rms=3.142 (0.000%) rms = 3.12, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=4773724.0, rms=3.122 (0.000%) positioning took 1.0 minutes mean border=51.6, 1154 (15) missing vertices, mean dist 0.1 [0.2 (%42.7)->0.4 (%57.3))] %60 local maxima, %20 large gradients and %15 min vals, 335 gradients ignored tol=1.0e-04, sigma=0.5, host= TRON, 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=4997872.0, rms=4.18 rms = 5.05, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=4805448.5, rms=3.576 (0.000%) 033: dt: 0.2500, sse=4898941.0, rms=3.358 (0.000%) rms = 3.36, time step reduction 2 of 3 to 0.125... 034: dt: 0.2500, sse=5104938.5, rms=3.356 (0.000%) 035: dt: 0.1250, sse=4867270.5, rms=3.072 (0.000%) 036: dt: 0.1250, sse=4858097.0, rms=3.010 (0.000%) rms = 3.00, time step reduction 3 of 3 to 0.062... 037: dt: 0.1250, sse=4856861.0, rms=3.001 (0.000%) positioning took 0.7 minutes mean border=50.5, 2189 (12) missing vertices, mean dist 0.1 [0.2 (%47.9)->0.3 (%52.1))] %62 local maxima, %18 large gradients and %14 min vals, 282 gradients ignored tol=1.0e-04, sigma=0.2, host= TRON, 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 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=4922149.0, rms=3.39 rms = 4.49, time step reduction 1 of 3 to 0.250... 038: dt: 0.2500, sse=4813526.0, rms=3.095 (0.000%) 039: dt: 0.2500, sse=5046354.0, rms=3.040 (0.000%) rms = 3.09, time step reduction 2 of 3 to 0.125... 040: dt: 0.1250, sse=4976752.0, rms=2.980 (0.000%) 041: dt: 0.1250, sse=4918731.5, rms=2.904 (0.000%) rms = 2.87, time step reduction 3 of 3 to 0.062... 042: dt: 0.1250, sse=4916162.0, rms=2.868 (0.000%) positioning took 0.7 minutes writing curvature file /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/surf/rh.area.pial vertex spacing 0.94 +- 0.40 (0.05-->6.96) (max @ vno 110386 --> 109430) face area 0.36 +- 0.27 (0.00-->6.57) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 144029 vertices processed 25000 of 144029 vertices processed 50000 of 144029 vertices processed 75000 of 144029 vertices processed 100000 of 144029 vertices processed 125000 of 144029 vertices processed 0 of 144029 vertices processed 25000 of 144029 vertices processed 50000 of 144029 vertices processed 75000 of 144029 vertices processed 100000 of 144029 vertices processed 125000 of 144029 vertices processed thickness calculation complete, 119:215 truncations. 38014 vertices at 0 distance 101644 vertices at 1 distance 86512 vertices at 2 distance 35053 vertices at 3 distance 10416 vertices at 4 distance 2945 vertices at 5 distance 866 vertices at 6 distance 258 vertices at 7 distance 92 vertices at 8 distance 44 vertices at 9 distance 24 vertices at 10 distance 28 vertices at 11 distance 18 vertices at 12 distance 11 vertices at 13 distance 7 vertices at 14 distance 7 vertices at 15 distance 5 vertices at 16 distance 6 vertices at 17 distance 7 vertices at 18 distance 1 vertices at 19 distance 2 vertices at 20 distance writing curvature file /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/surf/rh.thickness positioning took 12.4 minutes #-------------------------------------------- #@# Surf Volume rh Tue Jan 17 15:36:54 EST 2017 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.volume rh.area.mid mul rh.thickness Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ] #-------------------------------------------- #@# Refine Pial Surfs w/ T2/FLAIR Tue Jan 17 15:36:54 EST 2017 bbregister --s 1_S_5002_snp_bbr-init-header --mov /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/orig/FLAIRraw.mgz --lta /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/transforms/FLAIRraw.lta --init-header --T2 Log file is /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/transforms/FLAIRraw.dat.log Tue Jan 17 15:36:54 EST 2017 setenv SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL cd /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/scripts /usr/local/freesurfer/bin/bbregister --s 1_S_5002_snp_bbr-init-header --mov /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/orig/FLAIRraw.mgz --lta /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/transforms/FLAIRraw.lta --init-header --T2 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ Linux TRON 3.8.0-44-generic #66~precise1-Ubuntu SMP Tue Jul 15 04:01:04 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_convert /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/orig/FLAIRraw.mgz /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/transforms/tmp.bbregister.27845/template.nii mri_convert /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/orig/FLAIRraw.mgz /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/transforms/tmp.bbregister.27845/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/orig/FLAIRraw.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/transforms/tmp.bbregister.27845/template.nii... tkregister2_cmdl --s 1_S_5002_snp_bbr-init-header --mov /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/transforms/tmp.bbregister.27845/template.nii --regheader --reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/transforms/tmp.bbregister.27845/reg.init.dat --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/transforms/tmp.bbregister.27845/template.nii reg file /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/transforms/tmp.bbregister.27845/reg.init.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/transforms/tmp.bbregister.27845/template.nii Tmov: -------------------- -1.000 0.000 0.000 80.000; 0.000 0.000 0.977 -125.000; 0.000 -0.977 0.000 125.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- -1.000 0.000 0.000 -245.506; 0.000 0.000 1.000 533.401; 0.000 -1.000 0.000 -335.667; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- -1.000 0.000 0.000 -245.506; 0.000 0.000 1.000 533.401; 0.000 -1.000 0.000 -335.667; 0.000 0.000 0.000 1.000; Determinant -1 subject = 1_S_5002_snp_bbr-init-header RegMat --------------------------- -1.000 0.000 0.000 -245.506; 0.000 0.000 1.000 533.401; 0.000 -1.000 0.000 -335.667; 0.000 0.000 0.000 1.000; mri_segreg --mov /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/transforms/tmp.bbregister.27845/template.nii --init-reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/transforms/tmp.bbregister.27845/reg.init.dat --out-reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/transforms/tmp.bbregister.27845/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 1.103.2.1 2011/10/07 19:14:42 greve Exp $ setenv SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL cd /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/scripts mri_segreg --mov /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/transforms/tmp.bbregister.27845/template.nii --init-reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/transforms/tmp.bbregister.27845/reg.init.dat --out-reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/transforms/tmp.bbregister.27845/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 TRON machine x86_64 user sneha movvol /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/transforms/tmp.bbregister.27845/template.nii regfile /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/transforms/tmp.bbregister.27845/reg.init.dat subject 1_S_5002_snp_bbr-init-header dof 6 outregfile /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/transforms/tmp.bbregister.27845/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 1484884991 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg -1.000 0.000 0.000 -245.506; 0.000 0.000 1.000 533.401; 0.000 -1.000 0.000 -335.667; 0.000 0.000 0.000 1.000; 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 Projecting RH Surfs Computing relative cost 0 -25.0 -25.0 -25.0 10.000000 1 -25.0 -25.0 25.0 10.000000 2 -25.0 25.0 -25.0 10.000000 3 -25.0 25.0 25.0 10.000000 4 25.0 -25.0 -25.0 10.000000 5 25.0 -25.0 25.0 10.000000 6 25.0 25.0 -25.0 10.000000 7 25.0 25.0 25.0 10.000000 REL: 8 10.000000 80.000000 10.000000 rel = 1 Initial costs ---------------- Number of surface hits 0 WM Intensity -nan +/- -nan Ctx Intensity -nan +/- -nan Pct Contrast -nan +/- -nan Cost 10.0000 RelCost 1.0000 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 10.0000 10.0000 0.0 Brute Force -------------------------- Min cost was 10.000000 Number of iterations 729 Search time 1.274000 sec Parameters at best (transmm, rotdeg) -4.000 -4.000 -4.000 -4.000 -4.000 -4.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 -4 1 -4 2 -4 3 -4 4 -4 5 -4 Powell done niters = 0 Computing relative cost 0 -25.0 -25.0 -25.0 10.000000 1 -25.0 -25.0 25.0 10.000000 2 -25.0 25.0 -25.0 10.000000 3 -25.0 25.0 25.0 10.000000 4 25.0 -25.0 -25.0 10.000000 5 25.0 -25.0 25.0 10.000000 6 25.0 25.0 -25.0 10.000000 7 25.0 25.0 25.0 10.000000 REL: 8 10.000000 80.000000 10.000000 rel = 1 Number of iterations 0 Min cost was 10.000000 Number of FunctionCalls 109 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.193000 sec Parameters at optimum (transmm) -1.38389 -1.38389 -1.38389 Parameters at optimum (rotdeg) -1.38389 -1.38389 -1.38389 Final costs ---------------- Number of surface hits 0 WM Intensity -nan +/- -nan Ctx Intensity -nan +/- -nan Pct Contrast -nan +/- -nan Cost 10.0000 RelCost 1.0000 Reg at min cost was -0.999 0.024 0.025 -225.651; 0.024 -0.025 0.999 529.326; -0.024 -0.999 -0.024 -355.662; 0.000 0.000 0.000 1.000; Writing optimal reg to /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/transforms/tmp.bbregister.27845/bbr.pass1.dat, type = 14 Original Reg -1.000 0.000 0.000 -245.506; 0.000 0.000 1.000 533.401; 0.000 -1.000 0.000 -335.667; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.001 -0.024 -0.025 -19.855; -0.024 0.025 0.001 4.075; 0.024 -0.001 0.024 19.996; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 27.629613 Computing change in rh position Surface RMS Diff (mm) 28.133298 30.701124 mri_segreg done mri_segreg --mov /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/transforms/tmp.bbregister.27845/template.nii --init-reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/transforms/tmp.bbregister.27845/bbr.pass1.dat --out-reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/transforms/FLAIRraw.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/transforms/FLAIRraw.dat.mincost --dof 6 --nmax 36 --param /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/transforms/FLAIRraw.dat.param --surf white --cur-reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/transforms/tmp.bbregister.27845/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $ setenv SUBJECTS_DIR /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL cd /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/scripts mri_segreg --mov /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/transforms/tmp.bbregister.27845/template.nii --init-reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/transforms/tmp.bbregister.27845/bbr.pass1.dat --out-reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/transforms/FLAIRraw.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/transforms/FLAIRraw.dat.mincost --dof 6 --nmax 36 --param /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/transforms/FLAIRraw.dat.param --surf white --cur-reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/transforms/tmp.bbregister.27845/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname TRON machine x86_64 user sneha movvol /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/transforms/tmp.bbregister.27845/template.nii regfile /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/transforms/tmp.bbregister.27845/bbr.pass1.dat subject 1_S_5002_snp_bbr-init-header dof 6 outregfile /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/transforms/FLAIRraw.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 1485393579 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg -0.999 0.024 0.025 -225.651; 0.024 -0.025 0.999 529.326; -0.024 -0.999 -0.024 -355.662; 0.000 0.000 0.000 1.000; 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 Projecting RH Surfs Computing relative cost 0 -25.0 -25.0 -25.0 10.000000 1 -25.0 -25.0 25.0 10.000000 2 -25.0 25.0 -25.0 10.000000 3 -25.0 25.0 25.0 10.000000 4 25.0 -25.0 -25.0 10.000000 5 25.0 -25.0 25.0 10.000000 6 25.0 25.0 -25.0 10.000000 7 25.0 25.0 25.0 10.000000 REL: 8 10.000000 80.000000 10.000000 rel = 1 Initial costs ---------------- Number of surface hits 0 WM Intensity -nan +/- -nan Ctx Intensity -nan +/- -nan Pct Contrast -nan +/- -nan Cost 10.0000 RelCost 1.0000 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 10.0000 10.0000 0.0 Brute Force -------------------------- Min cost was 10.000000 Number of iterations 729 Search time 1.288000 sec Parameters at best (transmm, rotdeg) -0.100 -0.100 -0.100 -0.100 -0.100 -0.100 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 -0.1 1 -0.1 2 -0.1 3 -0.1 4 -0.1 5 -0.1 Powell done niters = 0 Computing relative cost 0 -25.0 -25.0 -25.0 10.000000 1 -25.0 -25.0 25.0 10.000000 2 -25.0 25.0 -25.0 10.000000 3 -25.0 25.0 25.0 10.000000 4 25.0 -25.0 -25.0 10.000000 5 25.0 -25.0 25.0 10.000000 6 25.0 25.0 -25.0 10.000000 7 25.0 25.0 25.0 10.000000 REL: 8 10.000000 80.000000 10.000000 rel = 1 Number of iterations 0 Min cost was 10.000000 Number of FunctionCalls 109 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 5.054000 sec Parameters at optimum (transmm) 2.51611 2.51611 2.51611 Parameters at optimum (rotdeg) 2.51611 2.51611 2.51611 Final costs ---------------- Number of surface hits 0 WM Intensity -nan +/- -nan Ctx Intensity -nan +/- -nan Pct Contrast -nan +/- -nan Cost 10.0000 RelCost 1.0000 Reg at min cost was -1.000 -0.021 -0.018 -261.165; -0.019 0.018 1.000 535.884; 0.021 -1.000 0.019 -319.339; 0.000 0.000 0.000 1.000; Writing optimal reg to /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/transforms/FLAIRraw.dat, type = 14 Original Reg -0.999 0.024 0.025 -225.651; 0.024 -0.025 0.999 529.326; -0.024 -0.999 -0.024 -355.662; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg 0.000 0.045 0.043 35.514; 0.043 -0.043 -0.000 -6.558; -0.045 0.000 -0.043 -36.323; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 49.632699 Computing change in rh position Surface RMS Diff (mm) 50.583082 55.240945 mri_segreg done tkregister2_cmdl --mov /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/orig/FLAIRraw.mgz --reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/transforms/FLAIRraw.dat --noedit --ltaout /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/transforms/FLAIRraw.lta tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/orig/FLAIRraw.mgz reg file /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/transforms/FLAIRraw.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- -1.000 -0.021 -0.018 -261.165; -0.019 0.018 1.000 535.884; 0.021 -1.000 0.019 -319.339; 0.000 0.000 0.000 1.000; float2int = 0 --------------------------------------- INFO: loading target /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/orig/FLAIRraw.mgz Tmov: -------------------- -1.000 0.000 0.000 80.000; 0.000 0.000 0.977 -125.000; 0.000 -0.977 0.000 125.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- -1.000 -0.021 -0.018 -261.165; -0.019 0.018 1.000 535.884; 0.021 -1.000 0.019 -319.339; 0.000 0.000 0.000 1.000; Determinant -1 subject = 1_S_5002_snp_bbr-init-header RegMat --------------------------- -1.000 -0.021 -0.018 -261.165; -0.019 0.018 1.000 535.884; 0.021 -1.000 0.019 -319.339; 0.000 0.000 0.000 1.000; transformed matrix: 1.000 -0.021 -0.019 1.146; 0.021 1.000 0.018 1.118; 0.018 -0.019 1.000 -1.132; 0.000 0.000 0.000 1.000; transformed matrix: -1.000 0.020 0.018 447.404; -0.018 0.018 -0.976 786.626; 0.021 0.976 0.018 -335.456; 0.000 0.000 0.000 1.000; Cleaning up Started at Tue Jan 17 15:36:54 EST 2017 Ended at Tue Jan 17 15:37:33 EST 2017 BBR-Run-Time-Sec 39 bbregister Done To check results, run: tkregister2 --mov /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/orig/FLAIRraw.mgz --reg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/transforms/FLAIRraw.dat --surf mri_convert -odt short -at /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/transforms/FLAIRraw.lta -rt cubic -ns 1 -rl /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/orig.mgz /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/orig/FLAIRraw.mgz /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/FLAIR.prenorm.mgz mri_convert -odt short -at /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/transforms/FLAIRraw.lta -rt cubic -ns 1 -rl /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/orig.mgz /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/orig/FLAIRraw.mgz /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/FLAIR.prenorm.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/orig/FLAIRraw.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) INFO: Reading transformation from file /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/transforms/FLAIRraw.lta... Reading transform with LTAreadEx() reading extra input line subject 1_S_5002_snp_bbr-init-header reading extra input line fscale 0.150000 reading template info from volume /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/orig.mgz... INFO: Applying transformation from file /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/transforms/FLAIRraw.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 1.000 -0.021 -0.019 1.146; 0.021 1.000 0.018 1.118; 0.018 -0.019 1.000 -1.132; 0.000 0.000 0.000 1.000; --------------------------------- Applying LTAtransformInterp (resample_type 5) MRItoBSpline degree 3 changing data type from float to short (noscale = 1)... writing to /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/FLAIR.prenorm.mgz... mri_normalize -sigma 0.5 -nonmax_suppress 0 -min_dist 1 -aseg /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/aseg.mgz -surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/surf/rh.white identity.nofile -surface /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/surf/lh.white identity.nofile /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/FLAIR.prenorm.mgz /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/FLAIR.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 /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/FLAIR.prenorm.mgz... computing distance transform computing distance transform 65748 non wm control points removed building Voronoi diagram... performing soap bubble smoothing, sigma = 0... smoothing bias field writing normalized volume to /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/FLAIR.mgz /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/scripts cp -v /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/surf/lh.pial /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/surf/lh.woFLAIR.pial `/shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/surf/lh.pial' -> `/shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/surf/lh.woFLAIR.pial' mris_make_surfaces -orig_white white -orig_pial woFLAIR.pial -white NOWRITE -mgz -T1 brain.finalsurfs -FLAIR ../mri/FLAIR -nsigma_above 3 -nsigma_below 3 1_S_5002_snp_bbr-init-header lh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... deforming surfaces based on FLAIR volume ../mri/FLAIR using T2 threshold of 3.00 sigmas above the mean (default=2) using T2 threshold of 3.00 sigmas below the mean (default=2) using white starting white location... using woFLAIR.pial starting pial locations... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/filled.mgz... reading volume /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/brain.finalsurfs.mgz... reading volume /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/wm.mgz... 33253 bright wm thresholded. 849 bright non-wm voxels segmented. reading original surface position from /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/surf/lh.orig... computing class statistics... border white: 294157 voxels (1.75%) border gray 303787 voxels (1.81%) WM (93.0): 93.7 +- 9.1 [70.0 --> 110.0] GM (79.0) : 76.6 +- 12.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 56.4 (was 70) setting MAX_BORDER_WHITE to 110.1 (was 105) setting MIN_BORDER_WHITE to 69.0 (was 85) setting MAX_CSF to 43.8 (was 40) setting MAX_GRAY to 91.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 62.7 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 31.3 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=101, GM=69 mean inside = 92.8, mean outside = 73.7 smoothing surface for 5 iterations... 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) repositioning cortical surface to gray/white boundary reading volume /shared_data2/sneha/4RTNI_processed/FreeSurfer/BL/1_S_5002_snp_bbr-init-header/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.87 +- 0.27 (0.02-->5.56) (max @ vno 64259 --> 139402) face area 0.32 +- 0.17 (0.00-->3.63) averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 33 points - only 15.15% unknown deleting segment 3 with 115 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 4 with 1 points - only 0.00% unknown deleting segment 5 with 9 points - only 0.00% unknown deleting segment 6 with 197 points - only 0.00% unknown deleting segment 8 with 112 points - only 0.00% unknown deleting segment 9 with 9 points - only 0.00% unknown deleting segment 10 with 10 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 11 with 2 points - only 0.00% unknown tol=1.0e-04, sigma=2.0, host= TRON, 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 0.87 +- 0.27 (0.03-->5.56) (max @ vno 64259 --> 139402) face area 0.32 +- 0.17 (0.00-->3.63) averaging target values for 5 iterations... 000: dt: 0.0000, sse=6056678.5, rms=0.00 rms = 1.71, time step reduction 1 of 3 to 0.250... rms = 0.47, time step reduction 2 of 3 to 0.125... rms = 0.06, time step reduction 3 of 3 to 0.062... 001: dt: 0.1250, sse=6056678.5, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 33 points - only 15.15% unknown deleting segment 1 with 115 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 1 points - only 0.00% unknown deleting segment 3 with 9 points - only 0.00% unknown deleting segment 4 with 197 points - only 0.00% unknown deleting segment 5 with 112 points - only 0.00% unknown deleting segment 6 with 9 points - only 0.00% unknown deleting segment 7 with 10 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown tol=1.0e-04, sigma=1.0, host= TRON, 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 0.87 +- 0.27 (0.03-->5.56) (max @ vno 64259 --> 139402) face area 0.32 +- 0.17 (0.00-->3.63) averaging target values for 5 iterations... 000: dt: 0.0000, sse=6056678.5, rms=0.00 rms = 1.72, time step reduction 1 of 3 to 0.250... rms = 0.47, time step reduction 2 of 3 to 0.125... rms = 0.06, time step reduction 3 of 3 to 0.062... 002: dt: 0.1250, sse=6056678.5, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 33 points - only 15.15% unknown deleting segment 1 with 115 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 1 points - only 0.00% unknown deleting segment 3 with 9 points - only 0.00% unknown deleting segment 4 with 197 points - only 0.00% unknown deleting segment 5 with 112 points - only 0.00% unknown deleting segment 6 with 9 points - only 0.00% unknown deleting segment 7 with 10 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown tol=1.0e-04, sigma=0.5, host= TRON, 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 0.87 +- 0.27 (0.03-->5.56) (max @ vno 64259 --> 139402) face area 0.32 +- 0.17 (0.00-->3.63) averaging target values for 5 iterations... 000: dt: 0.0000, sse=6056678.5, rms=0.00 rms = 1.71, time step reduction 1 of 3 to 0.250... rms = 0.47, time step reduction 2 of 3 to 0.125... rms = 0.06, time step reduction 3 of 3 to 0.062... 003: dt: 0.1250, sse=6056678.5, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 33 points - only 15.15% unknown deleting segment 1 with 115 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 1 points - only 0.00% unknown deleting segment 3 with 9 points - only 0.00% unknown deleting segment 4 with 197 points - only 0.00% unknown deleting segment 5 with 112 points - only 0.00% unknown deleting segment 6 with 9 points - only 0.00% unknown deleting segment 7 with 10 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown tol=1.0e-04, sigma=0.2, host= TRON, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 repositioning cortical surface to gray/csf boundary. HISTOalloc(-2147483648): could not allocate histogram 000: dt: 0.0000, sse=6056678.5, rms=0.00 rms = 1.72, time step reduction 1 of 3 to 0.250... rms = 0.47, time step reduction 2 of 3 to 0.125... rms = 0.06, time step reduction 3 of 3 to 0.062... 004: dt: 0.1250, sse=6056678.5, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group smoothing surface for 5 iterations... reading initial pial vertex positions from woFLAIR.pial... repositioning pial surface locations using ../mri/FLAIR.mgz compressed histogram detected, changing bin size to 0.000000 Cannot allocate memory Linux TRON 3.8.0-44-generic #66~precise1-Ubuntu SMP Tue Jul 15 04:01:04 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 1_S_5002_snp_bbr-init-header exited with ERRORS at Tue Jan 17 15:40:50 EST 2017 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting