Fri Nov 13 12:10:12 CET 2015 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0 /usr/local//freesurfer/bin/recon-all -autorecon1 -autorecon2 -autorecon3 -i /home/freesurfer/Documents/MRI_data/T1niftis/BCH_Subjects/T0/B_LU_02_MRI_E_T0/B_LU_02_MRI_E_T0_WIP_T1W_3D_TFE_3T_SENSE_6_1-0001.nii -s B_LU_02_MRI_E_T0 subjid B_LU_02_MRI_E_T0 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects 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 biosrv1 2.6.32-573.7.1.el6.x86_64 #1 SMP Tue Sep 22 22:00:00 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 63295 total used free shared buffers cached Mem: 16234576 15276800 957776 344 36896 4677480 -/+ buffers/cache: 10562424 5672152 Swap: 8183804 280580 7903224 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/13-11:10:12-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: root Machine: biosrv1 Platform: Linux PlatformVersion: 2.6.32-573.7.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/13-11:10:12-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: root Machine: biosrv1 Platform: Linux PlatformVersion: 2.6.32-573.7.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/13-11:10:12-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: root Machine: biosrv1 Platform: Linux PlatformVersion: 2.6.32-573.7.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/13-11:10:13-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: root Machine: biosrv1 Platform: Linux PlatformVersion: 2.6.32-573.7.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/13-11:10:13-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: root Machine: biosrv1 Platform: Linux PlatformVersion: 2.6.32-573.7.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/13-11:10:13-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: root Machine: biosrv1 Platform: Linux PlatformVersion: 2.6.32-573.7.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/13-11:10:13-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: root Machine: biosrv1 Platform: Linux PlatformVersion: 2.6.32-573.7.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/13-11:10:13-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: root Machine: biosrv1 Platform: Linux PlatformVersion: 2.6.32-573.7.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/13-11:10:13-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: root Machine: biosrv1 Platform: Linux PlatformVersion: 2.6.32-573.7.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/13-11:10:13-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: root Machine: biosrv1 Platform: Linux PlatformVersion: 2.6.32-573.7.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/13-11:10:13-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: root Machine: biosrv1 Platform: Linux PlatformVersion: 2.6.32-573.7.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/13-11:10:13-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: root Machine: biosrv1 Platform: Linux PlatformVersion: 2.6.32-573.7.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/13-11:10:14-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: root Machine: biosrv1 Platform: Linux PlatformVersion: 2.6.32-573.7.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/13-11:10:14-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: root Machine: biosrv1 Platform: Linux PlatformVersion: 2.6.32-573.7.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/13-11:10:14-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: root Machine: biosrv1 Platform: Linux PlatformVersion: 2.6.32-573.7.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/13-11:10:14-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: root Machine: biosrv1 Platform: Linux PlatformVersion: 2.6.32-573.7.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/13-11:10:14-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: root Machine: biosrv1 Platform: Linux PlatformVersion: 2.6.32-573.7.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/13-11:10:14-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: root Machine: biosrv1 Platform: Linux PlatformVersion: 2.6.32-573.7.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/13-11:10:14-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: root Machine: biosrv1 Platform: Linux PlatformVersion: 2.6.32-573.7.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/13-11:10:14-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: root Machine: biosrv1 Platform: Linux PlatformVersion: 2.6.32-573.7.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/13-11:10:15-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: root Machine: biosrv1 Platform: Linux PlatformVersion: 2.6.32-573.7.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/13-11:10:15-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: root Machine: biosrv1 Platform: Linux PlatformVersion: 2.6.32-573.7.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/13-11:10:15-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: root Machine: biosrv1 Platform: Linux PlatformVersion: 2.6.32-573.7.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/13-11:10:15-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: root Machine: biosrv1 Platform: Linux PlatformVersion: 2.6.32-573.7.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/13-11:10:15-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: root Machine: biosrv1 Platform: Linux PlatformVersion: 2.6.32-573.7.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/13-11:10:15-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: root Machine: biosrv1 Platform: Linux PlatformVersion: 2.6.32-573.7.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/13-11:10:15-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: root Machine: biosrv1 Platform: Linux PlatformVersion: 2.6.32-573.7.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/13-11:10:15-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: root Machine: biosrv1 Platform: Linux PlatformVersion: 2.6.32-573.7.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/13-11:10:16-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: root Machine: biosrv1 Platform: Linux PlatformVersion: 2.6.32-573.7.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/13-11:10:16-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: root Machine: biosrv1 Platform: Linux PlatformVersion: 2.6.32-573.7.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/13-11:10:16-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: root Machine: biosrv1 Platform: Linux PlatformVersion: 2.6.32-573.7.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/13-11:10:16-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: root Machine: biosrv1 Platform: Linux PlatformVersion: 2.6.32-573.7.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/13-11:10:16-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: root Machine: biosrv1 Platform: Linux PlatformVersion: 2.6.32-573.7.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/13-11:10:16-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: root Machine: biosrv1 Platform: Linux PlatformVersion: 2.6.32-573.7.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/13-11:10:16-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: root Machine: biosrv1 Platform: Linux PlatformVersion: 2.6.32-573.7.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/13-11:10:16-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: root Machine: biosrv1 Platform: Linux PlatformVersion: 2.6.32-573.7.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/13-11:10:17-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: root Machine: biosrv1 Platform: Linux PlatformVersion: 2.6.32-573.7.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/13-11:10:17-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: root Machine: biosrv1 Platform: Linux PlatformVersion: 2.6.32-573.7.1.el6.x86_64 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 ####################################### /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0 mri_convert /home/freesurfer/Documents/MRI_data/T1niftis/BCH_Subjects/T0/B_LU_02_MRI_E_T0/B_LU_02_MRI_E_T0_WIP_T1W_3D_TFE_3T_SENSE_6_1-0001.nii /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/orig/001.mgz mri_convert /home/freesurfer/Documents/MRI_data/T1niftis/BCH_Subjects/T0/B_LU_02_MRI_E_T0/B_LU_02_MRI_E_T0_WIP_T1W_3D_TFE_3T_SENSE_6_1-0001.nii /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/freesurfer/Documents/MRI_data/T1niftis/BCH_Subjects/T0/B_LU_02_MRI_E_T0/B_LU_02_MRI_E_T0_WIP_T1W_3D_TFE_3T_SENSE_6_1-0001.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -0.991785, -0.127913) j_ras = (0, -0.127913, 0.991785) k_ras = (1, 0, 0) writing to /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Fri Nov 13 12:10:24 CET 2015 Found 1 runs /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/orig/001.mgz /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/rawavg.mgz /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0 mri_convert /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/rawavg.mgz /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/orig.mgz --conform mri_convert /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/rawavg.mgz /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/rawavg.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -0.991785, -0.127913) j_ras = (0, -0.127913, 0.991785) k_ras = (1, 0, 0) Original Data has (1, 1, 1) mm size and (240, 240, 170) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/orig.mgz... mri_add_xform_to_header -c /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/transforms/talairach.xfm /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/orig.mgz /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Fri Nov 13 12:10:47 CET 2015 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Fri Nov 13 12:14:00 CET 2015 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.8168, pval=0.8469 >= threshold=0.0050) awk -f /usr/local//freesurfer/bin/extract_talairach_avi_QA.awk /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/transforms/talairach_avi.log tal_QC_AZS /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/transforms/talairach_avi.log TalAviQA: 0.97067 z-score: -1 #-------------------------------------------- #@# Nu Intensity Correction Fri Nov 13 12:14:00 CET 2015 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri /usr/local//freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux biosrv1 2.6.32-573.7.1.el6.x86_64 #1 SMP Tue Sep 22 22:00:00 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux Fri Nov 13 12:14:00 CET 2015 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.2138 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.2138/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.2138/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=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (-5.96046e-08, 0, -1) k_ras = (0, 1, 1.49012e-08) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.2138/nu0.mnc... -------------------------------------------------------- Iteration 1 Fri Nov 13 12:14:06 CET 2015 nu_correct -clobber ./tmp.mri_nu_correct.mni.2138/nu0.mnc ./tmp.mri_nu_correct.mni.2138/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.2138/0/ [root@biosrv1:/usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/] [2015-11-13 12:14:07] running: /usr/local//freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.2138/0/ ./tmp.mri_nu_correct.mni.2138/nu0.mnc ./tmp.mri_nu_correct.mni.2138/nu1.imp Processing:.................................................................Done 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Processing:.................................................................Done Number of iterations: 50 CV of field change: 0.00110344 [root@biosrv1:/usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/] [2015-11-13 12:14:58] running: /usr/local//freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.2138/nu0.mnc ./tmp.mri_nu_correct.mni.2138/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Fri Nov 13 12:15:03 CET 2015 nu_correct -clobber ./tmp.mri_nu_correct.mni.2138/nu1.mnc ./tmp.mri_nu_correct.mni.2138/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.2138/1/ [root@biosrv1:/usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/] [2015-11-13 12:15:03] running: /usr/local//freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.2138/1/ ./tmp.mri_nu_correct.mni.2138/nu1.mnc ./tmp.mri_nu_correct.mni.2138/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done 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Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 21 CV of field change: 0.000942033 [root@biosrv1:/usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/] [2015-11-13 12:15:27] running: /usr/local//freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.2138/nu1.mnc ./tmp.mri_nu_correct.mni.2138/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.2138/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.2138/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.2138/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.2138/ones.mgz sysname Linux hostname biosrv1 machine x86_64 user root input ./tmp.mri_nu_correct.mni.2138/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.2138/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.2138/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.2138/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2138/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.2138/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.2138/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2138/input.mean.dat sysname Linux hostname biosrv1 machine x86_64 user root UseRobust 0 Loading ./tmp.mri_nu_correct.mni.2138/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.2138/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.2138/ones.mgz --i ./tmp.mri_nu_correct.mni.2138/nu2.mnc --sum ./tmp.mri_nu_correct.mni.2138/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2138/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.2138/ones.mgz --i ./tmp.mri_nu_correct.mni.2138/nu2.mnc --sum ./tmp.mri_nu_correct.mni.2138/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2138/output.mean.dat sysname Linux hostname biosrv1 machine x86_64 user root UseRobust 0 Loading ./tmp.mri_nu_correct.mni.2138/ones.mgz Loading ./tmp.mri_nu_correct.mni.2138/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 16777216.000 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.2138/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.2138/nu2.mnc ./tmp.mri_nu_correct.mni.2138/nu2.mnc mul .99986440129023635635 Saving result to './tmp.mri_nu_correct.mni.2138/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.2138/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.2138/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.2138/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (-5.96046e-08, 0, -1) k_ras = (0, 1, 1.49012e-08) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 8 seconds. mapping ( 4, 152) to ( 3, 110) Fri Nov 13 12:16:23 CET 2015 mri_nu_correct.mni done mri_add_xform_to_header -c /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Fri Nov 13 12:16:25 CET 2015 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.154 0.023 -0.026 -2.504; -0.046 1.110 0.236 -14.312; 0.012 -0.261 1.126 3.656; 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 = 21 Starting OpenSpline(): npoints = 21 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 109 gm peak at 67 (67), valley at 56 (56) csf peak at 33, setting threshold to 55 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 65 (65), valley at 54 (54) csf peak at 33, setting threshold to 54 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 37 seconds. #-------------------------------------------- #@# Skull Stripping Fri Nov 13 12:19:03 CET 2015 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/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 = 1 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 5 reading 1 input volumes... logging results to talairach_with_skull.log reading '/usr/local//freesurfer/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=15.0 skull bounding box = (53, 38, 12) --> (206, 255, 222) using (104, 110, 117) as brain centroid... mean wm in atlas = 126, using box (85,83,91) --> (122, 136,142) to find MRI wm before smoothing, mri peak at 106 after smoothing, mri peak at 105, scaling input intensities by 1.200 scaling channel 0 by 1.2 initial log_p = -4.3 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.334370 @ (0.000, 0.000, 0.000) max log p = -4.334370 @ (0.000, 0.000, 0.000) max log p = -4.274609 @ (-2.273, -2.273, 2.273) max log p = -4.240578 @ (1.136, -1.136, 1.136) max log p = -4.236928 @ (0.568, -0.568, -0.568) max log p = -4.236928 @ (0.000, 0.000, 0.000) Found translation: (-0.6, -4.0, 2.8): log p = -4.237 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.2 (thresh=-4.2) 1.150 0.000 0.000 -19.518; 0.000 1.111 0.298 -41.054; 0.000 -0.278 1.038 33.685; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 1.150 0.000 0.000 -19.518; 0.000 1.111 0.298 -41.054; 0.000 -0.278 1.038 33.685; 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=-3.9, old_max_log_p =-4.0 (thresh=-4.0) 1.086 0.009 -0.032 -12.937; 0.000 1.132 0.303 -44.095; 0.036 -0.263 0.980 34.933; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.065 -0.035 -0.008 -7.418; 0.035 1.160 0.276 -49.347; -0.000 -0.230 1.009 32.797; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.065 -0.035 -0.008 -7.418; 0.034 1.131 0.303 -48.413; -0.001 -0.273 1.018 39.020; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.065 -0.035 -0.008 -7.418; 0.034 1.131 0.303 -48.413; -0.001 -0.273 1.018 39.020; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.063 -0.033 -0.017 -6.098; 0.034 1.137 0.296 -48.906; 0.008 -0.264 1.021 35.993; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.064 -0.024 -0.014 -7.650; 0.026 1.131 0.312 -49.214; 0.007 -0.283 1.016 38.784; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 8 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.065 -0.024 -0.014 -7.806; 0.026 1.129 0.311 -48.815; 0.007 -0.282 1.014 38.941; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 9 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.065 -0.024 -0.014 -7.806; 0.026 1.126 0.311 -48.417; 0.007 -0.283 1.016 38.784; 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 1.06544 -0.02381 -0.01412 -7.80588; 0.02561 1.12598 0.31069 -48.41675; 0.00728 -0.28260 1.01637 38.78412; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.06544 -0.02381 -0.01412 -7.80588; 0.02561 1.12598 0.31069 -48.41675; 0.00728 -0.28260 1.01637 38.78412; 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) = -0.0 tol 0.000010 Resulting transform: 1.065 -0.024 -0.014 -7.806; 0.026 1.126 0.311 -48.417; 0.007 -0.283 1.016 38.784; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.9 (old=-4.3) transform before final EM align: 1.065 -0.024 -0.014 -7.806; 0.026 1.126 0.311 -48.417; 0.007 -0.283 1.016 38.784; 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 1.06544 -0.02381 -0.01412 -7.80588; 0.02561 1.12598 0.31069 -48.41675; 0.00728 -0.28260 1.01637 38.78412; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.06544 -0.02381 -0.01412 -7.80588; 0.02561 1.12598 0.31069 -48.41675; 0.00728 -0.28260 1.01637 38.78412; 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: 014: -log(p) = 4.3 tol 0.000000 final transform: 1.065 -0.024 -0.014 -7.806; 0.026 1.126 0.311 -48.417; 0.007 -0.283 1.016 38.784; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 87 minutes and 25 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=130 y=114 z=102 r=88 first estimation of the main basin volume: 2933428 voxels Looking for seedpoints 2 found in the cerebellum 16 found in the rest of the brain global maximum in x=148, y=108, z=61, Imax=255 CSF=13, 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=20399612691 voxels, voxel volume =1.000 = 20399612691 mmm3 = 20399611.904 cm3 done. PostAnalyze...Basin Prior 21 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=129,y=118, z=97, r=10055 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ (2) Problem with the least square interpolation for CSF_MAX GLOBAL CSF_MIN=0, CSF_intensity=4, CSF_MAX=19 , nb = 44524 RIGHT_CER CSF_MIN=0, CSF_intensity=3, CSF_MAX=28 , nb = -1030530142 LEFT_CER CSF_MIN=0, CSF_intensity=3, CSF_MAX=21 , nb = -1060305750 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=4, CSF_MAX=18 , nb = 1077429401 LEFT_BRAIN CSF_MIN=0, CSF_intensity=4, CSF_MAX=19 , nb = 1079825826 OTHER CSF_MIN=5, CSF_intensity=11, CSF_MAX=40 , nb = 1071067242 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 19, 29, 45, 66 after analyzing : 19, 39, 45, 45 RIGHT_CER before analyzing : 28, 31, 37, 71 after analyzing : 28, 35, 37, 44 LEFT_CER before analyzing : 21, 30, 44, 71 after analyzing : 21, 39, 44, 47 RIGHT_BRAIN before analyzing : 18, 28, 45, 66 after analyzing : 18, 39, 45, 45 LEFT_BRAIN before analyzing : 19, 30, 46, 66 after analyzing : 19, 40, 46, 46 OTHER before analyzing : 40, 25, 22, 28 after analyzing : 21, 25, 25, 25 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...65 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.010 curvature mean = 69.119, std = 7.107 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 2.10, sigma = 2.92 after rotation: sse = 2.10, sigma = 2.92 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 2.17, its var is 2.48 before Erosion-Dilatation 0.01% 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...44 iterations mri_strip_skull: done peeling brain Brain Size = 1697242 voxels, voxel volume = 1.000 mm3 = 1697242 mmm3 = 1697.242 cm3 ****************************** Saving brainmask.auto.mgz done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Fri Nov 13 13:47:23 CET 2015 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/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 = 1 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/usr/local//freesurfer/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=24.0 skull bounding box = (64, 53, 25) --> (191, 197, 186) using (106, 101, 106) as brain centroid... mean wm in atlas = 107, using box (90,83,86) --> (121, 118,125) to find MRI wm before smoothing, mri peak at 106 after smoothing, mri peak at 105, scaling input intensities by 1.019 scaling channel 0 by 1.01905 initial log_p = -3.8 ************************************************ First Search limited to translation only. ************************************************ max log p = -3.813800 @ (0.000, 0.000, 0.000) max log p = -3.813800 @ (0.000, 0.000, 0.000) max log p = -3.739625 @ (-2.273, 2.273, 2.273) max log p = -3.706652 @ (-1.136, -1.136, 3.409) max log p = -3.702978 @ (0.568, -0.568, -1.705) max log p = -3.702978 @ (0.000, 0.000, 0.000) Found translation: (-2.8, 0.6, 4.0): log p = -3.703 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.4, old_max_log_p =-3.7 (thresh=-3.7) 1.064 0.000 0.000 -11.106; 0.000 1.135 0.169 -32.543; 0.000 -0.112 0.997 17.534; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.4, old_max_log_p =-3.4 (thresh=-3.4) 1.064 0.000 0.000 -11.106; 0.000 1.135 0.169 -32.543; 0.000 -0.112 0.997 17.534; 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=-3.3, old_max_log_p =-3.4 (thresh=-3.4) 1.084 0.000 0.000 -15.567; 0.000 1.119 0.266 -38.666; 0.000 -0.227 0.993 35.256; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3) 1.084 0.000 0.000 -15.567; 0.000 1.119 0.266 -38.666; 0.000 -0.227 0.993 35.256; 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=-3.3, old_max_log_p =-3.3 (thresh=-3.3) 1.080 0.011 -0.006 -14.399; -0.009 1.116 0.282 -39.287; 0.009 -0.244 0.985 36.935; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3) 1.080 0.011 -0.006 -14.399; -0.009 1.119 0.283 -39.658; 0.009 -0.243 0.982 37.175; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3) 1.080 0.011 -0.006 -14.399; -0.009 1.119 0.283 -39.658; 0.009 -0.243 0.982 37.175; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2772 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.07982 0.01111 -0.00576 -14.39860; -0.00888 1.11871 0.28311 -39.65777; 0.00880 -0.24310 0.98197 37.17511; 0.00000 0.00000 0.00000 1.00000; nsamples 2772 Quasinewton: input matrix 1.07982 0.01111 -0.00576 -14.39860; -0.00888 1.11871 0.28311 -39.65777; 0.00880 -0.24310 0.98197 37.17511; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.080 0.011 -0.006 -14.399; -0.009 1.119 0.283 -39.658; 0.009 -0.243 0.982 37.175; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.3 (old=-3.8) transform before final EM align: 1.080 0.011 -0.006 -14.399; -0.009 1.119 0.283 -39.658; 0.009 -0.243 0.982 37.175; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 312841 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.07982 0.01111 -0.00576 -14.39860; -0.00888 1.11871 0.28311 -39.65777; 0.00880 -0.24310 0.98197 37.17511; 0.00000 0.00000 0.00000 1.00000; nsamples 312841 Quasinewton: input matrix 1.07982 0.01111 -0.00576 -14.39860; -0.00888 1.11871 0.28311 -39.65777; 0.00880 -0.24310 0.98197 37.17511; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 010: -log(p) = 3.8 after pass:transform: ( 1.08, 0.01, -0.01, -14.40) ( -0.01, 1.12, 0.28, -39.66) ( 0.01, -0.24, 0.98, 37.18) dfp_em_step_func: 011: -log(p) = 3.8 after pass:transform: ( 1.08, 0.01, -0.01, -14.40) ( -0.01, 1.12, 0.28, -39.66) ( 0.01, -0.24, 0.98, 37.18) IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 013: -log(p) = 3.8 tol 0.000000 final transform: 1.080 0.011 -0.006 -14.399; -0.009 1.119 0.283 -39.658; 0.009 -0.243 0.982 37.175; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 50 minutes and 9 seconds. #-------------------------------------- #@# CA Normalize Fri Nov 13 14:37:31 CET 2015 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/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=24.0 skull bounding box = (64, 53, 25) --> (191, 197, 186) using (106, 101, 106) as brain centroid... mean wm in atlas = 107, using box (90,83,86) --> (121, 118,125) to find MRI wm before smoothing, mri peak at 106 after smoothing, mri peak at 105, scaling input intensities by 1.019 scaling channel 0 by 1.01905 using 244171 sample points... INFO: compute sample coordinates transform 1.080 0.011 -0.006 -14.399; -0.009 1.119 0.283 -39.658; 0.009 -0.243 0.982 37.175; 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 (127, 60, 23) --> (190, 163, 184) Left_Cerebral_White_Matter: limiting intensities to 99.0 --> 186.0 0 of 727 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (70, 60, 22) --> (130, 157, 185) Right_Cerebral_White_Matter: limiting intensities to 98.0 --> 186.0 0 of 423 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (131, 138, 51) --> (175, 178, 103) Left_Cerebellum_White_Matter: limiting intensities to 91.0 --> 186.0 0 of 14 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (86, 138, 48) --> (129, 177, 104) Right_Cerebellum_White_Matter: limiting intensities to 95.0 --> 186.0 0 of 8 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (114, 128, 85) --> (144, 189, 114) Brain_Stem: limiting intensities to 97.0 --> 186.0 0 of 17 (0.0%) samples deleted using 1189 total control points for intensity normalization... bias field = 0.980 +- 0.042 10 of 1189 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (127, 60, 23) --> (190, 163, 184) Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 168.0 0 of 826 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (70, 60, 22) --> (130, 157, 185) Right_Cerebral_White_Matter: limiting intensities to 92.0 --> 168.0 0 of 506 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (131, 138, 51) --> (175, 178, 103) Left_Cerebellum_White_Matter: limiting intensities to 85.0 --> 168.0 0 of 52 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (86, 138, 48) --> (129, 177, 104) Right_Cerebellum_White_Matter: limiting intensities to 85.0 --> 168.0 0 of 62 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (114, 128, 85) --> (144, 189, 114) Brain_Stem: limiting intensities to 89.0 --> 168.0 0 of 78 (0.0%) samples deleted using 1524 total control points for intensity normalization... bias field = 1.002 +- 0.049 10 of 1524 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (127, 60, 23) --> (190, 163, 184) Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 162.0 0 of 869 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (70, 60, 22) --> (130, 157, 185) Right_Cerebral_White_Matter: limiting intensities to 92.0 --> 162.0 0 of 559 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (131, 138, 51) --> (175, 178, 103) Left_Cerebellum_White_Matter: limiting intensities to 81.0 --> 162.0 0 of 108 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (86, 138, 48) --> (129, 177, 104) Right_Cerebellum_White_Matter: limiting intensities to 82.0 --> 162.0 0 of 81 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (114, 128, 85) --> (144, 189, 114) Brain_Stem: limiting intensities to 82.0 --> 162.0 0 of 192 (0.0%) samples deleted using 1809 total control points for intensity normalization... bias field = 1.000 +- 0.045 10 of 1809 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 2 minutes and 54 seconds. #-------------------------------------- #@# CA Reg Fri Nov 13 14:40:26 CET 2015 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /usr/local//freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log ======= NUMBER OF OPENMP THREADS = 1 ======= reading input volume 'norm.mgz'... reading GCA '/usr/local//freesurfer/average/RB_all_2008-03-26.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.26 (predicted orig area = 6.3) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.793, neg=0, invalid=96777 0001: dt=129.472000, rms=0.713 (10.139%), neg=0, invalid=96777 0002: dt=129.472000, rms=0.700 (1.815%), neg=0, invalid=96777 0003: dt=221.952000, rms=0.683 (2.414%), neg=0, invalid=96777 0004: dt=73.984000, rms=0.679 (0.518%), neg=0, invalid=96777 0005: dt=517.888000, rms=0.669 (1.457%), neg=0, invalid=96777 0006: dt=129.472000, rms=0.665 (0.592%), neg=0, invalid=96777 0007: dt=129.472000, rms=0.665 (0.119%), neg=0, invalid=96777 0008: dt=129.472000, rms=0.663 (0.285%), neg=0, invalid=96777 0009: dt=129.472000, rms=0.660 (0.425%), neg=0, invalid=96777 0010: dt=129.472000, rms=0.657 (0.420%), neg=0, invalid=96777 0011: dt=129.472000, rms=0.654 (0.410%), neg=0, invalid=96777 0012: dt=129.472000, rms=0.651 (0.538%), neg=0, invalid=96777 0013: dt=129.472000, rms=0.648 (0.495%), neg=0, invalid=96777 0014: dt=129.472000, rms=0.645 (0.442%), neg=0, invalid=96777 0015: dt=129.472000, rms=0.642 (0.375%), neg=0, invalid=96777 0016: dt=129.472000, rms=0.640 (0.437%), neg=0, invalid=96777 0017: dt=129.472000, rms=0.637 (0.352%), neg=0, invalid=96777 0018: dt=129.472000, rms=0.635 (0.302%), neg=0, invalid=96777 0019: dt=129.472000, rms=0.634 (0.273%), neg=0, invalid=96777 0020: dt=129.472000, rms=0.632 (0.314%), neg=0, invalid=96777 0021: dt=129.472000, rms=0.630 (0.269%), neg=0, invalid=96777 0022: dt=129.472000, rms=0.629 (0.223%), neg=0, invalid=96777 0023: dt=129.472000, rms=0.627 (0.175%), neg=0, invalid=96777 0024: dt=129.472000, rms=0.626 (0.251%), neg=0, invalid=96777 0025: dt=129.472000, rms=0.625 (0.182%), neg=0, invalid=96777 0026: dt=129.472000, rms=0.624 (0.161%), neg=0, invalid=96777 0027: dt=129.472000, rms=0.623 (0.090%), neg=0, invalid=96777 0028: dt=129.472000, rms=0.622 (0.197%), neg=0, invalid=96777 0029: dt=129.472000, rms=0.621 (0.183%), neg=0, invalid=96777 0030: dt=129.472000, rms=0.620 (0.114%), neg=0, invalid=96777 0031: dt=129.472000, rms=0.620 (-0.025%), neg=0, invalid=96777 0032: dt=0.000000, rms=0.620 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.620, neg=0, invalid=96777 0033: dt=32.368000, rms=0.620 (0.011%), neg=0, invalid=96777 0034: dt=129.472000, rms=0.620 (0.031%), neg=0, invalid=96777 0035: dt=443.904000, rms=0.618 (0.248%), neg=0, invalid=96777 0036: dt=23.120000, rms=0.618 (0.010%), neg=0, invalid=96777 0037: dt=23.120000, rms=0.618 (-0.005%), neg=0, invalid=96777 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.625, neg=0, invalid=96777 0038: dt=82.944000, rms=0.621 (0.614%), neg=0, invalid=96777 0039: dt=62.208000, rms=0.615 (0.962%), neg=0, invalid=96777 0040: dt=20.736000, rms=0.614 (0.122%), neg=0, invalid=96777 0041: dt=20.736000, rms=0.613 (0.219%), neg=0, invalid=96777 0042: dt=20.736000, rms=0.611 (0.304%), neg=0, invalid=96777 0043: dt=20.736000, rms=0.609 (0.405%), neg=0, invalid=96777 0044: dt=20.736000, rms=0.606 (0.469%), neg=0, invalid=96777 0045: dt=20.736000, rms=0.603 (0.506%), neg=0, invalid=96777 0046: dt=20.736000, rms=0.600 (0.506%), neg=0, invalid=96777 0047: dt=20.736000, rms=0.597 (0.485%), neg=0, invalid=96777 0048: dt=20.736000, rms=0.594 (0.453%), neg=0, invalid=96777 0049: dt=20.736000, rms=0.591 (0.424%), neg=0, invalid=96777 0050: dt=20.736000, rms=0.589 (0.424%), neg=0, invalid=96777 0051: dt=20.736000, rms=0.587 (0.407%), neg=0, invalid=96777 0052: dt=20.736000, rms=0.584 (0.384%), neg=0, invalid=96777 0053: dt=20.736000, rms=0.582 (0.351%), neg=0, invalid=96777 0054: dt=20.736000, rms=0.580 (0.330%), neg=0, invalid=96777 0055: dt=20.736000, rms=0.579 (0.299%), neg=0, invalid=96777 0056: dt=20.736000, rms=0.577 (0.271%), neg=0, invalid=96777 0057: dt=20.736000, rms=0.576 (0.251%), neg=0, invalid=96777 0058: dt=20.736000, rms=0.574 (0.225%), neg=0, invalid=96777 0059: dt=20.736000, rms=0.573 (0.206%), neg=0, invalid=96777 0060: dt=20.736000, rms=0.572 (0.176%), neg=0, invalid=96777 0061: dt=20.736000, rms=0.571 (0.143%), neg=0, invalid=96777 0062: dt=20.736000, rms=0.571 (0.117%), neg=0, invalid=96777 0063: dt=20.736000, rms=0.570 (0.113%), neg=0, invalid=96777 0064: dt=124.416000, rms=0.569 (0.121%), neg=0, invalid=96777 0065: dt=9.072000, rms=0.569 (-0.003%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.569, neg=0, invalid=96777 0066: dt=31.104000, rms=0.569 (0.091%), neg=0, invalid=96777 0067: dt=124.416000, rms=0.567 (0.317%), neg=0, invalid=96777 0068: dt=9.072000, rms=0.567 (0.007%), neg=0, invalid=96777 0069: dt=9.072000, rms=0.567 (0.020%), neg=0, invalid=96777 0070: dt=9.072000, rms=0.567 (0.005%), neg=0, invalid=96777 0071: dt=9.072000, rms=0.567 (-0.014%), neg=0, invalid=96777 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.591, neg=0, invalid=96777 0072: dt=8.224299, rms=0.590 (0.134%), neg=0, invalid=96777 0073: dt=2.800000, rms=0.590 (0.009%), neg=0, invalid=96777 0074: dt=2.800000, rms=0.590 (0.001%), neg=0, invalid=96777 0075: dt=2.800000, rms=0.590 (-0.021%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.590, neg=0, invalid=96777 0076: dt=0.175000, rms=0.590 (0.000%), neg=0, invalid=96777 0077: dt=0.115741, rms=0.590 (0.000%), neg=0, invalid=96777 0078: dt=0.031716, rms=0.590 (0.000%), neg=0, invalid=96777 0079: dt=0.031716, rms=0.590 (-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=0.652, neg=0, invalid=96777 0080: dt=5.668712, rms=0.637 (2.316%), neg=0, invalid=96777 0081: dt=2.493506, rms=0.636 (0.071%), neg=0, invalid=96777 0082: dt=2.493506, rms=0.636 (-0.007%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.636, neg=0, invalid=96777 0083: dt=0.000000, rms=0.636 (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=0.702, neg=0, invalid=96777 0084: dt=0.946950, rms=0.700 (0.378%), neg=0, invalid=96777 0085: dt=2.266667, rms=0.694 (0.772%), neg=0, invalid=96777 0086: dt=1.024000, rms=0.693 (0.146%), neg=0, invalid=96777 0087: dt=1.024000, rms=0.692 (0.191%), neg=0, invalid=96777 0088: dt=1.024000, rms=0.691 (0.169%), neg=0, invalid=96777 0089: dt=1.024000, rms=0.691 (-0.034%), neg=0, invalid=96777 0090: dt=0.448000, rms=0.691 (0.019%), neg=0, invalid=96777 0091: dt=1.280000, rms=0.690 (0.021%), neg=0, invalid=96777 0092: dt=1.792000, rms=0.690 (0.052%), neg=0, invalid=96777 0093: dt=0.448000, rms=0.690 (0.015%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.690, neg=0, invalid=96777 0094: dt=1.280000, rms=0.689 (0.116%), neg=0, invalid=96777 0095: dt=0.000000, rms=0.689 (-0.003%), 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=0.649, neg=0, invalid=96777 0096: dt=0.145579, rms=0.643 (0.954%), neg=0, invalid=96777 0097: dt=0.096000, rms=0.643 (0.022%), neg=0, invalid=96777 0098: dt=0.096000, rms=0.642 (0.127%), neg=0, invalid=96777 0099: dt=0.096000, rms=0.641 (0.207%), neg=0, invalid=96777 0100: dt=0.096000, rms=0.639 (0.235%), neg=0, invalid=96777 0101: dt=0.096000, rms=0.638 (0.228%), neg=0, invalid=96777 0102: dt=0.096000, rms=0.636 (0.206%), neg=0, invalid=96777 0103: dt=0.096000, rms=0.635 (0.169%), neg=0, invalid=96777 0104: dt=0.096000, rms=0.634 (0.123%), neg=0, invalid=96777 0105: dt=0.096000, rms=0.634 (0.080%), neg=0, invalid=96777 0106: dt=0.000000, rms=0.634 (-0.003%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.634, neg=0, invalid=96777 0107: dt=0.112000, rms=0.632 (0.220%), neg=0, invalid=96777 0108: dt=0.000000, rms=0.632 (-0.000%), neg=0, invalid=96777 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.10827 (24) Left_Lateral_Ventricle (4): linear fit = 0.94 x + 0.0 (1418 voxels, overlap=0.571) Left_Lateral_Ventricle (4): linear fit = 0.94 x + 0.0 (1418 voxels, peak = 23), gca=22.7 gca peak = 0.14022 (22) mri peak = 0.10919 (24) Right_Lateral_Ventricle (43): linear fit = 0.94 x + 0.0 (844 voxels, overlap=0.846) Right_Lateral_Ventricle (43): linear fit = 0.94 x + 0.0 (844 voxels, peak = 21), gca=20.8 gca peak = 0.24234 (100) mri peak = 0.08588 (104) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (441 voxels, overlap=1.002) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (441 voxels, peak = 102), gca=102.5 gca peak = 0.19192 (97) mri peak = 0.06812 (92) Left_Pallidum (13): linear fit = 0.95 x + 0.0 (368 voxels, overlap=0.892) Left_Pallidum (13): linear fit = 0.95 x + 0.0 (368 voxels, peak = 93), gca=92.6 gca peak = 0.24007 (63) mri peak = 0.08472 (68) Right_Hippocampus (53): linear fit = 1.05 x + 0.0 (801 voxels, overlap=0.974) Right_Hippocampus (53): linear fit = 1.05 x + 0.0 (801 voxels, peak = 66), gca=66.5 gca peak = 0.29892 (64) mri peak = 0.10793 (71) Left_Hippocampus (17): linear fit = 1.09 x + 0.0 (770 voxels, overlap=0.854) Left_Hippocampus (17): linear fit = 1.09 x + 0.0 (770 voxels, peak = 69), gca=69.4 gca peak = 0.12541 (104) mri peak = 0.08954 (107) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (66834 voxels, overlap=0.760) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (66834 voxels, peak = 108), gca=107.6 gca peak = 0.13686 (104) mri peak = 0.09823 (109) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (71347 voxels, overlap=0.713) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (71347 voxels, peak = 108), gca=107.6 gca peak = 0.11691 (63) mri peak = 0.04034 (66) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (27744 voxels, overlap=0.986) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (27744 voxels, peak = 65), gca=64.6 gca peak = 0.13270 (63) mri peak = 0.04047 (63) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (28532 voxels, overlap=0.998) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (28532 voxels, peak = 65), gca=64.6 gca peak = 0.15182 (70) mri peak = 0.14174 (81) Right_Caudate (50): linear fit = 1.12 x + 0.0 (412 voxels, overlap=0.203) Right_Caudate (50): linear fit = 1.12 x + 0.0 (412 voxels, peak = 79), gca=78.8 gca peak = 0.14251 (76) mri peak = 0.10243 (87) Left_Caudate (11): linear fit = 1.11 x + 0.0 (907 voxels, overlap=0.370) Left_Caudate (11): linear fit = 1.11 x + 0.0 (907 voxels, peak = 84), gca=84.0 gca peak = 0.12116 (60) mri peak = 0.03546 (68) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (26902 voxels, overlap=0.712) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (26902 voxels, peak = 68), gca=67.5 gca peak = 0.12723 (61) mri peak = 0.03547 (65) Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (32199 voxels, overlap=0.907) Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (32199 voxels, peak = 66), gca=65.6 gca peak = 0.22684 (88) mri peak = 0.07856 (92) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (8319 voxels, overlap=0.582) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (8319 voxels, peak = 94), gca=93.7 gca peak = 0.21067 (87) mri peak = 0.08823 (91) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (7333 voxels, overlap=0.618) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (7333 voxels, peak = 94), gca=93.5 gca peak = 0.25455 (62) mri peak = 0.10567 (74) Left_Amygdala (18): linear fit = 1.12 x + 0.0 (389 voxels, overlap=0.410) Left_Amygdala (18): linear fit = 1.12 x + 0.0 (389 voxels, peak = 69), gca=69.1 gca peak = 0.39668 (62) mri peak = 0.11628 (71) Right_Amygdala (54): linear fit = 1.11 x + 0.0 (386 voxels, overlap=0.387) Right_Amygdala (54): linear fit = 1.11 x + 0.0 (386 voxels, peak = 69), gca=68.5 gca peak = 0.10129 (93) mri peak = 0.06612 (98) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (5291 voxels, overlap=0.612) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (5291 voxels, peak = 99), gca=99.0 gca peak = 0.12071 (89) mri peak = 0.05639 (99) Right_Thalamus_Proper (49): linear fit = 1.10 x + 0.0 (3779 voxels, overlap=0.712) Right_Thalamus_Proper (49): linear fit = 1.10 x + 0.0 (3779 voxels, peak = 97), gca=97.5 gca peak = 0.13716 (82) mri peak = 0.07119 (91) Left_Putamen (12): linear fit = 1.07 x + 0.0 (2558 voxels, overlap=0.782) Left_Putamen (12): linear fit = 1.07 x + 0.0 (2558 voxels, peak = 87), gca=87.3 gca peak = 0.15214 (84) mri peak = 0.06335 (88) Right_Putamen (51): linear fit = 1.04 x + 0.0 (2629 voxels, overlap=0.851) Right_Putamen (51): linear fit = 1.04 x + 0.0 (2629 voxels, peak = 88), gca=87.8 gca peak = 0.08983 (85) mri peak = 0.08654 (95) Brain_Stem (16): linear fit = 1.12 x + 0.0 (11167 voxels, overlap=0.296) Brain_Stem (16): linear fit = 1.12 x + 0.0 (11167 voxels, peak = 95), gca=94.8 gca peak = 0.11809 (92) mri peak = 0.08221 (98) Right_VentralDC (60): linear fit = 1.07 x + 0.0 (903 voxels, overlap=0.506) Right_VentralDC (60): linear fit = 1.07 x + 0.0 (903 voxels, peak = 98), gca=98.0 gca peak = 0.12914 (94) mri peak = 0.07864 (98) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1045 voxels, overlap=0.510) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1045 voxels, peak = 101), gca=101.1 gca peak = 0.21100 (36) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13542 (27) mri peak = 0.17397 (26) Fourth_Ventricle (15): linear fit = 0.88 x + 0.0 (394 voxels, overlap=0.822) Fourth_Ventricle (15): linear fit = 0.88 x + 0.0 (394 voxels, peak = 24), gca=23.6 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21802 (40) 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_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 1.07 x + 0.0 estimating mean wm scale to be 1.03 x + 0.0 estimating mean csf scale to be 0.92 x + 0.0 saving intensity scales to talairach.label_intensities.txt **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.652, neg=0, invalid=96777 0109: dt=129.472000, rms=0.643 (1.397%), neg=0, invalid=96777 0110: dt=129.472000, rms=0.641 (0.353%), neg=0, invalid=96777 0111: dt=129.472000, rms=0.638 (0.479%), neg=0, invalid=96777 0112: dt=73.984000, rms=0.637 (0.091%), neg=0, invalid=96777 0113: dt=517.888000, rms=0.633 (0.589%), neg=0, invalid=96777 0114: dt=32.368000, rms=0.632 (0.177%), neg=0, invalid=96777 0115: dt=73.984000, rms=0.632 (0.100%), neg=0, invalid=96777 0116: dt=1183.744000, rms=0.627 (0.790%), neg=0, invalid=96777 0117: dt=32.368000, rms=0.624 (0.370%), neg=0, invalid=96777 0118: dt=32.368000, rms=0.624 (0.100%), neg=0, invalid=96777 0119: dt=32.368000, rms=0.623 (0.033%), neg=0, invalid=96777 0120: dt=32.368000, rms=0.623 (0.018%), neg=0, invalid=96777 0121: dt=32.368000, rms=0.623 (0.022%), neg=0, invalid=96777 0122: dt=32.368000, rms=0.623 (0.027%), neg=0, invalid=96777 0123: dt=32.368000, rms=0.623 (0.050%), neg=0, invalid=96777 0124: dt=32.368000, rms=0.622 (0.074%), neg=0, invalid=96777 0125: dt=32.368000, rms=0.622 (0.082%), neg=0, invalid=96777 0126: dt=32.368000, rms=0.621 (0.085%), neg=0, invalid=96777 0127: dt=32.368000, rms=0.621 (0.095%), neg=0, invalid=96777 0128: dt=32.368000, rms=0.620 (0.109%), neg=0, invalid=96777 0129: dt=32.368000, rms=0.619 (0.112%), neg=0, invalid=96777 0130: dt=32.368000, rms=0.618 (0.115%), neg=0, invalid=96777 0131: dt=32.368000, rms=0.618 (0.129%), neg=0, invalid=96777 0132: dt=32.368000, rms=0.617 (0.124%), neg=0, invalid=96777 0133: dt=32.368000, rms=0.616 (0.120%), neg=0, invalid=96777 0134: dt=32.368000, rms=0.615 (0.111%), neg=0, invalid=96777 0135: dt=32.368000, rms=0.615 (0.099%), neg=0, invalid=96777 0136: dt=32.368000, rms=0.614 (0.091%), neg=0, invalid=96777 0137: dt=32.368000, rms=0.614 (0.080%), neg=0, invalid=96777 0138: dt=32.368000, rms=0.613 (0.078%), neg=0, invalid=96777 0139: dt=32.368000, rms=0.613 (0.079%), neg=0, invalid=96777 0140: dt=32.368000, rms=0.612 (0.079%), neg=0, invalid=96777 0141: dt=32.368000, rms=0.612 (0.077%), neg=0, invalid=96777 0142: dt=32.368000, rms=0.611 (0.074%), neg=0, invalid=96777 0143: dt=32.368000, rms=0.611 (0.074%), neg=0, invalid=96777 0144: dt=32.368000, rms=0.611 (0.073%), neg=0, invalid=96777 0145: dt=32.368000, rms=0.610 (0.070%), neg=0, invalid=96777 0146: dt=32.368000, rms=0.610 (0.070%), neg=0, invalid=96777 0147: dt=32.368000, rms=0.609 (0.064%), neg=0, invalid=96777 0148: dt=32.368000, rms=0.609 (0.063%), neg=0, invalid=96777 0149: dt=32.368000, rms=0.609 (0.063%), neg=0, invalid=96777 0150: dt=32.368000, rms=0.608 (0.060%), neg=0, invalid=96777 0151: dt=32.368000, rms=0.608 (0.057%), neg=0, invalid=96777 0152: dt=32.368000, rms=0.607 (0.057%), neg=0, invalid=96777 0153: dt=32.368000, rms=0.607 (0.055%), neg=0, invalid=96777 0154: dt=32.368000, rms=0.607 (0.055%), neg=0, invalid=96777 0155: dt=32.368000, rms=0.606 (0.056%), neg=0, invalid=96777 0156: dt=32.368000, rms=0.606 (0.054%), neg=0, invalid=96777 0157: dt=32.368000, rms=0.606 (0.055%), neg=0, invalid=96777 0158: dt=32.368000, rms=0.606 (0.048%), neg=0, invalid=96777 0159: dt=32.368000, rms=0.605 (0.043%), neg=0, invalid=96777 0160: dt=32.368000, rms=0.605 (0.042%), neg=0, invalid=96777 0161: dt=32.368000, rms=0.605 (0.040%), neg=0, invalid=96777 0162: dt=32.368000, rms=0.605 (0.039%), neg=0, invalid=96777 0163: dt=32.368000, rms=0.604 (0.037%), neg=0, invalid=96777 0164: dt=32.368000, rms=0.604 (0.041%), neg=0, invalid=96777 0165: dt=32.368000, rms=0.604 (0.040%), neg=0, invalid=96777 0166: dt=32.368000, rms=0.604 (0.038%), neg=0, invalid=96777 0167: dt=32.368000, rms=0.603 (0.037%), neg=0, invalid=96777 0168: dt=32.368000, rms=0.603 (0.036%), neg=0, invalid=96777 0169: dt=32.368000, rms=0.603 (0.032%), neg=0, invalid=96777 0170: dt=32.368000, rms=0.603 (0.035%), neg=0, invalid=96777 0171: dt=32.368000, rms=0.603 (0.034%), neg=0, invalid=96777 0172: dt=32.368000, rms=0.602 (0.031%), neg=0, invalid=96777 0173: dt=32.368000, rms=0.602 (0.030%), neg=0, invalid=96777 0174: dt=32.368000, rms=0.602 (0.028%), neg=0, invalid=96777 0175: dt=32.368000, rms=0.602 (0.032%), neg=0, invalid=96777 0176: dt=32.368000, rms=0.602 (0.028%), neg=0, invalid=96777 0177: dt=32.368000, rms=0.601 (0.025%), neg=0, invalid=96777 0178: dt=32.368000, rms=0.601 (0.027%), neg=0, invalid=96777 0179: dt=32.368000, rms=0.601 (0.022%), neg=0, invalid=96777 0180: dt=32.368000, rms=0.601 (0.025%), neg=0, invalid=96777 0181: dt=32.368000, rms=0.601 (0.026%), neg=0, invalid=96777 0182: dt=32.368000, rms=0.601 (0.029%), neg=0, invalid=96777 0183: dt=32.368000, rms=0.601 (0.031%), neg=0, invalid=96777 0184: dt=32.368000, rms=0.600 (0.026%), neg=0, invalid=96777 0185: dt=32.368000, rms=0.600 (0.022%), neg=0, invalid=96777 0186: dt=32.368000, rms=0.600 (0.021%), neg=0, invalid=96777 0187: dt=517.888000, rms=0.600 (0.024%), neg=0, invalid=96777 0188: dt=32.368000, rms=0.600 (0.002%), neg=0, invalid=96777 0189: dt=32.368000, rms=0.600 (0.007%), neg=0, invalid=96777 0190: dt=32.368000, rms=0.600 (0.003%), neg=0, invalid=96777 0191: dt=32.368000, rms=0.600 (0.008%), neg=0, invalid=96777 0192: dt=32.368000, rms=0.600 (0.009%), neg=0, invalid=96777 0193: dt=32.368000, rms=0.600 (0.009%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.600, neg=0, invalid=96777 0194: dt=129.472000, rms=0.599 (0.089%), neg=0, invalid=96777 0195: dt=443.904000, rms=0.598 (0.198%), neg=0, invalid=96777 0196: dt=27.744000, rms=0.598 (0.011%), neg=0, invalid=96777 0197: dt=27.744000, rms=0.598 (0.002%), neg=0, invalid=96777 0198: dt=27.744000, rms=0.598 (-0.027%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.599, neg=0, invalid=96777 0199: dt=145.152000, rms=0.593 (0.958%), neg=0, invalid=96777 0200: dt=82.944000, rms=0.587 (1.034%), neg=0, invalid=96777 0201: dt=20.736000, rms=0.585 (0.395%), neg=0, invalid=96777 0202: dt=331.776000, rms=0.577 (1.358%), neg=0, invalid=96777 0203: dt=36.288000, rms=0.572 (0.784%), neg=0, invalid=96777 0204: dt=62.208000, rms=0.570 (0.351%), neg=0, invalid=96777 0205: dt=25.920000, rms=0.569 (0.147%), neg=0, invalid=96777 0206: dt=414.720000, rms=0.565 (0.817%), neg=0, invalid=96777 0207: dt=25.920000, rms=0.561 (0.612%), neg=0, invalid=96777 0208: dt=36.288000, rms=0.560 (0.152%), neg=0, invalid=96777 0209: dt=145.152000, rms=0.558 (0.449%), neg=0, invalid=96777 0210: dt=9.072000, rms=0.558 (0.024%), neg=0, invalid=96777 0211: dt=9.072000, rms=0.558 (0.031%), neg=0, invalid=96777 0212: dt=9.072000, rms=0.557 (0.018%), neg=0, invalid=96777 0213: dt=9.072000, rms=0.557 (0.022%), neg=0, invalid=96777 0214: dt=9.072000, rms=0.557 (0.048%), neg=0, invalid=96777 0215: dt=9.072000, rms=0.557 (0.086%), neg=0, invalid=96777 0216: dt=9.072000, rms=0.556 (0.121%), neg=0, invalid=96777 0217: dt=9.072000, rms=0.555 (0.128%), neg=0, invalid=96777 0218: dt=9.072000, rms=0.555 (0.129%), neg=0, invalid=96777 0219: dt=9.072000, rms=0.554 (0.120%), neg=0, invalid=96777 0220: dt=9.072000, rms=0.553 (0.119%), neg=0, invalid=96777 0221: dt=9.072000, rms=0.553 (0.116%), neg=0, invalid=96777 0222: dt=9.072000, rms=0.552 (0.112%), neg=0, invalid=96777 0223: dt=9.072000, rms=0.551 (0.112%), neg=0, invalid=96777 0224: dt=9.072000, rms=0.551 (0.127%), neg=0, invalid=96777 0225: dt=9.072000, rms=0.550 (0.140%), neg=0, invalid=96777 0226: dt=9.072000, rms=0.549 (0.147%), neg=0, invalid=96777 0227: dt=9.072000, rms=0.548 (0.144%), neg=0, invalid=96777 0228: dt=9.072000, rms=0.548 (0.132%), neg=0, invalid=96777 0229: dt=9.072000, rms=0.547 (0.125%), neg=0, invalid=96777 0230: dt=9.072000, rms=0.546 (0.115%), neg=0, invalid=96777 0231: dt=9.072000, rms=0.546 (0.115%), neg=0, invalid=96777 0232: dt=9.072000, rms=0.545 (0.100%), neg=0, invalid=96777 0233: dt=9.072000, rms=0.545 (0.087%), neg=0, invalid=96777 0234: dt=9.072000, rms=0.544 (0.107%), neg=0, invalid=96777 0235: dt=9.072000, rms=0.543 (0.112%), neg=0, invalid=96777 0236: dt=9.072000, rms=0.543 (0.110%), neg=0, invalid=96777 0237: dt=9.072000, rms=0.542 (0.107%), neg=0, invalid=96777 0238: dt=9.072000, rms=0.542 (0.096%), neg=0, invalid=96777 0239: dt=9.072000, rms=0.541 (0.092%), neg=0, invalid=96777 0240: dt=9.072000, rms=0.541 (0.086%), neg=0, invalid=96777 0241: dt=9.072000, rms=0.540 (0.083%), neg=0, invalid=96777 0242: dt=9.072000, rms=0.540 (0.079%), neg=0, invalid=96777 0243: dt=9.072000, rms=0.539 (0.076%), neg=0, invalid=96777 0244: dt=9.072000, rms=0.539 (0.077%), neg=0, invalid=96777 0245: dt=9.072000, rms=0.539 (0.081%), neg=0, invalid=96777 0246: dt=9.072000, rms=0.538 (0.084%), neg=0, invalid=96777 0247: dt=9.072000, rms=0.538 (0.081%), neg=0, invalid=96777 0248: dt=9.072000, rms=0.537 (0.073%), neg=0, invalid=96777 0249: dt=9.072000, rms=0.537 (0.070%), neg=0, invalid=96777 0250: dt=9.072000, rms=0.537 (0.065%), neg=0, invalid=96777 0251: dt=9.072000, rms=0.536 (0.063%), neg=0, invalid=96777 0252: dt=9.072000, rms=0.536 (0.061%), neg=0, invalid=96777 0253: dt=9.072000, rms=0.536 (0.063%), neg=0, invalid=96777 0254: dt=9.072000, rms=0.535 (0.071%), neg=0, invalid=96777 0255: dt=9.072000, rms=0.535 (0.065%), neg=0, invalid=96777 0256: dt=9.072000, rms=0.534 (0.070%), neg=0, invalid=96777 0257: dt=9.072000, rms=0.534 (0.056%), neg=0, invalid=96777 0258: dt=9.072000, rms=0.534 (0.056%), neg=0, invalid=96777 0259: dt=9.072000, rms=0.534 (0.052%), neg=0, invalid=96777 0260: dt=9.072000, rms=0.533 (0.051%), neg=0, invalid=96777 0261: dt=9.072000, rms=0.533 (0.052%), neg=0, invalid=96777 0262: dt=9.072000, rms=0.533 (0.049%), neg=0, invalid=96777 0263: dt=9.072000, rms=0.532 (0.054%), neg=0, invalid=96777 0264: dt=9.072000, rms=0.532 (0.051%), neg=0, invalid=96777 0265: dt=9.072000, rms=0.532 (0.053%), neg=0, invalid=96777 0266: dt=9.072000, rms=0.532 (0.047%), neg=0, invalid=96777 0267: dt=9.072000, rms=0.531 (0.046%), neg=0, invalid=96777 0268: dt=9.072000, rms=0.531 (0.042%), neg=0, invalid=96777 0269: dt=9.072000, rms=0.531 (0.042%), neg=0, invalid=96777 0270: dt=9.072000, rms=0.531 (0.046%), neg=0, invalid=96777 0271: dt=9.072000, rms=0.530 (0.045%), neg=0, invalid=96777 0272: dt=9.072000, rms=0.530 (0.047%), neg=0, invalid=96777 0273: dt=9.072000, rms=0.530 (0.048%), neg=0, invalid=96777 0274: dt=9.072000, rms=0.530 (0.046%), neg=0, invalid=96777 0275: dt=9.072000, rms=0.530 (0.040%), neg=0, invalid=96777 0276: dt=9.072000, rms=0.529 (0.042%), neg=0, invalid=96777 0277: dt=9.072000, rms=0.529 (0.034%), neg=0, invalid=96777 0278: dt=9.072000, rms=0.529 (0.038%), neg=0, invalid=96777 0279: dt=9.072000, rms=0.529 (0.030%), neg=0, invalid=96777 0280: dt=9.072000, rms=0.529 (0.039%), neg=0, invalid=96777 0281: dt=9.072000, rms=0.528 (0.043%), neg=0, invalid=96777 0282: dt=9.072000, rms=0.528 (0.042%), neg=0, invalid=96777 0283: dt=9.072000, rms=0.528 (0.041%), neg=0, invalid=96777 0284: dt=9.072000, rms=0.528 (0.035%), neg=0, invalid=96777 0285: dt=9.072000, rms=0.528 (0.034%), neg=0, invalid=96777 0286: dt=9.072000, rms=0.527 (0.029%), neg=0, invalid=96777 0287: dt=9.072000, rms=0.527 (0.036%), neg=0, invalid=96777 0288: dt=9.072000, rms=0.527 (0.032%), neg=0, invalid=96777 0289: dt=9.072000, rms=0.527 (0.043%), neg=0, invalid=96777 0290: dt=9.072000, rms=0.527 (0.039%), neg=0, invalid=96777 0291: dt=9.072000, rms=0.526 (0.039%), neg=0, invalid=96777 0292: dt=9.072000, rms=0.526 (0.031%), neg=0, invalid=96777 0293: dt=9.072000, rms=0.526 (0.031%), neg=0, invalid=96777 0294: dt=9.072000, rms=0.526 (0.029%), neg=0, invalid=96777 0295: dt=9.072000, rms=0.526 (0.027%), neg=0, invalid=96777 0296: dt=9.072000, rms=0.526 (0.023%), neg=0, invalid=96777 0297: dt=9.072000, rms=0.525 (0.032%), neg=0, invalid=96777 0298: dt=9.072000, rms=0.525 (0.038%), neg=0, invalid=96777 0299: dt=9.072000, rms=0.525 (0.042%), neg=0, invalid=96777 0300: dt=9.072000, rms=0.525 (0.040%), neg=0, invalid=96777 0301: dt=9.072000, rms=0.525 (0.037%), neg=0, invalid=96777 0302: dt=9.072000, rms=0.525 (0.026%), neg=0, invalid=96777 0303: dt=9.072000, rms=0.524 (0.025%), neg=0, invalid=96777 0304: dt=9.072000, rms=0.524 (0.027%), neg=0, invalid=96777 0305: dt=9.072000, rms=0.524 (0.024%), neg=0, invalid=96777 0306: dt=9.072000, rms=0.524 (0.024%), neg=0, invalid=96777 0307: dt=103.680000, rms=0.524 (0.064%), neg=0, invalid=96777 0308: dt=7.776000, rms=0.524 (-0.001%), neg=0, invalid=96777 0309: dt=7.776000, rms=0.524 (0.004%), neg=0, invalid=96777 0310: dt=7.776000, rms=0.524 (-0.014%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.524, neg=0, invalid=96777 0311: dt=36.288000, rms=0.523 (0.098%), neg=0, invalid=96777 0312: dt=82.944000, rms=0.522 (0.244%), neg=0, invalid=96777 0313: dt=9.072000, rms=0.522 (0.030%), neg=0, invalid=96777 0314: dt=9.072000, rms=0.522 (0.017%), neg=0, invalid=96777 0315: dt=9.072000, rms=0.522 (0.008%), neg=0, invalid=96777 0316: dt=9.072000, rms=0.522 (-0.004%), 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 0317: dt=44.800000, rms=0.525 (1.139%), neg=0, invalid=96777 0318: dt=11.200000, rms=0.522 (0.396%), neg=0, invalid=96777 0319: dt=153.600000, rms=0.511 (2.149%), neg=0, invalid=96777 0320: dt=8.000000, rms=0.508 (0.569%), neg=0, invalid=96777 0321: dt=12.642857, rms=0.506 (0.452%), neg=0, invalid=96777 0322: dt=11.200000, rms=0.505 (0.270%), neg=0, invalid=96777 0323: dt=32.000000, rms=0.504 (0.226%), neg=0, invalid=96777 0324: dt=11.200000, rms=0.502 (0.202%), neg=0, invalid=96777 0325: dt=11.200000, rms=0.502 (0.077%), neg=0, invalid=96777 0326: dt=32.000000, rms=0.501 (0.234%), neg=0, invalid=96777 0327: dt=6.518519, rms=0.500 (0.108%), neg=0, invalid=96777 0328: dt=44.800000, rms=0.499 (0.326%), neg=0, invalid=96777 0329: dt=11.200000, rms=0.498 (0.083%), neg=0, invalid=96777 0330: dt=11.200000, rms=0.498 (0.104%), neg=0, invalid=96777 0331: dt=25.600000, rms=0.497 (0.083%), neg=0, invalid=96777 0332: dt=11.200000, rms=0.497 (0.119%), neg=0, invalid=96777 0333: dt=9.600000, rms=0.497 (0.060%), neg=0, invalid=96777 0334: dt=32.000000, rms=0.496 (0.137%), neg=0, invalid=96777 0335: dt=6.400000, rms=0.496 (0.066%), neg=0, invalid=96777 0336: dt=44.800000, rms=0.495 (0.176%), neg=0, invalid=96777 0337: dt=9.600000, rms=0.494 (0.084%), neg=0, invalid=96777 0338: dt=25.600000, rms=0.494 (0.116%), neg=0, invalid=96777 0339: dt=4.800000, rms=0.494 (0.032%), neg=0, invalid=96777 0340: dt=4.800000, rms=0.493 (0.042%), neg=0, invalid=96777 0341: dt=4.800000, rms=0.493 (0.033%), neg=0, invalid=96777 0342: dt=4.800000, rms=0.493 (0.053%), neg=0, invalid=96777 0343: dt=4.800000, rms=0.493 (0.069%), neg=0, invalid=96777 0344: dt=4.800000, rms=0.492 (0.077%), neg=0, invalid=96777 0345: dt=4.800000, rms=0.492 (0.088%), neg=0, invalid=96777 0346: dt=4.800000, rms=0.491 (0.102%), neg=0, invalid=96777 0347: dt=4.800000, rms=0.491 (0.100%), neg=0, invalid=96777 0348: dt=4.800000, rms=0.490 (0.100%), neg=0, invalid=96777 0349: dt=4.800000, rms=0.490 (0.106%), neg=0, invalid=96777 0350: dt=4.800000, rms=0.489 (0.115%), neg=0, invalid=96777 0351: dt=4.800000, rms=0.489 (0.110%), neg=0, invalid=96777 0352: dt=4.800000, rms=0.488 (0.111%), neg=0, invalid=96777 0353: dt=4.800000, rms=0.488 (0.111%), neg=0, invalid=96777 0354: dt=4.800000, rms=0.487 (0.108%), neg=0, invalid=96777 0355: dt=4.800000, rms=0.487 (0.100%), neg=0, invalid=96777 0356: dt=4.800000, rms=0.486 (0.102%), neg=0, invalid=96777 0357: dt=4.800000, rms=0.485 (0.108%), neg=0, invalid=96777 0358: dt=4.800000, rms=0.485 (0.093%), neg=0, invalid=96777 0359: dt=4.800000, rms=0.485 (0.094%), neg=0, invalid=96777 0360: dt=4.800000, rms=0.484 (0.086%), neg=0, invalid=96777 0361: dt=4.800000, rms=0.484 (0.087%), neg=0, invalid=96777 0362: dt=4.800000, rms=0.483 (0.078%), neg=0, invalid=96777 0363: dt=4.800000, rms=0.483 (0.077%), neg=0, invalid=96777 0364: dt=4.800000, rms=0.483 (0.074%), neg=0, invalid=96777 0365: dt=4.800000, rms=0.482 (0.069%), neg=0, invalid=96777 0366: dt=4.800000, rms=0.482 (0.065%), neg=0, invalid=96777 0367: dt=4.800000, rms=0.482 (0.075%), neg=0, invalid=96777 0368: dt=4.800000, rms=0.481 (0.069%), neg=0, invalid=96777 0369: dt=4.800000, rms=0.481 (0.063%), neg=0, invalid=96777 0370: dt=4.800000, rms=0.481 (0.063%), neg=0, invalid=96777 0371: dt=4.800000, rms=0.480 (0.057%), neg=0, invalid=96777 0372: dt=4.800000, rms=0.480 (0.045%), neg=0, invalid=96777 0373: dt=4.800000, rms=0.480 (0.048%), neg=0, invalid=96777 0374: dt=4.800000, rms=0.480 (0.048%), neg=0, invalid=96777 0375: dt=4.800000, rms=0.479 (0.054%), neg=0, invalid=96777 0376: dt=4.800000, rms=0.479 (0.046%), neg=0, invalid=96777 0377: dt=4.800000, rms=0.479 (0.044%), neg=0, invalid=96777 0378: dt=4.800000, rms=0.479 (0.048%), neg=0, invalid=96777 0379: dt=4.800000, rms=0.479 (0.039%), neg=0, invalid=96777 0380: dt=4.800000, rms=0.478 (0.042%), neg=0, invalid=96777 0381: dt=4.800000, rms=0.478 (0.035%), neg=0, invalid=96777 0382: dt=4.800000, rms=0.478 (0.038%), neg=0, invalid=96777 0383: dt=4.800000, rms=0.478 (0.030%), neg=0, invalid=96777 0384: dt=4.800000, rms=0.478 (0.038%), neg=0, invalid=96777 0385: dt=4.800000, rms=0.478 (0.030%), neg=0, invalid=96777 0386: dt=4.800000, rms=0.477 (0.034%), neg=0, invalid=96777 0387: dt=4.800000, rms=0.477 (0.033%), neg=0, invalid=96777 0388: dt=4.800000, rms=0.477 (0.029%), neg=0, invalid=96777 0389: dt=4.800000, rms=0.477 (0.029%), neg=0, invalid=96777 0390: dt=4.800000, rms=0.477 (0.028%), neg=0, invalid=96777 0391: dt=4.800000, rms=0.477 (0.021%), neg=0, invalid=96777 0392: dt=4.800000, rms=0.477 (0.022%), neg=0, invalid=96777 0393: dt=4.800000, rms=0.477 (0.022%), neg=0, invalid=96777 0394: dt=11.200000, rms=0.477 (0.007%), neg=0, invalid=96777 0395: dt=11.200000, rms=0.476 (0.023%), neg=0, invalid=96777 0396: dt=11.200000, rms=0.476 (0.015%), neg=0, invalid=96777 0397: dt=11.200000, rms=0.476 (0.011%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.476, neg=0, invalid=96777 0398: dt=38.400000, rms=0.475 (0.296%), neg=0, invalid=96777 0399: dt=19.200000, rms=0.475 (0.058%), neg=0, invalid=96777 0400: dt=11.200000, rms=0.474 (0.055%), neg=0, invalid=96777 0401: dt=8.000000, rms=0.474 (0.006%), neg=0, invalid=96777 0402: dt=8.000000, rms=0.474 (0.017%), neg=0, invalid=96777 0403: dt=8.000000, rms=0.474 (0.024%), neg=0, invalid=96777 0404: dt=8.000000, rms=0.474 (0.027%), neg=0, invalid=96777 0405: dt=8.000000, rms=0.474 (0.028%), neg=0, invalid=96777 0406: dt=8.000000, rms=0.474 (0.023%), neg=0, invalid=96777 0407: dt=8.000000, rms=0.474 (0.031%), neg=0, invalid=96777 0408: dt=8.000000, rms=0.474 (0.014%), neg=0, invalid=96777 0409: dt=8.000000, rms=0.474 (0.003%), neg=0, invalid=96777 0410: dt=11.200000, rms=0.473 (0.014%), neg=0, invalid=96777 0411: dt=11.200000, rms=0.473 (0.016%), neg=0, invalid=96777 0412: dt=9.600000, rms=0.473 (0.006%), neg=0, invalid=96777 0413: dt=9.600000, rms=0.473 (0.012%), neg=0, invalid=96777 0414: dt=9.600000, rms=0.473 (0.017%), neg=0, invalid=96777 0415: dt=9.600000, rms=0.473 (0.015%), neg=0, invalid=96777 0416: dt=9.600000, rms=0.473 (0.021%), neg=0, invalid=96777 0417: dt=9.600000, rms=0.473 (0.035%), neg=0, invalid=96777 0418: dt=9.600000, rms=0.473 (0.024%), neg=0, invalid=96777 0419: dt=9.600000, rms=0.473 (0.021%), neg=0, invalid=96777 0420: dt=11.200000, rms=0.473 (0.007%), neg=0, invalid=96777 0421: dt=11.200000, rms=0.473 (0.011%), neg=0, invalid=96777 0422: dt=11.200000, rms=0.473 (0.003%), neg=0, invalid=96777 0423: dt=11.200000, rms=0.473 (0.010%), neg=0, invalid=96777 0424: dt=11.200000, rms=0.472 (0.016%), neg=0, invalid=96777 0425: dt=11.200000, rms=0.472 (0.024%), neg=0, invalid=96777 0426: dt=11.200000, rms=0.472 (0.009%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.494, neg=0, invalid=96777 0427: dt=0.000000, rms=0.494 (-0.004%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.494, neg=0, invalid=96777 0428: dt=0.000000, rms=0.494 (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=0.537, neg=0, invalid=96777 0429: dt=1.415020, rms=0.533 (0.729%), neg=0, invalid=96777 0430: dt=0.270833, rms=0.533 (0.015%), neg=0, invalid=96777 0431: dt=0.270833, rms=0.533 (-0.005%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.533, neg=0, invalid=96777 0432: dt=0.568182, rms=0.532 (0.079%), neg=0, invalid=96777 0433: dt=0.320000, rms=0.532 (0.013%), neg=0, invalid=96777 0434: dt=0.320000, rms=0.532 (-0.005%), 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=0.484, neg=0, invalid=96777 0435: dt=0.448000, rms=0.470 (2.829%), neg=0, invalid=96777 0436: dt=0.112000, rms=0.469 (0.146%), neg=0, invalid=96777 0437: dt=0.448000, rms=0.467 (0.519%), neg=0, invalid=96777 0438: dt=0.384000, rms=0.465 (0.303%), neg=0, invalid=96777 0439: dt=0.448000, rms=0.464 (0.241%), neg=0, invalid=96777 0440: dt=0.448000, rms=0.463 (0.187%), neg=0, invalid=96777 0441: dt=0.448000, rms=0.463 (0.130%), neg=0, invalid=96777 0442: dt=0.384000, rms=0.462 (0.093%), neg=0, invalid=96777 0443: dt=0.112000, rms=0.462 (0.026%), neg=0, invalid=96777 0444: dt=0.112000, rms=0.462 (0.020%), neg=0, invalid=96777 0445: dt=0.112000, rms=0.462 (0.044%), neg=0, invalid=96777 0446: dt=0.112000, rms=0.462 (0.021%), neg=0, invalid=96777 0447: dt=0.112000, rms=0.462 (0.032%), neg=0, invalid=96777 0448: dt=0.112000, rms=0.462 (0.045%), neg=0, invalid=96777 0449: dt=0.112000, rms=0.461 (0.058%), neg=0, invalid=96777 0450: dt=0.112000, rms=0.461 (0.065%), neg=0, invalid=96777 0451: dt=0.112000, rms=0.461 (0.066%), neg=0, invalid=96777 0452: dt=0.112000, rms=0.460 (0.071%), neg=0, invalid=96777 0453: dt=0.112000, rms=0.460 (0.060%), neg=0, invalid=96777 0454: dt=0.112000, rms=0.460 (0.064%), neg=0, invalid=96777 0455: dt=0.112000, rms=0.460 (0.054%), neg=0, invalid=96777 0456: dt=0.112000, rms=0.459 (0.045%), neg=0, invalid=96777 0457: dt=0.112000, rms=0.459 (0.039%), neg=0, invalid=96777 0458: dt=0.112000, rms=0.459 (-0.004%), neg=0, invalid=96777 0459: dt=0.080569, rms=0.459 (0.000%), neg=0, invalid=96777 0460: dt=0.000020, rms=0.459 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.459, neg=0, invalid=96777 0461: dt=0.448000, rms=0.455 (0.821%), neg=0, invalid=96777 0462: dt=0.112000, rms=0.455 (0.005%), neg=0, invalid=96777 0463: dt=0.112000, rms=0.455 (0.004%), neg=0, invalid=96777 0464: dt=0.112000, rms=0.455 (0.005%), neg=0, invalid=96777 0465: dt=0.112000, rms=0.455 (0.001%), neg=0, invalid=96777 0466: dt=0.112000, rms=0.455 (0.006%), neg=0, invalid=96777 0467: dt=0.112000, rms=0.455 (-0.006%), 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=0.453, neg=0, invalid=96777 0468: dt=0.000000, rms=0.453 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.453, neg=0, invalid=96777 0469: dt=443.904000, rms=0.453 (0.127%), neg=0, invalid=96777 0470: dt=73.984000, rms=0.452 (0.033%), neg=0, invalid=96777 0471: dt=73.984000, rms=0.452 (0.024%), neg=0, invalid=96777 0472: dt=73.984000, rms=0.452 (0.017%), neg=0, invalid=96777 0473: dt=73.984000, rms=0.452 (0.022%), neg=0, invalid=96777 0474: dt=73.984000, rms=0.452 (0.024%), neg=0, invalid=96777 0475: dt=73.984000, rms=0.452 (0.042%), neg=0, invalid=96777 0476: dt=73.984000, rms=0.452 (0.037%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.452, neg=0, invalid=96777 0477: dt=31.104000, rms=0.452 (0.044%), neg=0, invalid=96777 0478: dt=36.288000, rms=0.451 (0.056%), neg=0, invalid=96777 0479: dt=15.552000, rms=0.451 (0.012%), neg=0, invalid=96777 0480: dt=15.552000, rms=0.451 (0.030%), neg=0, invalid=96777 0481: dt=15.552000, rms=0.451 (0.035%), neg=0, invalid=96777 0482: dt=15.552000, rms=0.451 (0.041%), neg=0, invalid=96777 0483: dt=15.552000, rms=0.451 (0.033%), neg=0, invalid=96777 0484: dt=15.552000, rms=0.450 (0.024%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.450, neg=0, invalid=96777 0485: dt=103.680000, rms=0.448 (0.519%), neg=0, invalid=96777 0486: dt=31.104000, rms=0.447 (0.155%), neg=0, invalid=96777 0487: dt=31.104000, rms=0.447 (0.056%), neg=0, invalid=96777 0488: dt=31.104000, rms=0.447 (0.052%), neg=0, invalid=96777 0489: dt=31.104000, rms=0.446 (0.111%), neg=0, invalid=96777 0490: dt=31.104000, rms=0.446 (0.103%), neg=0, invalid=96777 0491: dt=25.920000, rms=0.446 (0.059%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.446, neg=0, invalid=96777 iter 0, gcam->neg = 6 after 6 iterations, nbhd size=1, neg = 0 0492: dt=44.800000, rms=0.443 (0.687%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0493: dt=10.105263, rms=0.442 (0.235%), neg=0, invalid=96777 0494: dt=10.105263, rms=0.441 (0.241%), neg=0, invalid=96777 0495: dt=10.105263, rms=0.440 (0.277%), neg=0, invalid=96777 iter 0, gcam->neg = 7 after 6 iterations, nbhd size=1, neg = 0 0496: dt=10.105263, rms=0.438 (0.304%), neg=0, invalid=96777 0497: dt=10.105263, rms=0.437 (0.309%), neg=0, invalid=96777 0498: dt=10.105263, rms=0.436 (0.293%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0499: dt=10.105263, rms=0.435 (0.216%), neg=0, invalid=96777 0500: dt=10.105263, rms=0.434 (0.185%), neg=0, invalid=96777 0501: dt=10.105263, rms=0.433 (0.160%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0502: dt=10.105263, rms=0.433 (0.157%), neg=0, invalid=96777 0503: dt=10.105263, rms=0.432 (0.176%), neg=0, invalid=96777 0504: dt=10.105263, rms=0.431 (0.141%), neg=0, invalid=96777 0505: dt=10.105263, rms=0.430 (0.154%), neg=0, invalid=96777 0506: dt=10.105263, rms=0.430 (0.128%), neg=0, invalid=96777 0507: dt=10.105263, rms=0.429 (0.136%), neg=0, invalid=96777 0508: dt=10.105263, rms=0.429 (0.121%), neg=0, invalid=96777 0509: dt=10.105263, rms=0.428 (0.074%), neg=0, invalid=96777 0510: dt=11.200000, rms=0.428 (0.062%), neg=0, invalid=96777 0511: dt=11.200000, rms=0.428 (0.011%), neg=0, invalid=96777 0512: dt=11.200000, rms=0.428 (0.034%), neg=0, invalid=96777 0513: dt=11.200000, rms=0.428 (0.058%), neg=0, invalid=96777 0514: dt=11.200000, rms=0.428 (0.028%), neg=0, invalid=96777 0515: dt=11.200000, rms=0.428 (0.033%), neg=0, invalid=96777 0516: dt=11.200000, rms=0.427 (0.033%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.427, neg=0, invalid=96777 0517: dt=38.400000, rms=0.425 (0.512%), neg=0, invalid=96777 0518: dt=5.611111, rms=0.425 (0.095%), neg=0, invalid=96777 0519: dt=5.611111, rms=0.424 (0.092%), neg=0, invalid=96777 0520: dt=5.611111, rms=0.424 (0.080%), neg=0, invalid=96777 0521: dt=5.611111, rms=0.424 (0.073%), neg=0, invalid=96777 0522: dt=8.000000, rms=0.424 (0.017%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.430, neg=0, invalid=96777 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0523: dt=4.032000, rms=0.430 (0.119%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0524: dt=4.032000, rms=0.430 (0.046%), neg=0, invalid=96777 0525: dt=4.032000, rms=0.429 (0.035%), neg=0, invalid=96777 iter 0, gcam->neg = 12 after 9 iterations, nbhd size=1, neg = 0 0526: dt=4.032000, rms=0.429 (-0.033%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.429, neg=0, invalid=96777 iter 0, gcam->neg = 21 after 17 iterations, nbhd size=2, neg = 0 0527: dt=10.905830, rms=0.428 (0.321%), neg=0, invalid=96777 iter 0, gcam->neg = 10 after 9 iterations, nbhd size=1, neg = 0 0528: dt=2.880000, rms=0.428 (0.048%), neg=0, invalid=96777 0529: dt=2.880000, rms=0.428 (0.075%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 5 iterations, nbhd size=1, neg = 0 0530: dt=2.880000, rms=0.427 (0.116%), neg=0, invalid=96777 iter 0, gcam->neg = 8 after 6 iterations, nbhd size=1, neg = 0 0531: dt=2.880000, rms=0.426 (0.122%), neg=0, invalid=96777 iter 0, gcam->neg = 6 after 7 iterations, nbhd size=1, neg = 0 0532: dt=2.880000, rms=0.426 (0.095%), neg=0, invalid=96777 0533: dt=2.880000, rms=0.426 (0.109%), neg=0, invalid=96777 0534: dt=2.880000, rms=0.425 (0.106%), neg=0, invalid=96777 iter 0, gcam->neg = 37 after 16 iterations, nbhd size=1, neg = 0 0535: dt=16.128000, rms=0.424 (0.346%), neg=0, invalid=96777 0536: dt=2.068966, rms=0.424 (0.015%), neg=0, invalid=96777 0537: dt=2.068966, rms=0.424 (0.013%), neg=0, invalid=96777 iter 0, gcam->neg = 13 after 1 iterations, nbhd size=0, neg = 0 0538: dt=2.068966, rms=0.423 (0.030%), neg=0, invalid=96777 iter 0, gcam->neg = 10 after 9 iterations, nbhd size=1, neg = 0 0539: dt=2.068966, rms=0.423 (0.035%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0540: dt=2.068966, rms=0.423 (0.041%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0541: dt=2.068966, rms=0.423 (0.046%), neg=0, invalid=96777 0542: dt=2.068966, rms=0.423 (0.053%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0543: dt=2.068966, rms=0.422 (0.062%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 5 iterations, nbhd size=1, neg = 0 0544: dt=2.068966, rms=0.422 (0.072%), neg=0, invalid=96777 0545: dt=2.068966, rms=0.422 (0.071%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 6 iterations, nbhd size=1, neg = 0 0546: dt=2.068966, rms=0.422 (0.080%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 5 iterations, nbhd size=1, neg = 0 0547: dt=2.068966, rms=0.421 (0.081%), neg=0, invalid=96777 iter 0, gcam->neg = 5 after 0 iterations, nbhd size=0, neg = 0 0548: dt=2.068966, rms=0.421 (0.081%), neg=0, invalid=96777 iter 0, gcam->neg = 7 after 6 iterations, nbhd size=1, neg = 0 0549: dt=2.068966, rms=0.421 (0.058%), neg=0, invalid=96777 0550: dt=0.063000, 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=0.425, neg=0, invalid=96777 0551: dt=0.000000, rms=0.425 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.425, neg=0, invalid=96777 0552: dt=0.000000, rms=0.425 (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=0.417, neg=0, invalid=96777 iter 0, gcam->neg = 567 after 55 iterations, nbhd size=2, neg = 0 0553: dt=1.792000, rms=0.391 (6.427%), neg=0, invalid=96777 0554: dt=0.000188, rms=0.391 (0.003%), neg=0, invalid=96777 0555: dt=0.000188, rms=0.391 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.391, neg=0, invalid=96777 0556: dt=0.000750, rms=0.391 (0.001%), neg=0, invalid=96777 0557: dt=0.000000, rms=0.391 (0.003%), neg=0, invalid=96777 0558: dt=0.000000, rms=0.391 (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=0.379, neg=0, invalid=96777 0559: dt=0.000000, rms=0.380 (-0.232%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.380, neg=0, invalid=96777 0560: dt=27.744000, rms=0.380 (0.002%), neg=0, invalid=96777 0561: dt=0.361250, rms=0.380 (0.000%), neg=0, invalid=96777 0562: dt=0.361250, rms=0.380 (0.000%), neg=0, invalid=96777 0563: dt=0.361250, rms=0.380 (-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=0.380, neg=0, invalid=96777 0564: dt=0.006326, rms=0.380 (0.000%), neg=0, invalid=96777 0565: dt=0.006326, rms=0.380 (0.000%), neg=0, invalid=96777 0566: dt=0.006326, rms=0.380 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.380, neg=0, invalid=96777 0567: dt=62.208000, rms=0.380 (0.048%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 200 iterations, nbhd size=4, neg = 2 starting rms=0.005, neg=2, removing folds in lattice.... iter 1, dt=0.000055: new neg 0, old_neg 2, delta 2, rms=0.003 (43.230%) 0568: dt=124.416000, rms=0.380 (0.019%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0569: dt=124.416000, rms=0.380 (0.003%), neg=0, invalid=96777 0570: dt=124.416000, rms=0.380 (-0.059%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.380, neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0571: dt=6.400000, rms=0.380 (0.044%), neg=0, invalid=96777 iter 0, gcam->neg = 6 after 14 iterations, nbhd size=2, neg = 0 0572: dt=11.200000, rms=0.380 (0.059%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0573: dt=11.200000, rms=0.380 (0.046%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0574: dt=11.200000, rms=0.380 (-0.011%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.380, neg=0, invalid=96777 iter 0, gcam->neg = 4 after 5 iterations, nbhd size=1, neg = 0 0575: dt=25.600000, rms=0.379 (0.239%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 31 iterations, nbhd size=1, neg = 0 0576: dt=44.800000, rms=0.377 (0.376%), neg=0, invalid=96777 0577: dt=0.002344, rms=0.377 (0.000%), neg=0, invalid=96777 0578: dt=0.002344, rms=0.377 (0.000%), neg=0, invalid=96777 0579: dt=0.002344, rms=0.377 (0.000%), neg=0, invalid=96777 0580: dt=0.002344, rms=0.377 (0.000%), neg=0, invalid=96777 0581: dt=0.002344, rms=0.377 (0.000%), neg=0, invalid=96777 0582: dt=0.002344, rms=0.377 (0.000%), neg=0, invalid=96777 0583: dt=0.002344, rms=0.377 (0.000%), neg=0, invalid=96777 0584: dt=0.002344, rms=0.377 (0.000%), neg=0, invalid=96777 0585: dt=0.002344, rms=0.377 (0.000%), neg=0, invalid=96777 0586: dt=0.002344, rms=0.377 (0.000%), neg=0, invalid=96777 0587: dt=0.002344, rms=0.377 (0.000%), neg=0, invalid=96777 0588: dt=0.002344, rms=0.377 (0.000%), neg=0, invalid=96777 0589: dt=0.002344, rms=0.377 (0.000%), neg=0, invalid=96777 0590: dt=0.002344, rms=0.377 (0.000%), neg=0, invalid=96777 0591: dt=0.002344, rms=0.377 (0.000%), neg=0, invalid=96777 0592: dt=0.002344, rms=0.377 (0.000%), neg=0, invalid=96777 0593: dt=0.002344, rms=0.377 (0.000%), neg=0, invalid=96777 0594: dt=0.002344, rms=0.377 (0.000%), neg=0, invalid=96777 0595: dt=0.002344, rms=0.377 (0.000%), neg=0, invalid=96777 0596: dt=0.002344, rms=0.377 (0.000%), neg=0, invalid=96777 0597: dt=0.002344, rms=0.377 (0.000%), neg=0, invalid=96777 0598: dt=0.002344, rms=0.377 (0.000%), neg=0, invalid=96777 0599: dt=0.002344, rms=0.377 (0.000%), neg=0, invalid=96777 0600: dt=0.002344, rms=0.377 (0.000%), neg=0, invalid=96777 0601: dt=0.002344, rms=0.377 (0.000%), neg=0, invalid=96777 0602: dt=0.002344, rms=0.377 (0.000%), neg=0, invalid=96777 0603: dt=0.002344, rms=0.377 (0.000%), neg=0, invalid=96777 0604: dt=0.002344, rms=0.377 (0.000%), neg=0, invalid=96777 0605: dt=0.002344, rms=0.377 (0.000%), neg=0, invalid=96777 0606: dt=0.002344, rms=0.377 (0.000%), neg=0, invalid=96777 0607: dt=0.002344, rms=0.377 (0.000%), neg=0, invalid=96777 0608: dt=0.002344, rms=0.377 (0.000%), neg=0, invalid=96777 0609: dt=0.002344, rms=0.377 (0.000%), neg=0, invalid=96777 iter 0, gcam->neg = 10 after 200 iterations, nbhd size=3, neg = 1 starting rms=0.006, neg=1, removing folds in lattice.... iter 1, dt=0.000088: new neg 0, old_neg 1, delta 1, rms=0.002 (64.725%) 0610: dt=38.400000, rms=0.377 (0.180%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0611: dt=38.400000, rms=0.376 (0.144%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.378, neg=0, invalid=96777 iter 0, gcam->neg = 15 after 8 iterations, nbhd size=1, neg = 0 0612: dt=4.032000, rms=0.378 (0.087%), neg=0, invalid=96777 0613: dt=0.252000, rms=0.378 (0.004%), neg=0, invalid=96777 0614: dt=0.252000, rms=0.378 (0.010%), neg=0, invalid=96777 0615: dt=0.252000, rms=0.378 (0.018%), neg=0, invalid=96777 0616: dt=0.252000, rms=0.378 (0.024%), neg=0, invalid=96777 0617: dt=0.252000, rms=0.378 (0.028%), neg=0, invalid=96777 0618: dt=0.252000, rms=0.377 (0.031%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0619: dt=0.252000, rms=0.377 (0.026%), neg=0, invalid=96777 0620: dt=0.252000, rms=0.377 (0.026%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0621: dt=0.252000, rms=0.377 (0.025%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.377, neg=0, invalid=96777 iter 0, gcam->neg = 17 after 9 iterations, nbhd size=1, neg = 0 0622: dt=4.083333, rms=0.377 (0.141%), neg=0, invalid=96777 iter 0, gcam->neg = 9 after 47 iterations, nbhd size=2, neg = 0 0623: dt=2.880000, rms=0.376 (0.048%), neg=0, invalid=96777 iter 0, gcam->neg = 59 after 16 iterations, nbhd size=1, neg = 0 0624: dt=2.880000, rms=0.376 (-0.003%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.381, neg=0, invalid=96777 0625: dt=0.000060, rms=0.381 (0.000%), neg=0, invalid=96777 0626: dt=0.000000, rms=0.381 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.381, neg=0, invalid=96777 0627: dt=0.000000, rms=0.381 (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=0.373, neg=0, invalid=96777 iter 0, gcam->neg = 328 after 46 iterations, nbhd size=2, neg = 0 0628: dt=0.784024, rms=0.364 (2.440%), neg=0, invalid=96777 0629: dt=0.000094, rms=0.364 (0.002%), neg=0, invalid=96777 0630: dt=0.000094, rms=0.364 (0.000%), neg=0, invalid=96777 0631: dt=0.000094, rms=0.364 (0.000%), neg=0, invalid=96777 0632: dt=0.000094, rms=0.364 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.364, neg=0, invalid=96777 0633: dt=0.001750, rms=0.364 (0.000%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0634: dt=0.064000, rms=0.364 (0.015%), neg=0, invalid=96777 0635: dt=0.001750, rms=0.364 (0.000%), neg=0, invalid=96777 0636: dt=0.001750, rms=0.364 (0.001%), neg=0, invalid=96777 0637: dt=0.001750, rms=0.364 (0.001%), neg=0, invalid=96777 0638: dt=0.001750, rms=0.364 (0.001%), neg=0, invalid=96777 0639: dt=0.001750, rms=0.364 (0.002%), neg=0, invalid=96777 0640: dt=0.001750, rms=0.364 (0.002%), neg=0, invalid=96777 0641: dt=0.001750, rms=0.364 (0.002%), neg=0, invalid=96777 0642: dt=0.001750, rms=0.364 (0.002%), neg=0, invalid=96777 0643: dt=0.001750, rms=0.364 (0.003%), neg=0, invalid=96777 0644: dt=0.001750, rms=0.364 (0.003%), neg=0, invalid=96777 0645: dt=0.001750, rms=0.364 (0.003%), neg=0, invalid=96777 0646: dt=0.001750, rms=0.364 (0.003%), neg=0, invalid=96777 0647: dt=0.001750, rms=0.364 (0.003%), neg=0, invalid=96777 writing output transformation to transforms/talairach.m3z... GCAMwrite registration took 7 hours, 3 minutes and 55 seconds. #-------------------------------------- #@# CA Reg Inv Fri Nov 13 21:44:21 CET 2015 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z Inverting GCAM Saving inverse #-------------------------------------- #@# Remove Neck Fri Nov 13 21:46:16 CET 2015 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... 11284456 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 1 minutes and 53 seconds. #-------------------------------------- #@# SkullLTA Fri Nov 13 21:48:09 CET 2015 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 = 1 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 5 using previously computed transform transforms/talairach.lta reading 1 input volumes... logging results to talairach_with_skull_2.log reading '/usr/local//freesurfer/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=13.0 skull bounding box = (53, 38, 10) --> (206, 225, 208) using (104, 100, 109) as brain centroid... mean wm in atlas = 126, using box (85,77,85) --> (122, 123,133) to find MRI wm before smoothing, mri peak at 105 after smoothing, mri peak at 105, scaling input intensities by 1.200 scaling channel 0 by 1.2 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.080 0.011 -0.006 -14.399; -0.009 1.119 0.283 -39.658; 0.009 -0.261 1.056 32.011; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 1 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.059 -0.024 -0.014 -6.740; 0.028 1.139 0.288 -47.296; 0.009 -0.247 0.997 34.247; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.059 -0.024 -0.014 -6.740; 0.028 1.139 0.288 -47.296; 0.009 -0.247 0.997 34.247; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 3 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.061 -0.024 -0.014 -7.364; 0.028 1.135 0.296 -47.671; 0.009 -0.255 0.991 36.343; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.061 -0.024 -0.014 -7.364; 0.028 1.137 0.296 -47.869; 0.009 -0.255 0.991 36.343; 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 1.06060 -0.02371 -0.01441 -7.36357; 0.02831 1.13652 0.29599 -47.86916; 0.00868 -0.25522 0.99110 36.34255; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.06060 -0.02371 -0.01441 -7.36357; 0.02831 1.13652 0.29599 -47.86916; 0.00868 -0.25522 0.99110 36.34255; 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: 006: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.061 -0.024 -0.014 -7.364; 0.028 1.137 0.296 -47.869; 0.009 -0.255 0.991 36.343; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.9 (old=-3.9) transform before final EM align: 1.061 -0.024 -0.014 -7.364; 0.028 1.137 0.296 -47.869; 0.009 -0.255 0.991 36.343; 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 1.06060 -0.02371 -0.01441 -7.36357; 0.02831 1.13652 0.29599 -47.86916; 0.00868 -0.25522 0.99110 36.34255; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.06060 -0.02371 -0.01441 -7.36357; 0.02831 1.13652 0.29599 -47.86916; 0.00868 -0.25522 0.99110 36.34255; 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: 008: -log(p) = 4.3 tol 0.000000 final transform: 1.061 -0.024 -0.014 -7.364; 0.028 1.137 0.296 -47.869; 0.009 -0.255 0.991 36.343; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull_2.lta... registration took 38 minutes and 40 seconds. #-------------------------------------- #@# SubCort Seg Fri Nov 13 22:26:50 CET 2015 mri_ca_label -align norm.mgz transforms/talairach.m3z /usr/local//freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz sysname Linux hostname biosrv1 machine x86_64 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects cd /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri mri_ca_label -align norm.mgz transforms/talairach.m3z /usr/local//freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes... reading classifier array from /usr/local//freesurfer/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 = 0.12147 (23) Left_Lateral_Ventricle (4): linear fit = 0.87 x + 0.0 (1557 voxels, overlap=0.809) Left_Lateral_Ventricle (4): linear fit = 0.87 x + 0.0 (1557 voxels, peak = 23), gca=23.4 gca peak = 0.14982 (20) mri peak = 0.10238 (22) Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (1422 voxels, overlap=0.821) Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (1422 voxels, peak = 20), gca=20.5 gca peak = 0.28003 (97) mri peak = 0.13374 (103) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (329 voxels, overlap=1.023) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (329 voxels, peak = 99), gca=99.4 gca peak = 0.18160 (96) mri peak = 0.13566 (101) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (251 voxels, overlap=1.014) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (251 voxels, peak = 100), gca=100.3 gca peak = 0.27536 (62) mri peak = 0.09360 (68) Right_Hippocampus (53): linear fit = 1.05 x + 0.0 (809 voxels, overlap=1.007) Right_Hippocampus (53): linear fit = 1.05 x + 0.0 (809 voxels, peak = 65), gca=65.4 gca peak = 0.32745 (63) mri peak = 0.11055 (71) Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (782 voxels, overlap=0.644) Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (782 voxels, peak = 69), gca=69.0 gca peak = 0.08597 (105) mri peak = 0.10162 (108) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (32458 voxels, overlap=0.656) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (32458 voxels, peak = 108), gca=107.6 gca peak = 0.09209 (106) mri peak = 0.11164 (109) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (36725 voxels, overlap=0.613) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (36725 voxels, peak = 109), gca=108.6 gca peak = 0.07826 (63) mri peak = 0.04390 (67) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (25629 voxels, overlap=0.927) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (25629 voxels, peak = 65), gca=64.6 gca peak = 0.08598 (64) mri peak = 0.03904 (63) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (23829 voxels, overlap=0.940) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (23829 voxels, peak = 63), gca=63.0 gca peak = 0.24164 (71) mri peak = 0.13037 (81) Right_Caudate (50): linear fit = 1.13 x + 0.0 (603 voxels, overlap=0.015) Right_Caudate (50): linear fit = 1.13 x + 0.0 (603 voxels, peak = 81), gca=80.6 gca peak = 0.18227 (75) mri peak = 0.12719 (85) Left_Caudate (11): linear fit = 1.12 x + 0.0 (764 voxels, overlap=0.492) Left_Caudate (11): linear fit = 1.12 x + 0.0 (764 voxels, peak = 84), gca=83.6 gca peak = 0.10629 (62) mri peak = 0.04928 (68) Left_Cerebellum_Cortex (8): linear fit = 1.11 x + 0.0 (26390 voxels, overlap=0.717) Left_Cerebellum_Cortex (8): linear fit = 1.11 x + 0.0 (26390 voxels, peak = 69), gca=68.5 gca peak = 0.11668 (59) mri peak = 0.05013 (65) Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (25697 voxels, overlap=0.926) Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (25697 voxels, peak = 63), gca=63.4 gca peak = 0.17849 (88) mri peak = 0.10250 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (6409 voxels, overlap=0.603) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (6409 voxels, peak = 93), gca=92.8 gca peak = 0.16819 (86) mri peak = 0.09758 (91) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (6404 voxels, overlap=0.592) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (6404 voxels, peak = 92), gca=92.5 gca peak = 0.41688 (64) mri peak = 0.10646 (74) Left_Amygdala (18): linear fit = 1.13 x + 0.0 (263 voxels, overlap=0.056) Left_Amygdala (18): linear fit = 1.13 x + 0.0 (263 voxels, peak = 73), gca=72.6 gca peak = 0.42394 (62) mri peak = 0.13097 (71) Right_Amygdala (54): linear fit = 1.13 x + 0.0 (281 voxels, overlap=0.046) Right_Amygdala (54): linear fit = 1.13 x + 0.0 (281 voxels, peak = 70), gca=70.4 gca peak = 0.10041 (96) mri peak = 0.08420 (98) Left_Thalamus_Proper (10): linear fit = 1.04 x + 0.0 (4228 voxels, overlap=0.822) Left_Thalamus_Proper (10): linear fit = 1.04 x + 0.0 (4228 voxels, peak = 100), gca=100.3 gca peak = 0.13978 (88) mri peak = 0.07829 (97) Right_Thalamus_Proper (49): linear fit = 1.09 x + 0.0 (3539 voxels, overlap=0.586) Right_Thalamus_Proper (49): linear fit = 1.09 x + 0.0 (3539 voxels, peak = 95), gca=95.5 gca peak = 0.08514 (81) mri peak = 0.08000 (90) Left_Putamen (12): linear fit = 1.05 x + 0.0 (1759 voxels, overlap=0.703) Left_Putamen (12): linear fit = 1.05 x + 0.0 (1759 voxels, peak = 85), gca=85.5 gca peak = 0.09624 (82) mri peak = 0.10341 (86) Right_Putamen (51): linear fit = 1.05 x + 0.0 (1876 voxels, overlap=0.686) Right_Putamen (51): linear fit = 1.05 x + 0.0 (1876 voxels, peak = 87), gca=86.5 gca peak = 0.07543 (88) mri peak = 0.08171 (95) Brain_Stem (16): linear fit = 1.09 x + 0.0 (11869 voxels, overlap=0.422) Brain_Stem (16): linear fit = 1.09 x + 0.0 (11869 voxels, peak = 95), gca=95.5 gca peak = 0.12757 (95) mri peak = 0.08138 (102) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1084 voxels, overlap=0.522) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1084 voxels, peak = 104), gca=104.0 gca peak = 0.17004 (92) mri peak = 0.07761 (101) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (1253 voxels, overlap=0.632) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (1253 voxels, peak = 100), gca=99.8 gca peak = 0.21361 (36) mri peak = 0.17028 (30) gca peak = 0.26069 (23) mri peak = 0.15536 (23) Fourth_Ventricle (15): linear fit = 0.94 x + 0.0 (100 voxels, overlap=0.701) Fourth_Ventricle (15): linear fit = 0.94 x + 0.0 (100 voxels, peak = 22), gca=21.7 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 1.07 x + 0.0 estimating mean wm scale to be 1.02 x + 0.0 estimating mean csf scale to be 0.94 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.16084 (24) mri peak = 0.12147 (23) Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (1557 voxels, overlap=0.945) Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (1557 voxels, peak = 25), gca=24.6 gca peak = 0.19384 (21) mri peak = 0.10238 (22) Right_Lateral_Ventricle (43): linear fit = 0.94 x + 0.0 (1422 voxels, overlap=0.786) Right_Lateral_Ventricle (43): linear fit = 0.94 x + 0.0 (1422 voxels, peak = 20), gca=19.8 gca peak = 0.30362 (100) mri peak = 0.13374 (103) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (329 voxels, overlap=1.019) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (329 voxels, peak = 100), gca=100.5 gca peak = 0.18298 (100) mri peak = 0.13566 (101) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (251 voxels, overlap=1.013) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (251 voxels, peak = 100), gca=100.0 gca peak = 0.22045 (65) mri peak = 0.09360 (68) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (809 voxels, overlap=1.003) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (809 voxels, peak = 64), gca=64.0 gca peak = 0.29168 (69) mri peak = 0.11055 (71) Left_Hippocampus (17): linear fit = 0.98 x + 0.0 (782 voxels, overlap=1.003) Left_Hippocampus (17): linear fit = 0.98 x + 0.0 (782 voxels, peak = 67), gca=67.3 gca peak = 0.08345 (108) mri peak = 0.10162 (108) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (32458 voxels, overlap=0.735) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (32458 voxels, peak = 108), gca=108.0 gca peak = 0.08541 (108) mri peak = 0.11164 (109) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (36725 voxels, overlap=0.708) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (36725 voxels, peak = 108), gca=108.0 gca peak = 0.07462 (65) mri peak = 0.04390 (67) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (25629 voxels, overlap=0.908) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (25629 voxels, peak = 67), gca=66.6 gca peak = 0.08737 (63) mri peak = 0.03904 (63) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (23829 voxels, overlap=0.960) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (23829 voxels, peak = 65), gca=64.6 gca peak = 0.23227 (80) mri peak = 0.13037 (81) Right_Caudate (50): linear fit = 1.00 x + 0.0 (603 voxels, overlap=1.000) Right_Caudate (50): linear fit = 1.00 x + 0.0 (603 voxels, peak = 80), gca=80.0 gca peak = 0.16079 (83) mri peak = 0.12719 (85) Left_Caudate (11): linear fit = 0.99 x + 0.0 (764 voxels, overlap=0.741) Left_Caudate (11): linear fit = 0.99 x + 0.0 (764 voxels, peak = 82), gca=81.8 gca peak = 0.09417 (69) mri peak = 0.04928 (68) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (26390 voxels, overlap=0.982) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (26390 voxels, peak = 69), gca=69.0 gca peak = 0.12026 (64) mri peak = 0.05013 (65) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (25697 voxels, overlap=0.999) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (25697 voxels, peak = 66), gca=65.6 gca peak = 0.17166 (92) mri peak = 0.10250 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6409 voxels, overlap=0.949) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6409 voxels, peak = 92), gca=91.5 gca peak = 0.15715 (93) mri peak = 0.09758 (91) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6404 voxels, overlap=0.983) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6404 voxels, peak = 93), gca=92.5 gca peak = 0.30692 (72) mri peak = 0.10646 (74) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (263 voxels, overlap=1.014) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (263 voxels, peak = 72), gca=72.0 gca peak = 0.30977 (71) mri peak = 0.13097 (71) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (281 voxels, overlap=1.001) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (281 voxels, peak = 71), gca=71.0 gca peak = 0.11249 (100) mri peak = 0.08420 (98) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4228 voxels, overlap=0.978) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4228 voxels, peak = 100), gca=100.5 gca peak = 0.11561 (95) mri peak = 0.07829 (97) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3539 voxels, overlap=0.966) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3539 voxels, peak = 95), gca=95.0 gca peak = 0.08918 (92) mri peak = 0.08000 (90) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1759 voxels, overlap=0.876) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1759 voxels, peak = 92), gca=91.5 gca peak = 0.10648 (80) mri peak = 0.10341 (86) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1876 voxels, overlap=0.830) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1876 voxels, peak = 80), gca=80.0 gca peak = 0.07104 (93) mri peak = 0.08171 (95) Brain_Stem (16): linear fit = 1.00 x + 0.0 (11869 voxels, overlap=0.752) Brain_Stem (16): linear fit = 1.00 x + 0.0 (11869 voxels, peak = 93), gca=93.5 gca peak = 0.11322 (104) mri peak = 0.08138 (102) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1084 voxels, overlap=0.825) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1084 voxels, peak = 105), gca=104.5 gca peak = 0.16446 (100) mri peak = 0.07761 (101) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1253 voxels, overlap=0.870) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1253 voxels, peak = 100), gca=100.5 gca peak = 0.21361 (34) mri peak = 0.17028 (30) gca peak = 0.18638 (22) mri peak = 0.15536 (23) Fourth_Ventricle (15): linear fit = 0.99 x + 0.0 (100 voxels, overlap=0.785) Fourth_Ventricle (15): linear fit = 0.99 x + 0.0 (100 voxels, peak = 22), gca=21.7 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.19797 (38) gca peak Third_Ventricle = 0.21361 (34) gca peak CSF = 0.23022 (43) gca peak Left_Accumbens_area = 0.60200 (78) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65116 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.19666 (35) gca peak Right_Accumbens_area = 0.26414 (82) gca peak Right_vessel = 0.83457 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.82185 (39) gca peak WM_hypointensities = 0.14754 (84) gca peak non_WM_hypointensities = 0.11940 (54) gca peak Optic_Chiasm = 0.34488 (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 0.98 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 17957 gm and wm labels changed (%20 to gray, %80 to white out of all changed labels) 223 hippocampal voxels changed. 1 amygdala voxels changed. pass 1: 71300 changed. image ll: -2.159, PF=1.000 pass 2: 10372 changed. image ll: -2.157, PF=1.000 pass 3: 3367 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 31 minutes and 43 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/transforms/cc_up.lta B_LU_02_MRI_E_T0 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/transforms/cc_up.lta reading aseg from /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/aseg.auto_noCCseg.mgz reading norm from /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/norm.mgz 19756 voxels in left wm, 30635 in right wm, xrange [125, 132] searching rotation angles z=[-6 8], y=[-8 6] searching scale 1 Z rot -6.3 searching scale 1 Z rot -6.1 searching scale 1 Z rot -5.8 searching scale 1 Z rot -5.6 searching scale 1 Z rot -5.3 searching scale 1 Z rot -5.1 searching scale 1 Z rot -4.8 searching scale 1 Z rot -4.6 searching scale 1 Z rot -4.3 searching scale 1 Z rot -4.1 searching scale 1 Z rot -3.8 searching scale 1 Z rot -3.6 searching scale 1 Z rot -3.3 searching scale 1 Z rot -3.1 searching scale 1 Z rot -2.8 searching scale 1 Z rot -2.6 searching scale 1 Z rot -2.3 searching scale 1 Z rot -2.1 searching scale 1 Z rot -1.8 searching scale 1 Z rot -1.6 searching scale 1 Z rot -1.3 searching scale 1 Z rot -1.1 searching scale 1 Z rot -0.8 searching scale 1 Z rot -0.6 searching scale 1 Z rot -0.3 searching scale 1 Z rot -0.1 searching scale 1 Z rot 0.2 searching scale 1 Z rot 0.4 searching scale 1 Z rot 0.7 searching scale 1 Z rot 0.9 searching scale 1 Z rot 1.2 searching scale 1 Z rot 1.4 searching scale 1 Z rot 1.7 searching scale 1 Z rot 1.9 searching scale 1 Z rot 2.2 searching scale 1 Z rot 2.4 searching scale 1 Z rot 2.7 searching scale 1 Z rot 2.9 searching scale 1 Z rot 3.2 searching scale 1 Z rot 3.4 searching scale 1 Z rot 3.7 searching scale 1 Z rot 3.9 searching scale 1 Z rot 4.2 searching scale 1 Z rot 4.4 searching scale 1 Z rot 4.7 searching scale 1 Z rot 4.9 searching scale 1 Z rot 5.2 searching scale 1 Z rot 5.4 searching scale 1 Z rot 5.7 searching scale 1 Z rot 5.9 searching scale 1 Z rot 6.2 searching scale 1 Z rot 6.4 searching scale 1 Z rot 6.7 searching scale 1 Z rot 6.9 searching scale 1 Z rot 7.2 searching scale 1 Z rot 7.4 global minimum found at slice 128.6, rotations (-1.33, 0.65) final transformation (x=128.6, yr=-1.331, zr=0.651): 1.000 -0.011 -0.023 3.028; 0.011 1.000 -0.000 23.573; 0.023 -0.000 1.000 21.041; 0.000 0.000 0.000 1.000; updating x range to be [126, 130] in xformed coordinates best xformed slice 128 cc center is found at 128 144 106 eigenvectors: -0.000 -0.003 1.000; -0.066 -0.998 -0.003; 0.998 -0.066 -0.000; error in mid anterior detected - correcting... error in mid anterior detected - correcting... writing aseg with callosum to /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/aseg.auto.mgz... corpus callosum matter segmentation took 1.1 minutes #-------------------------------------- #@# Merge ASeg Fri Nov 13 22:59:41 CET 2015 cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# Intensity Normalization2 Fri Nov 13 22:59:41 CET 2015 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 2783 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 70 (70), valley at 43 (43) csf peak at 28, setting threshold to 56 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 71 (71), valley at 38 (38) csf peak at 35, setting threshold to 59 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 6 minutes and 56 seconds. #-------------------------------------------- #@# Mask BFS Fri Nov 13 23:06:42 CET 2015 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1625094 voxels in mask (pct= 9.69) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Fri Nov 13 23:06:46 CET 2015 mri_segment brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (104.0): 103.9 +- 6.6 [80.0 --> 125.0] GM (73.0) : 72.2 +- 10.3 [30.0 --> 96.0] setting bottom of white matter range to 82.5 setting top of gray matter range to 92.8 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 4237 sparsely connected voxels removed... thickening thin strands.... 20 segments, 5059 filled 1755 bright non-wm voxels segmented. 2394 diagonally connected voxels added... white matter segmentation took 3.1 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 1.24 minutes reading wm segmentation from wm.seg.mgz... 29 voxels added to wm to prevent paths from MTL structures to cortex 1818 additional wm voxels added 0 additional wm voxels added SEG EDIT: 41923 voxels turned on, 51223 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 90 new 90 115,126,128 old 90 new 90 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.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-): 19 found - 19 modified | TOTAL: 23 pass 2 (xy-): 0 found - 19 modified | TOTAL: 23 pass 1 (yz+): 20 found - 20 modified | TOTAL: 43 pass 2 (yz+): 0 found - 20 modified | TOTAL: 43 pass 1 (yz-): 17 found - 17 modified | TOTAL: 60 pass 2 (yz-): 0 found - 17 modified | TOTAL: 60 pass 1 (xz+): 9 found - 9 modified | TOTAL: 69 pass 2 (xz+): 0 found - 9 modified | TOTAL: 69 pass 1 (xz-): 9 found - 9 modified | TOTAL: 78 pass 2 (xz-): 0 found - 9 modified | TOTAL: 78 Iteration Number : 1 pass 1 (+++): 10 found - 10 modified | TOTAL: 10 pass 2 (+++): 0 found - 10 modified | TOTAL: 10 pass 1 (+++): 4 found - 4 modified | TOTAL: 14 pass 2 (+++): 0 found - 4 modified | TOTAL: 14 pass 1 (+++): 4 found - 4 modified | TOTAL: 18 pass 2 (+++): 0 found - 4 modified | TOTAL: 18 pass 1 (+++): 6 found - 6 modified | TOTAL: 24 pass 2 (+++): 0 found - 6 modified | TOTAL: 24 Iteration Number : 1 pass 1 (++): 114 found - 114 modified | TOTAL: 114 pass 2 (++): 0 found - 114 modified | TOTAL: 114 pass 1 (+-): 92 found - 92 modified | TOTAL: 206 pass 2 (+-): 0 found - 92 modified | TOTAL: 206 pass 1 (--): 81 found - 81 modified | TOTAL: 287 pass 2 (--): 0 found - 81 modified | TOTAL: 287 pass 1 (-+): 86 found - 86 modified | TOTAL: 373 pass 2 (-+): 0 found - 86 modified | TOTAL: 373 Iteration Number : 2 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 1 found - 1 modified | TOTAL: 2 pass 2 (xy-): 0 found - 1 modified | TOTAL: 2 pass 1 (yz+): 2 found - 2 modified | TOTAL: 4 pass 2 (yz+): 0 found - 2 modified | TOTAL: 4 pass 1 (yz-): 3 found - 3 modified | TOTAL: 7 pass 2 (yz-): 0 found - 3 modified | TOTAL: 7 pass 1 (xz+): 2 found - 2 modified | TOTAL: 9 pass 2 (xz+): 0 found - 2 modified | TOTAL: 9 pass 1 (xz-): 0 found - 0 modified | TOTAL: 9 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 (++): 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 (-+): 2 found - 2 modified | TOTAL: 5 pass 2 (-+): 0 found - 2 modified | TOTAL: 5 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 489 (out of 535896: 0.091249) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Fri Nov 13 23:11:16 CET 2015 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.080 0.011 -0.006 -14.399; -0.009 1.119 0.283 -39.658; 0.009 -0.243 0.982 37.175; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.080 0.011 -0.006 -14.399; -0.009 1.119 0.283 -39.658; 0.009 -0.243 0.982 37.175; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1090 (min = 350, max = 1400), aspect = 0.47 (min = 0.10, max = 0.75) no need to search using seed (126, 119, 149), TAL = (2.0, 21.0, 9.0) talairach voxel to voxel transform 0.926 -0.008 0.008 12.751; 0.009 0.841 -0.242 42.498; -0.006 0.208 0.958 -27.451; 0.000 0.000 0.000 1.000; segmentation indicates cc at (126, 119, 149) --> (2.0, 21.0, 9.0) done. writing output to filled.mgz... filling took 1.4 minutes talairach cc position changed to (2.00, 21.00, 9.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, 21.00, 9.00) SRC: (112.99, 107.43, 139.46) search lh wm seed point around talairach space (-16.00, 21.00, 9.00), SRC: (146.32, 107.75, 139.24) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Fri Nov 13 23:12:43 CET 2015 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/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-): 1 found - 1 modified | TOTAL: 2 pass 2 (xy-): 0 found - 1 modified | TOTAL: 2 pass 1 (yz+): 1 found - 1 modified | TOTAL: 3 pass 2 (yz+): 0 found - 1 modified | TOTAL: 3 pass 1 (yz-): 0 found - 0 modified | TOTAL: 3 pass 1 (xz+): 1 found - 1 modified | TOTAL: 4 pass 2 (xz+): 0 found - 1 modified | TOTAL: 4 pass 1 (xz-): 1 found - 1 modified | TOTAL: 5 pass 2 (xz-): 0 found - 1 modified | TOTAL: 5 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 1 found - 1 modified | TOTAL: 1 pass 2 (--): 0 found - 1 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 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 = 8 (out of 260086: 0.003076) 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: 1842 vertices, 1993 faces slice 40: 8608 vertices, 8914 faces slice 50: 18888 vertices, 19253 faces slice 60: 29768 vertices, 30158 faces slice 70: 40945 vertices, 41338 faces slice 80: 52425 vertices, 52820 faces slice 90: 64349 vertices, 64732 faces slice 100: 75123 vertices, 75491 faces slice 110: 85786 vertices, 86199 faces slice 120: 96292 vertices, 96686 faces slice 130: 106071 vertices, 106435 faces slice 140: 114566 vertices, 114883 faces slice 150: 122332 vertices, 122618 faces slice 160: 128564 vertices, 128788 faces slice 170: 133985 vertices, 134187 faces slice 180: 137269 vertices, 137398 faces slice 190: 138038 vertices, 138080 faces slice 200: 138038 vertices, 138080 faces slice 210: 138038 vertices, 138080 faces slice 220: 138038 vertices, 138080 faces slice 230: 138038 vertices, 138080 faces slice 240: 138038 vertices, 138080 faces slice 250: 138038 vertices, 138080 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... 138038 voxel in cpt #1: X=-42 [v=138038,e=414240,f=276160] located at (-27.861059, -32.172649, 17.600269) For the whole surface: X=-42 [v=138038,e=414240,f=276160] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Fri Nov 13 23:12:58 CET 2015 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/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 Fri Nov 13 23:13:06 CET 2015 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/scripts avg radius = 47.0 mm, total surface area = 72978 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 1.2 minutes Not saving sulc step 000: RMS=0.101 (target=0.015) step 005: RMS=0.074 (target=0.015) step 010: RMS=0.055 (target=0.015) step 015: RMS=0.046 (target=0.015) step 020: RMS=0.040 (target=0.015) step 025: RMS=0.035 (target=0.015) step 030: RMS=0.031 (target=0.015) step 035: RMS=0.029 (target=0.015) step 040: RMS=0.028 (target=0.015) step 045: RMS=0.027 (target=0.015) step 050: RMS=0.027 (target=0.015) step 055: RMS=0.026 (target=0.015) step 060: RMS=0.026 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Fri Nov 13 23:14:16 CET 2015 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/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 0.99 +- 0.57 (0.00-->6.90) (max @ vno 58266 --> 59477) face area 0.03 +- 0.03 (-0.12-->0.53) scaling brain by 0.311... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.467, avgs=0 005/300: dt: 0.9000, rms radial error=176.210, avgs=0 010/300: dt: 0.9000, rms radial error=175.658, avgs=0 015/300: dt: 0.9000, rms radial error=174.933, avgs=0 020/300: dt: 0.9000, rms radial error=174.107, avgs=0 025/300: dt: 0.9000, rms radial error=173.223, avgs=0 030/300: dt: 0.9000, rms radial error=172.307, avgs=0 035/300: dt: 0.9000, rms radial error=171.374, avgs=0 040/300: dt: 0.9000, rms radial error=170.434, avgs=0 045/300: dt: 0.9000, rms radial error=169.491, avgs=0 050/300: dt: 0.9000, rms radial error=168.548, avgs=0 055/300: dt: 0.9000, rms radial error=167.608, avgs=0 060/300: dt: 0.9000, rms radial error=166.671, avgs=0 065/300: dt: 0.9000, rms radial error=165.739, avgs=0 070/300: dt: 0.9000, rms radial error=164.811, avgs=0 075/300: dt: 0.9000, rms radial error=163.888, avgs=0 080/300: dt: 0.9000, rms radial error=162.969, avgs=0 085/300: dt: 0.9000, rms radial error=162.055, avgs=0 090/300: dt: 0.9000, rms radial error=161.146, avgs=0 095/300: dt: 0.9000, rms radial error=160.242, avgs=0 100/300: dt: 0.9000, rms radial error=159.342, avgs=0 105/300: dt: 0.9000, rms radial error=158.447, avgs=0 110/300: dt: 0.9000, rms radial error=157.557, avgs=0 115/300: dt: 0.9000, rms radial error=156.672, avgs=0 120/300: dt: 0.9000, rms radial error=155.791, avgs=0 125/300: dt: 0.9000, rms radial error=154.916, avgs=0 130/300: dt: 0.9000, rms radial error=154.045, avgs=0 135/300: dt: 0.9000, rms radial error=153.178, avgs=0 140/300: dt: 0.9000, rms radial error=152.317, avgs=0 145/300: dt: 0.9000, rms radial error=151.460, avgs=0 150/300: dt: 0.9000, rms radial error=150.607, avgs=0 155/300: dt: 0.9000, rms radial error=149.760, avgs=0 160/300: dt: 0.9000, rms radial error=148.917, avgs=0 165/300: dt: 0.9000, rms radial error=148.078, avgs=0 170/300: dt: 0.9000, rms radial error=147.244, avgs=0 175/300: dt: 0.9000, rms radial error=146.415, avgs=0 180/300: dt: 0.9000, rms radial error=145.590, avgs=0 185/300: dt: 0.9000, rms radial error=144.770, avgs=0 190/300: dt: 0.9000, rms radial error=143.955, avgs=0 195/300: dt: 0.9000, rms radial error=143.144, avgs=0 200/300: dt: 0.9000, rms radial error=142.337, avgs=0 205/300: dt: 0.9000, rms radial error=141.535, avgs=0 210/300: dt: 0.9000, rms radial error=140.738, avgs=0 215/300: dt: 0.9000, rms radial error=139.945, avgs=0 220/300: dt: 0.9000, rms radial error=139.156, avgs=0 225/300: dt: 0.9000, rms radial error=138.371, 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=136.044, avgs=0 245/300: dt: 0.9000, rms radial error=135.277, avgs=0 250/300: dt: 0.9000, rms radial error=134.514, avgs=0 255/300: dt: 0.9000, rms radial error=133.756, avgs=0 260/300: dt: 0.9000, rms radial error=133.002, avgs=0 265/300: dt: 0.9000, rms radial error=132.252, avgs=0 270/300: dt: 0.9000, rms radial error=131.506, avgs=0 275/300: dt: 0.9000, rms radial error=130.765, avgs=0 280/300: dt: 0.9000, rms radial error=130.027, avgs=0 285/300: dt: 0.9000, rms radial error=129.294, avgs=0 290/300: dt: 0.9000, rms radial error=128.565, avgs=0 295/300: dt: 0.9000, rms radial error=127.841, avgs=0 300/300: dt: 0.9000, rms radial error=127.120, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 16142.76 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 = 2702.84 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00004 epoch 3 (K=160.0), pass 1, starting sse = 280.06 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/10 = 0.00465 epoch 4 (K=640.0), pass 1, starting sse = 20.13 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.11/14 = 0.00821 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.14 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Fri Nov 13 23:22:30 CET 2015 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 B_LU_02_MRI_E_T0 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=-42 (nv=138038, nf=276160, ne=414240, g=22) 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... 5006 ambiguous faces found in tessellation segmenting defects... 26 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 21 into 16 25 defects to be corrected 0 vertices coincident reading input surface /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.2929 (-4.6465) -vertex loglikelihood: -6.0756 (-3.0378) -normal dot loglikelihood: -3.6965 (-3.6965) -quad curv loglikelihood: -6.4114 (-3.2057) Total Loglikelihood : -25.4763 CORRECTING DEFECT 0 (vertices=25, convex hull=54) After retessellation of defect 0, euler #=-23 (135115,404410,269272) : difference with theory (-22) = 1 CORRECTING DEFECT 1 (vertices=20, convex hull=58) After retessellation of defect 1, euler #=-22 (135127,404468,269319) : difference with theory (-21) = 1 CORRECTING DEFECT 2 (vertices=33, convex hull=37) After retessellation of defect 2, euler #=-21 (135131,404490,269338) : difference with theory (-20) = 1 CORRECTING DEFECT 3 (vertices=12, convex hull=29) After retessellation of defect 3, euler #=-20 (135131,404498,269347) : difference with theory (-19) = 1 CORRECTING DEFECT 4 (vertices=99, convex hull=69) After retessellation of defect 4, euler #=-19 (135152,404592,269421) : difference with theory (-18) = 1 CORRECTING DEFECT 5 (vertices=57, convex hull=85) After retessellation of defect 5, euler #=-18 (135179,404708,269511) : difference with theory (-17) = 1 CORRECTING DEFECT 6 (vertices=702, convex hull=290) After retessellation of defect 6, euler #=-17 (135310,405256,269929) : difference with theory (-16) = 1 CORRECTING DEFECT 7 (vertices=162, convex hull=141) After retessellation of defect 7, euler #=-16 (135347,405428,270065) : difference with theory (-15) = 1 CORRECTING DEFECT 8 (vertices=37, convex hull=58) After retessellation of defect 8, euler #=-15 (135370,405523,270138) : difference with theory (-14) = 1 CORRECTING DEFECT 9 (vertices=521, convex hull=257) After retessellation of defect 9, euler #=-14 (135389,405703,270300) : difference with theory (-13) = 1 CORRECTING DEFECT 10 (vertices=76, convex hull=102) After retessellation of defect 10, euler #=-13 (135430,405872,270429) : difference with theory (-12) = 1 CORRECTING DEFECT 11 (vertices=13, convex hull=41) After retessellation of defect 11, euler #=-12 (135432,405891,270447) : difference with theory (-11) = 1 CORRECTING DEFECT 12 (vertices=46, convex hull=74) After retessellation of defect 12, euler #=-11 (135453,405983,270519) : difference with theory (-10) = 1 CORRECTING DEFECT 13 (vertices=25, convex hull=47) After retessellation of defect 13, euler #=-10 (135466,406040,270564) : difference with theory (-9) = 1 CORRECTING DEFECT 14 (vertices=38, convex hull=69) After retessellation of defect 14, euler #=-9 (135487,406133,270637) : difference with theory (-8) = 1 CORRECTING DEFECT 15 (vertices=71, convex hull=99) After retessellation of defect 15, euler #=-8 (135519,406275,270748) : difference with theory (-7) = 1 CORRECTING DEFECT 16 (vertices=433, convex hull=220) After retessellation of defect 16, euler #=-6 (135614,406662,271042) : difference with theory (-6) = 0 CORRECTING DEFECT 17 (vertices=83, convex hull=64) After retessellation of defect 17, euler #=-5 (135644,406778,271129) : difference with theory (-5) = 0 CORRECTING DEFECT 18 (vertices=242, convex hull=33) After retessellation of defect 18, euler #=-4 (135653,406816,271159) : difference with theory (-4) = 0 CORRECTING DEFECT 19 (vertices=81, convex hull=70) After retessellation of defect 19, euler #=-3 (135671,406898,271224) : difference with theory (-3) = 0 CORRECTING DEFECT 20 (vertices=18, convex hull=18) After retessellation of defect 20, euler #=-2 (135672,406906,271232) : difference with theory (-2) = 0 CORRECTING DEFECT 21 (vertices=18, convex hull=22) After retessellation of defect 21, euler #=-1 (135675,406923,271247) : difference with theory (-1) = 0 CORRECTING DEFECT 22 (vertices=30, convex hull=68) After retessellation of defect 22, euler #=0 (135684,406974,271290) : difference with theory (0) = 0 CORRECTING DEFECT 23 (vertices=22, convex hull=57) After retessellation of defect 23, euler #=1 (135693,407023,271331) : difference with theory (1) = 0 CORRECTING DEFECT 24 (vertices=67, convex hull=108) After retessellation of defect 24, euler #=2 (135722,407160,271440) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.23 (0.05-->13.04) (max @ vno 77985 --> 81877) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.23 (0.05-->13.04) (max @ vno 77985 --> 81877) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 96 mutations (36.0%), 171 crossovers (64.0%), 294 vertices were eliminated building final representation... 2316 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=135722, nf=271440, ne=407160, g=0) writing corrected surface to /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 43.8 minutes 0 defective edges removing intersecting faces 000: 250 intersecting 001: 24 intersecting 002: 2 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 135722 - 407160 + 271440 = 2 --> 0 holes F =2V-4: 271440 = 271444-4 (0) 2E=3F: 814320 = 814320 (0) total defect index = 0 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 75 intersecting 001: 13 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Sat Nov 14 00:06:27 CET 2015 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs B_LU_02_MRI_E_T0 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 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/filled.mgz... reading volume /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/brain.finalsurfs.mgz... reading volume /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/wm.mgz... 12463 bright wm thresholded. 1921 bright non-wm voxels segmented. reading original surface position from /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/lh.orig... computing class statistics... border white: 246839 voxels (1.47%) border gray 281365 voxels (1.68%) WM (95.0): 96.0 +- 7.9 [70.0 --> 110.0] GM (83.0) : 81.2 +- 11.2 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 59.8 (was 70) setting MAX_BORDER_WHITE to 112.9 (was 105) setting MIN_BORDER_WHITE to 71.0 (was 85) setting MAX_CSF to 48.6 (was 40) setting MAX_GRAY to 97.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 65.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 37.5 (was 40) repositioning cortical surface to gray/white boundary reading volume /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.04-->4.50) (max @ vno 56380 --> 135321) face area 0.28 +- 0.12 (0.00-->4.83) mean absolute distance = 0.75 +- 0.92 3564 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=71 mean inside = 95.5, mean outside = 78.3 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group mean border=81.5, 75 (75) missing vertices, mean dist 0.3 [0.6 (%33.4)->0.8 (%66.6))] %61 local maxima, %34 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=biosr, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.26 (0.10-->7.31) (max @ vno 60709 --> 53985) face area 0.28 +- 0.14 (0.00-->5.32) mean absolute distance = 0.37 +- 0.60 3012 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5235132.0, rms=10.28 001: dt: 0.5000, sse=5729338.0, rms=7.456 (0.000%) 002: dt: 0.5000, sse=5993121.5, rms=5.666 (0.000%) 003: dt: 0.5000, sse=6277099.5, rms=4.532 (0.000%) 004: dt: 0.5000, sse=6443013.0, rms=3.807 (0.000%) 005: dt: 0.5000, sse=6592409.0, rms=3.438 (0.000%) 006: dt: 0.5000, sse=6664586.5, rms=3.199 (0.000%) 007: dt: 0.5000, sse=6715328.5, rms=3.131 (0.000%) 008: dt: 0.5000, sse=6725067.5, rms=3.040 (0.000%) rms = 3.00, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=6747159.0, rms=3.005 (0.000%) 010: dt: 0.2500, sse=4050105.8, rms=2.038 (0.000%) 011: dt: 0.2500, sse=3720453.5, rms=1.823 (0.000%) 012: dt: 0.2500, sse=3592847.5, rms=1.750 (0.000%) rms = 1.74, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=3556300.5, rms=1.737 (0.000%) rms = 1.70, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=3510758.2, rms=1.704 (0.000%) positioning took 2.5 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group mean border=84.6, 48 (10) missing vertices, mean dist -0.2 [0.4 (%72.9)->0.3 (%27.1))] %73 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=biosr, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.11-->7.90) (max @ vno 60709 --> 53985) face area 0.35 +- 0.17 (0.00-->7.69) mean absolute distance = 0.27 +- 0.39 3738 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4138235.2, rms=4.67 015: dt: 0.5000, sse=4413800.0, rms=2.959 (0.000%) 016: dt: 0.5000, sse=4780966.5, rms=2.678 (0.000%) 017: dt: 0.5000, sse=5202767.5, rms=2.505 (0.000%) rms = 2.73, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=4282635.0, rms=1.850 (0.000%) 019: dt: 0.2500, sse=3960395.0, rms=1.524 (0.000%) 020: dt: 0.2500, sse=3837968.2, rms=1.422 (0.000%) rms = 1.41, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=3796055.2, rms=1.408 (0.000%) rms = 1.38, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=3756962.8, rms=1.378 (0.000%) positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=87.3, 33 (3) missing vertices, mean dist -0.2 [0.3 (%74.9)->0.2 (%25.1))] %84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=biosr, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.04-->7.75) (max @ vno 135261 --> 135231) face area 0.34 +- 0.17 (0.00-->7.74) mean absolute distance = 0.21 +- 0.31 3003 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4004386.8, rms=3.54 023: dt: 0.5000, sse=4223882.5, rms=2.324 (0.000%) rms = 2.43, time step reduction 1 of 3 to 0.250... 024: dt: 0.2500, sse=3980668.0, rms=1.731 (0.000%) 025: dt: 0.2500, sse=3873088.2, rms=1.378 (0.000%) 026: dt: 0.2500, sse=3844342.0, rms=1.275 (0.000%) rms = 1.25, time step reduction 2 of 3 to 0.125... 027: dt: 0.2500, sse=3813962.5, rms=1.253 (0.000%) rms = 1.22, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=3793412.8, rms=1.223 (0.000%) positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=88.3, 28 (1) missing vertices, mean dist -0.0 [0.2 (%58.9)->0.2 (%41.1))] %88 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=biosr, 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 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=3806865.8, rms=1.64 029: dt: 0.5000, sse=4690238.5, rms=1.552 (0.000%) rms = 1.96, time step reduction 1 of 3 to 0.250... 030: dt: 0.2500, sse=4272667.0, rms=1.128 (0.000%) 031: dt: 0.2500, sse=4111114.2, rms=1.036 (0.000%) rms = 1.00, time step reduction 2 of 3 to 0.125... 032: dt: 0.2500, sse=4206619.5, rms=0.997 (0.000%) rms = 0.98, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=4201744.5, rms=0.985 (0.000%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 12 non-cortical segments detected only using segment with 1630 vertices erasing segment 0 (vno[0] = 52829) erasing segment 2 (vno[0] = 64059) erasing segment 3 (vno[0] = 81708) erasing segment 4 (vno[0] = 81725) erasing segment 5 (vno[0] = 90010) erasing segment 6 (vno[0] = 100883) erasing segment 7 (vno[0] = 100926) erasing segment 8 (vno[0] = 104282) erasing segment 9 (vno[0] = 105210) erasing segment 10 (vno[0] = 105241) erasing segment 11 (vno[0] = 135281) writing cortex label to /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/label/lh.cortex.label... writing curvature file /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/lh.curv writing smoothed area to lh.area writing curvature file /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/lh.area vertex spacing 0.89 +- 0.25 (0.05-->8.00) (max @ vno 135261 --> 135231) face area 0.33 +- 0.16 (0.00-->7.98) refinement took 9.8 minutes #-------------------------------------------- #@# Smooth2 lh Sat Nov 14 00:16:14 CET 2015 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/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 Sat Nov 14 00:16:21 CET 2015 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 47.2 mm, total surface area = 82535 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.114 (target=0.015) step 005: RMS=0.079 (target=0.015) step 010: RMS=0.057 (target=0.015) step 015: RMS=0.046 (target=0.015) step 020: RMS=0.038 (target=0.015) step 025: RMS=0.031 (target=0.015) step 030: RMS=0.026 (target=0.015) step 035: RMS=0.022 (target=0.015) step 040: RMS=0.019 (target=0.015) step 045: RMS=0.017 (target=0.015) step 050: RMS=0.015 (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 161 vertices thresholded to be in k1 ~ [-0.25 0.61], k2 ~ [-0.11 0.06] total integrated curvature = 0.551*4pi (6.929) --> 0 handles ICI = 1.7, FI = 11.0, variation=186.991 111 vertices thresholded to be in [-0.02 0.02] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 123 vertices thresholded to be in [-0.15 0.16] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.017, std = 0.024 done. #----------------------------------------- #@# Curvature Stats lh Sat Nov 14 00:19:25 CET 2015 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm B_LU_02_MRI_E_T0 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 [ B_LU_02_MRI_E_T0/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 [ 284 ] Gb_filter = 0 WARN: S lookup min: -0.083493 WARN: S explicit min: 0.000000 vertex = 229 #-------------------------------------------- #@# Sphere lh Sat Nov 14 00:19:34 CET 2015 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/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 0.292... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=biosr, 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 %19.65 pass 1: epoch 2 of 3 starting distance error %19.56 unfolding complete - removing small folds... starting distance error %19.50 removing remaining folds... final distance error %19.52 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/lh.sphere spherical transformation took 1.08 hours #-------------------------------------------- #@# Surf Reg lh Sat Nov 14 01:24:21 CET 2015 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/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=biosr, 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=biosr, 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 = 0.575 curvature mean = 0.046, std = 0.941 curvature mean = 0.025, std = 0.853 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 0.00) sse = 292595.8, tmin=1.5623 d=32.00 min @ (8.00, 0.00, 0.00) sse = 252916.3, tmin=3.0307 d=16.00 min @ (0.00, 4.00, 0.00) sse = 234824.9, tmin=4.5211 d=8.00 min @ (0.00, 0.00, -2.00) sse = 233856.9, tmin=6.0523 d=4.00 min @ (0.00, -1.00, 1.00) sse = 232008.7, tmin=7.6128 d=2.00 min @ (0.00, 0.00, -0.50) sse = 231978.8, tmin=9.2227 d=1.00 min @ (0.00, 0.00, 0.25) sse = 231931.0, tmin=10.7985 d=0.50 min @ (-0.12, 0.00, 0.00) sse = 231911.6, tmin=12.3383 tol=1.0e+00, sigma=0.5, host=biosr, 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 12.34 min curvature mean = 0.018, std = 0.951 curvature mean = 0.011, std = 0.939 curvature mean = 0.015, std = 0.962 curvature mean = 0.005, std = 0.973 curvature mean = 0.012, std = 0.963 curvature mean = 0.001, std = 0.989 2 Reading smoothwm curvature mean = -0.029, std = 0.284 curvature mean = 0.003, std = 0.067 curvature mean = 0.074, std = 0.359 curvature mean = 0.003, std = 0.079 curvature mean = 0.034, std = 0.566 curvature mean = 0.003, std = 0.085 curvature mean = 0.018, std = 0.713 curvature mean = 0.003, std = 0.088 curvature mean = 0.007, std = 0.822 MRISregister() return, current seed 0 writing registered surface to ../surf/lh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white lh Sat Nov 14 02:04:16 CET 2015 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 Sat Nov 14 02:04:20 CET 2015 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/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 Sat Nov 14 02:04:23 CET 2015 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 B_LU_02_MRI_E_T0 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... 1313 labels changed using aseg relabeling using gibbs priors... 000: 3013 changed, 135722 examined... 001: 641 changed, 12940 examined... 002: 175 changed, 3553 examined... 003: 49 changed, 1024 examined... 004: 20 changed, 315 examined... 005: 11 changed, 115 examined... 006: 2 changed, 64 examined... 007: 1 changed, 16 examined... 008: 0 changed, 7 examined... 262 labels changed using aseg 000: 127 total segments, 78 labels (427 vertices) changed 001: 46 total segments, 7 labels (29 vertices) changed 002: 39 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 40 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1944 vertices marked for relabeling... 1944 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 1 minutes and 30 seconds. #-------------------------------------------- #@# Make Pial Surf lh Sat Nov 14 02:05:53 CET 2015 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs B_LU_02_MRI_E_T0 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 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/filled.mgz... reading volume /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/brain.finalsurfs.mgz... reading volume /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/wm.mgz... 12463 bright wm thresholded. 1921 bright non-wm voxels segmented. reading original surface position from /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/lh.orig... computing class statistics... border white: 246839 voxels (1.47%) border gray 281365 voxels (1.68%) WM (95.0): 96.0 +- 7.9 [70.0 --> 110.0] GM (83.0) : 81.2 +- 11.2 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 59.8 (was 70) setting MAX_BORDER_WHITE to 112.9 (was 105) setting MIN_BORDER_WHITE to 71.0 (was 85) setting MAX_CSF to 48.6 (was 40) setting MAX_GRAY to 97.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 65.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 37.5 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=71 mean inside = 95.5, mean outside = 78.3 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 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.04-->4.50) (max @ vno 56380 --> 135321) face area 0.28 +- 0.12 (0.00-->4.83) mean absolute distance = 0.75 +- 0.93 3683 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 1 with 540 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 3 points - only 0.00% unknown mean border=81.5, 75 (75) missing vertices, mean dist 0.3 [0.6 (%33.4)->0.8 (%66.6))] %62 local maxima, %34 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=biosr, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.26 (0.10-->7.31) (max @ vno 60709 --> 53985) face area 0.28 +- 0.14 (0.00-->5.31) mean absolute distance = 0.37 +- 0.61 3072 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5247662.0, rms=10.27 001: dt: 0.5000, sse=5749902.5, rms=7.447 (0.000%) 002: dt: 0.5000, sse=6015538.0, rms=5.659 (0.000%) 003: dt: 0.5000, sse=6299436.5, rms=4.526 (0.000%) 004: dt: 0.5000, sse=6467885.0, rms=3.802 (0.000%) 005: dt: 0.5000, sse=6614983.5, rms=3.434 (0.000%) 006: dt: 0.5000, sse=6691776.5, rms=3.196 (0.000%) 007: dt: 0.5000, sse=6740477.5, rms=3.128 (0.000%) 008: dt: 0.5000, sse=6753285.0, rms=3.036 (0.000%) rms = 3.00, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=6773203.5, rms=3.002 (0.000%) 010: dt: 0.2500, sse=4067952.0, rms=2.037 (0.000%) 011: dt: 0.2500, sse=3737950.2, rms=1.823 (0.000%) 012: dt: 0.2500, sse=3610394.5, rms=1.750 (0.000%) rms = 1.74, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=3573561.5, rms=1.737 (0.000%) rms = 1.70, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=3527816.5, rms=1.704 (0.000%) positioning took 2.4 minutes inhibiting deformation at non-cortical midline structures... deleting segment 2 with 383 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 3 with 1 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 4 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 6 with 72 points - only 0.00% unknown deleting segment 8 with 9 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 9 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 10 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group mean border=84.6, 48 (10) missing vertices, mean dist -0.2 [0.4 (%72.9)->0.3 (%27.1))] %73 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=biosr, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.11-->7.90) (max @ vno 60709 --> 53985) face area 0.35 +- 0.17 (0.00-->7.69) mean absolute distance = 0.27 +- 0.39 3131 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4159434.8, rms=4.67 015: dt: 0.5000, sse=4434818.5, rms=2.959 (0.000%) 016: dt: 0.5000, sse=4807151.5, rms=2.677 (0.000%) 017: dt: 0.5000, sse=5227290.0, rms=2.504 (0.000%) rms = 2.73, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=4304372.5, rms=1.851 (0.000%) 019: dt: 0.2500, sse=3982477.8, rms=1.525 (0.000%) 020: dt: 0.2500, sse=3858804.8, rms=1.423 (0.000%) rms = 1.41, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=3816592.8, rms=1.410 (0.000%) rms = 1.38, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=3776192.2, rms=1.377 (0.000%) positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... deleting segment 1 with 416 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 3 with 104 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 5 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 7 with 11 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 8 with 4 points - only 0.00% unknown removing 4 vertex label from ripped group mean border=87.3, 33 (3) missing vertices, mean dist -0.2 [0.3 (%74.8)->0.2 (%25.2))] %85 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=biosr, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.04-->7.75) (max @ vno 135261 --> 135231) face area 0.34 +- 0.16 (0.00-->7.74) mean absolute distance = 0.21 +- 0.31 3062 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4024102.5, rms=3.54 023: dt: 0.5000, sse=4243492.5, rms=2.312 (0.000%) rms = 2.43, time step reduction 1 of 3 to 0.250... 024: dt: 0.2500, sse=3999549.5, rms=1.719 (0.000%) 025: dt: 0.2500, sse=3890893.2, rms=1.363 (0.000%) 026: dt: 0.2500, sse=3863227.2, rms=1.259 (0.000%) rms = 1.25, time step reduction 2 of 3 to 0.125... 027: dt: 0.2500, sse=3833985.5, rms=1.249 (0.000%) rms = 1.22, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=3813222.2, rms=1.222 (0.000%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... deleting segment 1 with 527 points - only 0.00% unknown removing 4 vertex label from ripped group removing 1 vertex label from ripped group deleting segment 3 with 1 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 3 points - only 0.00% unknown deleting segment 6 with 11 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 7 with 4 points - only 0.00% unknown deleting segment 8 with 7 points - only 0.00% unknown removing 4 vertex label from ripped group mean border=88.3, 28 (1) missing vertices, mean dist -0.0 [0.2 (%58.9)->0.2 (%41.1))] %88 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=biosr, 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=3826968.2, rms=1.64 029: dt: 0.5000, sse=4714692.0, rms=1.550 (0.000%) rms = 1.96, time step reduction 1 of 3 to 0.250... 030: dt: 0.2500, sse=4296133.0, rms=1.129 (0.000%) 031: dt: 0.2500, sse=4134290.0, rms=1.034 (0.000%) rms = 0.99, time step reduction 2 of 3 to 0.125... 032: dt: 0.2500, sse=4230157.0, rms=0.990 (0.000%) rms = 0.98, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=4224775.0, rms=0.982 (0.000%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... smoothing surface for 5 iterations... mean border=61.2, 71 (71) missing vertices, mean dist 1.7 [0.1 (%0.0)->2.4 (%100.0))] %24 local maxima, %45 large gradients and %28 min vals, 1410 gradients ignored tol=1.0e-04, sigma=2.0, host=biosr, 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=22140426.0, rms=27.33 001: dt: 0.5000, sse=17131394.0, rms=23.541 (0.000%) 002: dt: 0.5000, sse=13343847.0, rms=20.258 (0.000%) 003: dt: 0.5000, sse=10651356.0, rms=17.497 (0.000%) 004: dt: 0.5000, sse=8920331.0, rms=15.190 (0.000%) 005: dt: 0.5000, sse=7720295.5, rms=13.296 (0.000%) 006: dt: 0.5000, sse=6974265.0, rms=11.772 (0.000%) 007: dt: 0.5000, sse=6517795.5, rms=10.455 (0.000%) 008: dt: 0.5000, sse=6242580.0, rms=9.246 (0.000%) 009: dt: 0.5000, sse=6029530.0, rms=8.077 (0.000%) 010: dt: 0.5000, sse=5887255.0, rms=6.935 (0.000%) 011: dt: 0.5000, sse=5839574.0, rms=5.929 (0.000%) 012: dt: 0.5000, sse=5893813.5, rms=5.119 (0.000%) 013: dt: 0.5000, sse=6018030.5, rms=4.564 (0.000%) 014: dt: 0.5000, sse=6102355.5, rms=4.211 (0.000%) 015: dt: 0.5000, sse=6219044.5, rms=4.021 (0.000%) 016: dt: 0.5000, sse=6258280.5, rms=3.908 (0.000%) 017: dt: 0.5000, sse=6315831.5, rms=3.839 (0.000%) rms = 3.79, time step reduction 1 of 3 to 0.250... 018: dt: 0.5000, sse=6339240.5, rms=3.789 (0.000%) 019: dt: 0.2500, sse=4335768.5, rms=3.038 (0.000%) 020: dt: 0.2500, sse=4158771.0, rms=2.833 (0.000%) rms = 2.79, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=4048505.8, rms=2.795 (0.000%) 022: dt: 0.1250, sse=3868545.5, rms=2.684 (0.000%) rms = 2.67, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=3842007.5, rms=2.672 (0.000%) positioning took 4.0 minutes mean border=58.5, 929 (12) missing vertices, mean dist 0.2 [0.2 (%41.9)->0.5 (%58.1))] %43 local maxima, %31 large gradients and %21 min vals, 698 gradients ignored tol=1.0e-04, sigma=1.0, host=biosr, 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=4576095.5, rms=5.19 024: dt: 0.5000, sse=4643262.0, rms=3.907 (0.000%) 025: dt: 0.5000, sse=5920202.0, rms=3.844 (0.000%) rms = 3.88, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=4931746.0, rms=3.137 (0.000%) 027: dt: 0.2500, sse=4524259.0, rms=2.841 (0.000%) 028: dt: 0.2500, sse=4489276.0, rms=2.765 (0.000%) rms = 2.73, time step reduction 2 of 3 to 0.125... 029: dt: 0.2500, sse=4444835.0, rms=2.726 (0.000%) 030: dt: 0.1250, sse=4301155.5, rms=2.614 (0.000%) rms = 2.60, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=4289413.5, rms=2.597 (0.000%) positioning took 1.5 minutes mean border=56.8, 1147 (8) missing vertices, mean dist 0.1 [0.2 (%37.5)->0.3 (%62.5))] %57 local maxima, %17 large gradients and %21 min vals, 657 gradients ignored tol=1.0e-04, sigma=0.5, host=biosr, 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=4458616.0, rms=3.52 rms = 3.60, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=4290027.0, rms=3.021 (0.000%) 033: dt: 0.2500, sse=4302487.5, rms=2.716 (0.000%) 034: dt: 0.2500, sse=4455654.0, rms=2.637 (0.000%) rms = 2.62, time step reduction 2 of 3 to 0.125... 035: dt: 0.2500, sse=4535475.5, rms=2.622 (0.000%) 036: dt: 0.1250, sse=4416101.0, rms=2.533 (0.000%) rms = 2.52, time step reduction 3 of 3 to 0.062... 037: dt: 0.1250, sse=4426925.0, rms=2.517 (0.000%) positioning took 1.2 minutes mean border=55.9, 2491 (7) missing vertices, mean dist 0.1 [0.2 (%44.3)->0.3 (%55.7))] %61 local maxima, %13 large gradients and %20 min vals, 563 gradients ignored tol=1.0e-04, sigma=0.2, host=biosr, 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 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=4455568.5, rms=2.73 rms = 3.18, time step reduction 1 of 3 to 0.250... 038: dt: 0.2500, sse=4376951.5, rms=2.548 (0.000%) 039: dt: 0.2500, sse=4539140.5, rms=2.486 (0.000%) rms = 2.46, time step reduction 2 of 3 to 0.125... 040: dt: 0.2500, sse=4607688.5, rms=2.464 (0.000%) 041: dt: 0.1250, sse=4543229.0, rms=2.388 (0.000%) rms = 2.37, time step reduction 3 of 3 to 0.062... 042: dt: 0.1250, sse=4569052.0, rms=2.368 (0.000%) positioning took 0.9 minutes writing curvature file /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/lh.area.pial vertex spacing 1.00 +- 0.41 (0.05-->10.14) (max @ vno 135261 --> 135231) face area 0.40 +- 0.30 (0.00-->12.90) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 135722 vertices processed 25000 of 135722 vertices processed 50000 of 135722 vertices processed 75000 of 135722 vertices processed 100000 of 135722 vertices processed 125000 of 135722 vertices processed 0 of 135722 vertices processed 25000 of 135722 vertices processed 50000 of 135722 vertices processed 75000 of 135722 vertices processed 100000 of 135722 vertices processed 125000 of 135722 vertices processed thickness calculation complete, 507:850 truncations. 31410 vertices at 0 distance 92385 vertices at 1 distance 83481 vertices at 2 distance 35915 vertices at 3 distance 11859 vertices at 4 distance 3665 vertices at 5 distance 1269 vertices at 6 distance 459 vertices at 7 distance 223 vertices at 8 distance 107 vertices at 9 distance 82 vertices at 10 distance 35 vertices at 11 distance 38 vertices at 12 distance 34 vertices at 13 distance 29 vertices at 14 distance 14 vertices at 15 distance 17 vertices at 16 distance 21 vertices at 17 distance 17 vertices at 18 distance 7 vertices at 19 distance 15 vertices at 20 distance writing curvature file /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/lh.thickness positioning took 19.1 minutes #-------------------------------------------- #@# Surf Volume lh Sat Nov 14 02:25:01 CET 2015 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.volume lh.area.mid mul lh.thickness Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# WM/GM Contrast lh Sat Nov 14 02:25:02 CET 2015 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/scripts pctsurfcon --s B_LU_02_MRI_E_T0 --lh-only Log file is /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/scripts/pctsurfcon.log Sat Nov 14 02:25:02 CET 2015 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects cd /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/scripts /usr/local//freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux biosrv1 2.6.32-573.7.1.el6.x86_64 #1 SMP Tue Sep 22 22:00:00 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local//freesurfer mri_vol2surf --mov /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/tmp.pctsurfcon.32383/lh.wm.mgh --regheader B_LU_02_MRI_E_T0 --cortex srcvol = /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/orig.mgz as target reference. Loading label /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/label/lh.cortex.label Reading surface /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/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 = 73568 Masking with /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/label/lh.cortex.label Writing to /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/tmp.pctsurfcon.32383/lh.wm.mgh Dim: 135722 1 1 mri_vol2surf --mov /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/tmp.pctsurfcon.32383/lh.gm.mgh --projfrac 0.3 --regheader B_LU_02_MRI_E_T0 --cortex srcvol = /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/orig.mgz as target reference. Loading label /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/label/lh.cortex.label Reading surface /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/lh.white Done reading source surface Reading thickness /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/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 = 89221 Masking with /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/label/lh.cortex.label Writing to /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/tmp.pctsurfcon.32383/lh.gm.mgh Dim: 135722 1 1 mri_concat /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/tmp.pctsurfcon.32383/lh.wm.mgh /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/tmp.pctsurfcon.32383/lh.gm.mgh --paired-diff-norm --mul 100 --o /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/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 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/lh.w-g.pct.mgh mri_segstats --in /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/lh.w-g.pct.mgh --annot B_LU_02_MRI_E_T0 lh aparc --sum /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/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 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/lh.w-g.pct.mgh --annot B_LU_02_MRI_E_T0 lh aparc --sum /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/stats/lh.w-g.pct.stats --snr sysname Linux hostname biosrv1 machine x86_64 user root 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 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/lh.w-g.pct.mgh Vertex Area is 0.662636 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 1000 unknown 0 0.000 1 1001 bankssts 1331 949.908 2 1002 caudalanteriorcingulate 1391 882.591 3 1003 caudalmiddlefrontal 4002 2660.173 4 1004 corpuscallosum 0 0.000 5 1005 cuneus 2224 1381.407 6 1006 entorhinal 738 532.006 7 1007 fusiform 5346 3641.896 8 1008 inferiorparietal 7105 4693.421 9 1009 inferiortemporal 4522 3103.630 10 1010 isthmuscingulate 1531 981.126 11 1011 lateraloccipital 6881 4378.130 12 1012 lateralorbitofrontal 3977 2628.760 13 1013 lingual 4424 2941.250 14 1014 medialorbitofrontal 2951 1950.321 15 1015 middletemporal 4138 2816.784 16 1016 parahippocampal 1006 657.814 17 1017 paracentral 2425 1475.510 18 1018 parsopercularis 2354 1603.935 19 1019 parsorbitalis 975 606.567 20 1020 parstriangularis 1891 1246.465 21 1021 pericalcarine 1913 1287.369 22 1022 postcentral 6856 4439.027 23 1023 posteriorcingulate 1676 1138.343 24 1024 precentral 8225 5049.671 25 1025 precuneus 6015 4071.052 26 1026 rostralanteriorcingulate 1406 917.622 27 1027 rostralmiddlefrontal 9026 6150.217 28 1028 superiorfrontal 10549 7103.638 29 1029 superiorparietal 8474 5535.293 30 1030 superiortemporal 4911 3273.946 31 1031 supramarginal 5336 3631.455 32 1032 frontalpole 329 227.652 33 1033 temporalpole 590 417.690 34 1034 transversetemporal 720 450.654 35 1035 insula 3348 2172.187 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats lh Sat Nov 14 02:25:16 CET 2015 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/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 B_LU_02_MRI_E_T0 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/lh.white... reading input pial surface /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/lh.pial... reading input white surface /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/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 1331 950 2218 2.443 0.416 0.097 0.021 6 1.1 bankssts 1391 883 2793 2.818 0.541 0.153 0.257 153 2.6 caudalanteriorcingulate 4002 2660 7849 2.695 0.485 0.127 0.035 43 5.8 caudalmiddlefrontal 2224 1381 2498 1.653 0.430 0.147 0.051 37 4.6 cuneus 738 532 2700 3.276 0.927 0.165 0.073 14 2.0 entorhinal 5346 3642 10738 2.635 0.572 0.147 0.048 86 10.5 fusiform 7105 4693 12570 2.393 0.520 0.137 0.040 102 11.6 inferiorparietal 4522 3104 10481 2.847 0.561 0.146 0.059 88 9.9 inferiortemporal 1531 981 2758 2.667 0.740 0.156 0.077 59 4.7 isthmuscingulate 6881 4378 10377 2.081 0.634 0.151 0.048 105 13.8 lateraloccipital 3977 2629 7384 2.697 0.694 0.158 0.077 96 11.6 lateralorbitofrontal 4424 2941 6150 1.971 0.570 0.161 0.061 84 10.5 lingual 2951 1950 5074 2.250 0.777 0.168 0.190 156 12.5 medialorbitofrontal 4138 2817 9406 2.849 0.561 0.147 0.051 76 8.1 middletemporal 1006 658 2206 2.949 0.592 0.108 0.032 8 1.3 parahippocampal 2425 1476 3917 2.454 0.636 0.114 0.049 31 5.1 paracentral 2354 1604 5038 2.862 0.440 0.135 0.035 30 3.3 parsopercularis 975 607 2057 2.688 0.662 0.158 0.058 21 2.0 parsorbitalis 1891 1246 3750 2.641 0.479 0.126 0.031 23 2.5 parstriangularis 1913 1287 1744 1.449 0.354 0.156 0.058 35 4.4 pericalcarine 6856 4439 10434 2.055 0.586 0.127 0.038 89 10.4 postcentral 1676 1138 3103 2.536 0.619 0.158 0.053 32 3.7 posteriorcingulate 8225 5050 14479 2.631 0.558 0.111 0.034 88 11.1 precentral 6015 4071 10265 2.363 0.570 0.146 0.046 96 11.0 precuneus 1406 918 3327 3.364 0.648 0.158 0.062 27 3.5 rostralanteriorcingulate 9026 6150 16443 2.302 0.621 0.155 0.057 165 20.9 rostralmiddlefrontal 10549 7104 22313 2.745 0.607 0.140 0.044 150 18.6 superiorfrontal 8474 5535 12917 2.052 0.497 0.137 0.042 119 13.8 superiorparietal 4911 3274 10453 2.869 0.579 0.124 0.032 57 6.5 superiortemporal 5336 3631 9945 2.477 0.601 0.146 0.046 90 10.1 supramarginal 329 228 832 2.692 0.486 0.201 0.111 11 1.1 frontalpole 590 418 2395 3.749 0.638 0.173 0.082 14 2.3 temporalpole 720 451 1149 2.414 0.439 0.140 0.038 9 1.1 transversetemporal 3348 2172 7010 3.210 0.886 0.124 0.074 78 10.8 insula #----------------------------------------- #@# Cortical Parc 2 lh Sat Nov 14 02:25:46 CET 2015 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 B_LU_02_MRI_E_T0 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... 21 labels changed using aseg relabeling using gibbs priors... 000: 9269 changed, 135722 examined... 001: 2248 changed, 35323 examined... 002: 650 changed, 11465 examined... 003: 264 changed, 3654 examined... 004: 136 changed, 1566 examined... 005: 71 changed, 756 examined... 006: 32 changed, 396 examined... 007: 17 changed, 177 examined... 008: 13 changed, 107 examined... 009: 5 changed, 76 examined... 010: 8 changed, 36 examined... 011: 2 changed, 38 examined... 012: 1 changed, 14 examined... 013: 2 changed, 7 examined... 014: 2 changed, 10 examined... 015: 0 changed, 13 examined... 2 labels changed using aseg 000: 289 total segments, 207 labels (2958 vertices) changed 001: 104 total segments, 22 labels (167 vertices) changed 002: 82 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 120 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 938 vertices marked for relabeling... 938 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 1 minutes and 36 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Sat Nov 14 02:27:22 CET 2015 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/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 B_LU_02_MRI_E_T0 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/lh.white... reading input pial surface /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/lh.pial... reading input white surface /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/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 1164 789 1980 2.256 0.656 0.159 0.058 21 2.7 G_and_S_frontomargin 1620 1067 3074 2.438 0.695 0.155 0.044 26 3.0 G_and_S_occipital_inf 1707 939 2762 2.384 0.656 0.122 0.067 40 4.4 G_and_S_paracentral 1632 1081 3210 2.583 0.407 0.161 0.055 33 3.4 G_and_S_subcentral 726 506 1637 2.425 0.583 0.178 0.091 19 2.2 G_and_S_transv_frontopol 2401 1615 4778 2.826 0.727 0.148 0.051 38 4.7 G_and_S_cingul-Ant 1853 1220 3339 2.685 0.418 0.131 0.192 149 2.6 G_and_S_cingul-Mid-Ant 1167 822 2260 2.704 0.430 0.130 0.033 13 1.5 G_and_S_cingul-Mid-Post 640 411 1715 3.016 0.435 0.190 0.102 20 2.6 G_cingul-Post-dorsal 292 184 430 2.404 0.781 0.197 0.183 24 2.1 G_cingul-Post-ventral 1898 1176 2188 1.618 0.389 0.155 0.059 38 4.5 G_cuneus 1466 989 3739 2.978 0.429 0.151 0.046 26 2.7 G_front_inf-Opercular 288 175 705 2.878 0.330 0.164 0.053 6 0.6 G_front_inf-Orbital 993 644 2442 2.769 0.514 0.149 0.039 18 1.8 G_front_inf-Triangul 5490 3697 12031 2.579 0.599 0.160 0.060 114 13.3 G_front_middle 7283 4845 17367 2.858 0.622 0.153 0.054 129 16.4 G_front_sup 584 359 1196 2.920 0.826 0.156 0.079 17 1.8 G_Ins_lg_and_S_cent_ins 647 390 2068 3.964 0.610 0.122 0.061 11 1.6 G_insular_short 2230 1359 4514 2.510 0.542 0.156 0.053 44 4.9 G_occipital_middle 1839 1137 2456 1.901 0.457 0.150 0.051 31 3.9 G_occipital_sup 2315 1463 5019 2.667 0.616 0.156 0.060 49 5.8 G_oc-temp_lat-fusifor 2863 1858 4156 1.937 0.570 0.173 0.067 65 7.7 G_oc-temp_med-Lingual 1467 1016 4579 3.203 0.742 0.145 0.056 21 3.2 G_oc-temp_med-Parahip 2763 1768 5798 2.610 0.765 0.169 0.092 84 9.5 G_orbital 2488 1584 5556 2.677 0.490 0.156 0.055 53 5.6 G_pariet_inf-Angular 2809 1933 6205 2.620 0.564 0.162 0.057 61 6.5 G_pariet_inf-Supramar 3219 2115 5942 2.221 0.528 0.150 0.052 60 6.3 G_parietal_sup 2585 1598 4566 2.268 0.536 0.139 0.045 45 4.7 G_postcentral 3312 1799 6914 2.921 0.440 0.113 0.039 39 5.1 G_precentral 3080 2058 6105 2.401 0.577 0.158 0.053 64 6.6 G_precuneus 1120 732 2407 2.357 0.808 0.209 0.356 98 5.3 G_rectus 488 283 649 2.301 0.836 0.187 0.250 66 5.6 G_subcallosal 649 404 1240 2.537 0.463 0.138 0.036 9 1.0 G_temp_sup-G_T_transv 1731 1104 4659 3.012 0.522 0.144 0.047 31 3.3 G_temp_sup-Lateral 684 472 1964 3.550 0.722 0.128 0.038 8 1.0 G_temp_sup-Plan_polar 696 478 1268 2.387 0.445 0.106 0.027 9 0.7 G_temp_sup-Plan_tempo 2637 1794 6869 2.895 0.559 0.160 0.079 69 7.4 G_temporal_inf 2662 1794 6852 2.872 0.582 0.155 0.059 60 6.1 G_temporal_middle 362 243 509 2.443 0.382 0.095 0.018 2 0.2 Lat_Fis-ant-Horizont 303 222 505 2.674 0.326 0.087 0.019 1 0.2 Lat_Fis-ant-Vertical 1025 684 1337 2.513 0.649 0.127 0.034 9 1.4 Lat_Fis-post 1920 1209 2309 1.725 0.443 0.159 0.054 32 4.3 Pole_occipital 1654 1164 5237 3.225 0.782 0.169 0.068 36 4.8 Pole_temporal 2434 1660 2661 1.796 0.743 0.148 0.056 37 5.2 S_calcarine 3348 2242 3781 1.827 0.570 0.106 0.024 19 3.5 S_central 1033 710 1481 2.241 0.522 0.116 0.026 8 1.1 S_cingul-Marginalis 389 264 811 3.574 0.723 0.121 0.178 9 4.8 S_circular_insula_ant 1379 932 2408 3.034 0.743 0.095 0.028 8 1.3 S_circular_insula_inf 1681 1145 2578 2.654 0.467 0.113 0.026 11 1.8 S_circular_insula_sup 1164 851 2122 2.703 0.407 0.114 0.024 7 1.2 S_collat_transv_ant 403 280 426 1.734 0.503 0.167 0.043 5 0.8 S_collat_transv_post 2370 1605 3629 2.385 0.532 0.125 0.033 22 3.0 S_front_inf 1278 870 1934 2.130 0.543 0.146 0.045 18 2.2 S_front_middle 3335 2267 5525 2.482 0.559 0.121 0.033 28 4.6 S_front_sup 261 170 471 2.828 0.574 0.154 0.054 5 0.4 S_interm_prim-Jensen 3076 2088 4068 1.954 0.468 0.117 0.029 28 3.5 S_intrapariet_and_P_trans 1013 664 1177 1.892 0.460 0.141 0.044 10 1.8 S_oc_middle_and_Lunatus 1569 1053 2014 1.947 0.383 0.123 0.029 14 1.9 S_oc_sup_and_transversal 739 521 1018 2.250 0.491 0.134 0.034 7 1.0 S_occipital_ant 1026 708 1624 2.493 0.349 0.133 0.039 14 1.6 S_oc-temp_lat 2101 1444 3172 2.430 0.513 0.121 0.029 17 2.4 S_oc-temp_med_and_Lingual 446 301 597 2.122 0.562 0.126 0.028 4 0.6 S_orbital_lateral 985 675 1302 2.228 0.836 0.122 0.032 10 1.3 S_orbital_med-olfact 1351 908 2325 2.672 0.603 0.149 0.058 24 2.7 S_orbital-H_Shaped 2143 1421 2838 2.127 0.664 0.134 0.038 24 3.3 S_parieto_occipital 1444 896 2120 2.646 0.994 0.150 0.043 40 2.6 S_pericallosal 3141 2103 3969 2.002 0.428 0.111 0.027 25 3.5 S_postcentral 1670 1137 2588 2.589 0.457 0.095 0.019 9 1.4 S_precentral-inf-part 1379 933 2068 2.514 0.450 0.106 0.023 8 1.4 S_precentral-sup-part 855 581 1256 2.329 0.705 0.135 0.062 11 1.6 S_suborbital 1184 831 1848 2.308 0.430 0.136 0.042 13 1.9 S_subparietal 1093 768 1790 2.700 0.511 0.120 0.025 7 1.2 S_temporal_inf 5183 3528 8130 2.497 0.521 0.117 0.028 44 5.7 S_temporal_sup 361 263 503 2.441 0.392 0.137 0.026 4 0.4 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Sat Nov 14 02:27:57 CET 2015 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 B_LU_02_MRI_E_T0 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... 913 labels changed using aseg relabeling using gibbs priors... 000: 2829 changed, 135722 examined... 001: 631 changed, 12016 examined... 002: 150 changed, 3402 examined... 003: 47 changed, 893 examined... 004: 24 changed, 268 examined... 005: 7 changed, 135 examined... 006: 1 changed, 37 examined... 007: 0 changed, 7 examined... 74 labels changed using aseg 000: 65 total segments, 32 labels (433 vertices) changed 001: 35 total segments, 2 labels (7 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 50 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 904 vertices marked for relabeling... 904 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas40.annot... classification took 1 minutes and 33 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Sat Nov 14 02:29:31 CET 2015 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/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 B_LU_02_MRI_E_T0 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot. reading volume /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/lh.white... reading input pial surface /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/lh.pial... reading input white surface /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/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 1955 1257 3747 2.817 0.498 0.148 0.193 160 3.4 caudalanteriorcingulate 4179 2778 8262 2.703 0.503 0.127 0.035 45 6.0 caudalmiddlefrontal 3239 2012 3902 1.768 0.460 0.145 0.051 54 6.8 cuneus 776 554 2777 3.273 0.878 0.165 0.071 14 2.1 entorhinal 4822 3280 9628 2.634 0.567 0.148 0.048 77 9.5 fusiform 6593 4361 11727 2.397 0.527 0.135 0.039 91 10.4 inferiorparietal 4636 3194 10390 2.797 0.566 0.145 0.059 90 10.2 inferiortemporal 1539 987 2775 2.665 0.740 0.156 0.077 59 4.7 isthmuscingulate 7154 4557 10753 2.068 0.624 0.149 0.047 106 14.0 lateraloccipital 4252 2802 7940 2.623 0.741 0.160 0.080 106 13.2 lateralorbitofrontal 4368 2903 6091 1.971 0.571 0.161 0.060 82 10.2 lingual 2649 1735 4471 2.218 0.784 0.169 0.211 174 11.7 medialorbitofrontal 5614 3824 12277 2.791 0.569 0.141 0.046 91 10.1 middletemporal 1024 665 2225 2.948 0.591 0.107 0.033 9 1.3 parahippocampal 2805 1715 4696 2.475 0.631 0.113 0.049 35 5.9 paracentral 2130 1441 4559 2.899 0.422 0.135 0.036 27 3.0 parsopercularis 1022 655 2011 2.621 0.540 0.142 0.047 16 1.8 parsorbitalis 2272 1509 4325 2.580 0.489 0.127 0.031 27 3.1 parstriangularis 1924 1296 1765 1.452 0.356 0.158 0.059 35 4.5 pericalcarine 7533 4902 11421 2.067 0.586 0.128 0.038 98 11.4 postcentral 1851 1261 3527 2.563 0.600 0.155 0.051 34 3.8 posteriorcingulate 8115 4974 14138 2.625 0.554 0.112 0.034 87 10.9 precentral 5724 3889 10003 2.383 0.579 0.147 0.046 93 10.4 precuneus 1817 1202 4001 3.156 0.754 0.153 0.059 32 4.2 rostralanteriorcingulate 6349 4310 11873 2.357 0.637 0.153 0.055 114 13.7 rostralmiddlefrontal 12139 8231 25369 2.651 0.648 0.149 0.051 198 24.4 superiorfrontal 6801 4456 10428 2.060 0.501 0.137 0.042 96 11.1 superiorparietal 6546 4422 14676 2.890 0.674 0.128 0.038 86 10.5 superiortemporal 5375 3649 9997 2.478 0.605 0.147 0.047 94 10.3 supramarginal 704 442 1153 2.429 0.446 0.139 0.037 9 1.1 transversetemporal 2679 1735 5864 3.335 0.827 0.119 0.068 39 9.0 insula #-------------------------------------------- #@# Tessellate rh Sat Nov 14 02:30:08 CET 2015 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 2 found - 2 modified | TOTAL: 4 pass 2 (xy-): 0 found - 2 modified | TOTAL: 4 pass 1 (yz+): 0 found - 0 modified | TOTAL: 4 pass 1 (yz-): 2 found - 2 modified | TOTAL: 6 pass 2 (yz-): 0 found - 2 modified | TOTAL: 6 pass 1 (xz+): 2 found - 2 modified | TOTAL: 8 pass 2 (xz+): 0 found - 2 modified | TOTAL: 8 pass 1 (xz-): 3 found - 3 modified | TOTAL: 11 pass 2 (xz-): 0 found - 3 modified | TOTAL: 11 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 1 found - 1 modified | TOTAL: 1 pass 2 (--): 0 found - 1 modified | TOTAL: 1 pass 1 (-+): 2 found - 2 modified | TOTAL: 3 pass 2 (-+): 0 found - 2 modified | TOTAL: 3 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 14 (out of 254432: 0.005502) 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 30: 497 vertices, 548 faces slice 40: 5281 vertices, 5507 faces slice 50: 13003 vertices, 13351 faces slice 60: 23611 vertices, 24010 faces slice 70: 34213 vertices, 34592 faces slice 80: 45321 vertices, 45679 faces slice 90: 57390 vertices, 57848 faces slice 100: 68609 vertices, 69005 faces slice 110: 79253 vertices, 79652 faces slice 120: 89725 vertices, 90124 faces slice 130: 100368 vertices, 100735 faces slice 140: 109655 vertices, 109975 faces slice 150: 117779 vertices, 118047 faces slice 160: 124501 vertices, 124771 faces slice 170: 130512 vertices, 130722 faces slice 180: 134087 vertices, 134234 faces slice 190: 135194 vertices, 135234 faces slice 200: 135194 vertices, 135234 faces slice 210: 135194 vertices, 135234 faces slice 220: 135194 vertices, 135234 faces slice 230: 135194 vertices, 135234 faces slice 240: 135194 vertices, 135234 faces slice 250: 135194 vertices, 135234 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... 135194 voxel in cpt #1: X=-40 [v=135194,e=405702,f=270468] located at (26.637905, -27.854639, 18.530645) For the whole surface: X=-40 [v=135194,e=405702,f=270468] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Sat Nov 14 02:30:22 CET 2015 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/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 Sat Nov 14 02:30:28 CET 2015 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/scripts avg radius = 46.2 mm, total surface area = 71695 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.8 minutes Not saving sulc step 000: RMS=0.100 (target=0.015) step 005: RMS=0.074 (target=0.015) step 010: RMS=0.055 (target=0.015) step 015: RMS=0.046 (target=0.015) step 020: RMS=0.039 (target=0.015) step 025: RMS=0.035 (target=0.015) step 030: RMS=0.032 (target=0.015) step 035: RMS=0.029 (target=0.015) step 040: RMS=0.027 (target=0.015) step 045: RMS=0.025 (target=0.015) step 050: RMS=0.025 (target=0.015) step 055: RMS=0.024 (target=0.015) step 060: RMS=0.023 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere rh Sat Nov 14 02:31:18 CET 2015 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.01 +- 0.56 (0.00-->5.99) (max @ vno 99123 --> 99124) face area 0.03 +- 0.03 (-0.24-->0.63) scaling brain by 0.315... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.503, avgs=0 005/300: dt: 0.9000, rms radial error=176.243, avgs=0 010/300: dt: 0.9000, rms radial error=175.686, avgs=0 015/300: dt: 0.9000, rms radial error=174.955, avgs=0 020/300: dt: 0.9000, rms radial error=174.125, avgs=0 025/300: dt: 0.9000, rms radial error=173.239, avgs=0 030/300: dt: 0.9000, rms radial error=172.321, avgs=0 035/300: dt: 0.9000, rms radial error=171.387, avgs=0 040/300: dt: 0.9000, rms radial error=170.444, avgs=0 045/300: dt: 0.9000, rms radial error=169.499, avgs=0 050/300: dt: 0.9000, rms radial error=168.555, avgs=0 055/300: dt: 0.9000, rms radial error=167.613, avgs=0 060/300: dt: 0.9000, rms radial error=166.675, avgs=0 065/300: dt: 0.9000, rms radial error=165.741, avgs=0 070/300: dt: 0.9000, rms radial error=164.811, avgs=0 075/300: dt: 0.9000, rms radial error=163.886, avgs=0 080/300: dt: 0.9000, rms radial error=162.966, avgs=0 085/300: dt: 0.9000, rms radial error=162.051, avgs=0 090/300: dt: 0.9000, rms radial error=161.141, avgs=0 095/300: dt: 0.9000, rms radial error=160.235, avgs=0 100/300: dt: 0.9000, rms radial error=159.335, avgs=0 105/300: dt: 0.9000, rms radial error=158.439, avgs=0 110/300: dt: 0.9000, rms radial error=157.548, avgs=0 115/300: dt: 0.9000, rms radial error=156.662, avgs=0 120/300: dt: 0.9000, rms radial error=155.781, avgs=0 125/300: dt: 0.9000, rms radial error=154.904, avgs=0 130/300: dt: 0.9000, rms radial error=154.033, avgs=0 135/300: dt: 0.9000, rms radial error=153.165, avgs=0 140/300: dt: 0.9000, rms radial error=152.303, avgs=0 145/300: dt: 0.9000, rms radial error=151.445, avgs=0 150/300: dt: 0.9000, rms radial error=150.592, avgs=0 155/300: dt: 0.9000, rms radial error=149.743, avgs=0 160/300: dt: 0.9000, rms radial error=148.899, avgs=0 165/300: dt: 0.9000, rms radial error=148.060, avgs=0 170/300: dt: 0.9000, rms radial error=147.225, avgs=0 175/300: dt: 0.9000, rms radial error=146.395, avgs=0 180/300: dt: 0.9000, rms radial error=145.570, avgs=0 185/300: dt: 0.9000, rms radial error=144.749, avgs=0 190/300: dt: 0.9000, rms radial error=143.933, avgs=0 195/300: dt: 0.9000, rms radial error=143.121, avgs=0 200/300: dt: 0.9000, rms radial error=142.314, avgs=0 205/300: dt: 0.9000, rms radial error=141.511, avgs=0 210/300: dt: 0.9000, rms radial error=140.713, avgs=0 215/300: dt: 0.9000, rms radial error=139.919, avgs=0 220/300: dt: 0.9000, rms radial error=139.129, avgs=0 225/300: dt: 0.9000, rms radial error=138.344, avgs=0 230/300: dt: 0.9000, rms radial error=137.563, avgs=0 235/300: dt: 0.9000, rms radial error=136.786, avgs=0 240/300: dt: 0.9000, rms radial error=136.014, avgs=0 245/300: dt: 0.9000, rms radial error=135.246, avgs=0 250/300: dt: 0.9000, rms radial error=134.482, avgs=0 255/300: dt: 0.9000, rms radial error=133.723, avgs=0 260/300: dt: 0.9000, rms radial error=132.968, avgs=0 265/300: dt: 0.9000, rms radial error=132.217, avgs=0 270/300: dt: 0.9000, rms radial error=131.470, avgs=0 275/300: dt: 0.9000, rms radial error=130.727, avgs=0 280/300: dt: 0.9000, rms radial error=129.989, avgs=0 285/300: dt: 0.9000, rms radial error=129.255, avgs=0 290/300: dt: 0.9000, rms radial error=128.525, avgs=0 295/300: dt: 0.9000, rms radial error=127.800, avgs=0 300/300: dt: 0.9000, rms radial error=127.078, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 15704.06 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00018 epoch 2 (K=40.0), pass 1, starting sse = 2558.92 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00008 epoch 3 (K=160.0), pass 1, starting sse = 252.32 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.08/11 = 0.00766 epoch 4 (K=640.0), pass 1, starting sse = 16.52 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.14/16 = 0.00885 final writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.12 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology rh Sat Nov 14 02:38:38 CET 2015 cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 B_LU_02_MRI_E_T0 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=-40 (nv=135194, nf=270468, ne=405702, g=21) 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... 3170 ambiguous faces found in tessellation segmenting defects... 30 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 30 defects to be corrected 0 vertices coincident reading input surface /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.3342 (-4.6671) -vertex loglikelihood: -6.1167 (-3.0584) -normal dot loglikelihood: -3.6231 (-3.6231) -quad curv loglikelihood: -6.4536 (-3.2268) Total Loglikelihood : -25.5276 CORRECTING DEFECT 0 (vertices=80, convex hull=121) After retessellation of defect 0, euler #=-27 (133284,399110,265799) : difference with theory (-27) = 0 CORRECTING DEFECT 1 (vertices=21, convex hull=66) After retessellation of defect 1, euler #=-26 (133292,399160,265842) : difference with theory (-26) = 0 CORRECTING DEFECT 2 (vertices=50, convex hull=86) After retessellation of defect 2, euler #=-25 (133321,399284,265938) : difference with theory (-25) = 0 CORRECTING DEFECT 3 (vertices=26, convex hull=54) After retessellation of defect 3, euler #=-24 (133336,399352,265992) : difference with theory (-24) = 0 CORRECTING DEFECT 4 (vertices=37, convex hull=64) After retessellation of defect 4, euler #=-23 (133354,399429,266052) : difference with theory (-23) = 0 CORRECTING DEFECT 5 (vertices=81, convex hull=61) After retessellation of defect 5, euler #=-22 (133373,399512,266117) : difference with theory (-22) = 0 CORRECTING DEFECT 6 (vertices=46, convex hull=72) After retessellation of defect 6, euler #=-21 (133402,399632,266209) : difference with theory (-21) = 0 CORRECTING DEFECT 7 (vertices=125, convex hull=52) After retessellation of defect 7, euler #=-20 (133425,399721,266276) : difference with theory (-20) = 0 CORRECTING DEFECT 8 (vertices=319, convex hull=205) After retessellation of defect 8, euler #=-19 (133444,399871,266408) : difference with theory (-19) = 0 CORRECTING DEFECT 9 (vertices=10, convex hull=22) After retessellation of defect 9, euler #=-18 (133446,399883,266419) : difference with theory (-18) = 0 CORRECTING DEFECT 10 (vertices=18, convex hull=47) After retessellation of defect 10, euler #=-17 (133455,399927,266455) : difference with theory (-17) = 0 CORRECTING DEFECT 11 (vertices=24, convex hull=59) After retessellation of defect 11, euler #=-16 (133467,399989,266506) : difference with theory (-16) = 0 CORRECTING DEFECT 12 (vertices=39, convex hull=57) After retessellation of defect 12, euler #=-15 (133476,400041,266550) : difference with theory (-15) = 0 CORRECTING DEFECT 13 (vertices=20, convex hull=25) After retessellation of defect 13, euler #=-14 (133479,400057,266564) : difference with theory (-14) = 0 CORRECTING DEFECT 14 (vertices=6, convex hull=21) After retessellation of defect 14, euler #=-13 (133479,400062,266570) : difference with theory (-13) = 0 CORRECTING DEFECT 15 (vertices=33, convex hull=61) After retessellation of defect 15, euler #=-12 (133493,400130,266625) : difference with theory (-12) = 0 CORRECTING DEFECT 16 (vertices=19, convex hull=28) After retessellation of defect 16, euler #=-11 (133497,400151,266643) : difference with theory (-11) = 0 CORRECTING DEFECT 17 (vertices=49, convex hull=30) After retessellation of defect 17, euler #=-10 (133501,400174,266663) : difference with theory (-10) = 0 CORRECTING DEFECT 18 (vertices=375, convex hull=184) After retessellation of defect 18, euler #=-9 (133528,400335,266798) : difference with theory (-9) = 0 CORRECTING DEFECT 19 (vertices=89, convex hull=30) After retessellation of defect 19, euler #=-8 (133541,400385,266836) : difference with theory (-8) = 0 CORRECTING DEFECT 20 (vertices=5, convex hull=25) Warning - incorrect dp selected!!!!(-91.844365 >= -91.844368 ) After retessellation of defect 20, euler #=-7 (133542,400394,266845) : difference with theory (-7) = 0 CORRECTING DEFECT 21 (vertices=6, convex hull=24) After retessellation of defect 21, euler #=-6 (133544,400407,266857) : difference with theory (-6) = 0 CORRECTING DEFECT 22 (vertices=23, convex hull=29) After retessellation of defect 22, euler #=-5 (133548,400432,266879) : difference with theory (-5) = 0 CORRECTING DEFECT 23 (vertices=24, convex hull=56) After retessellation of defect 23, euler #=-4 (133563,400500,266933) : difference with theory (-4) = 0 CORRECTING DEFECT 24 (vertices=153, convex hull=115) After retessellation of defect 24, euler #=-3 (133590,400631,267038) : difference with theory (-3) = 0 CORRECTING DEFECT 25 (vertices=79, convex hull=86) After retessellation of defect 25, euler #=-2 (133615,400742,267125) : difference with theory (-2) = 0 CORRECTING DEFECT 26 (vertices=64, convex hull=70) After retessellation of defect 26, euler #=-1 (133628,400810,267181) : difference with theory (-1) = 0 CORRECTING DEFECT 27 (vertices=14, convex hull=18) After retessellation of defect 27, euler #=0 (133629,400818,267189) : difference with theory (0) = 0 CORRECTING DEFECT 28 (vertices=58, convex hull=65) After retessellation of defect 28, euler #=1 (133650,400907,267258) : difference with theory (1) = 0 CORRECTING DEFECT 29 (vertices=44, convex hull=91) After retessellation of defect 29, euler #=2 (133676,401022,267348) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.23 (0.12-->13.02) (max @ vno 116218 --> 124800) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.23 (0.12-->13.02) (max @ vno 116218 --> 124800) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 114 mutations (35.4%), 208 crossovers (64.6%), 219 vertices were eliminated building final representation... 1518 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=133676, nf=267348, ne=401022, g=0) writing corrected surface to /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 32.0 minutes 0 defective edges removing intersecting faces 000: 180 intersecting 001: 6 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 133676 - 401022 + 267348 = 2 --> 0 holes F =2V-4: 267348 = 267352-4 (0) 2E=3F: 802044 = 802044 (0) total defect index = 0 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 11 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Sat Nov 14 03:10:42 CET 2015 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs B_LU_02_MRI_E_T0 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 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/filled.mgz... reading volume /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/brain.finalsurfs.mgz... reading volume /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/wm.mgz... 12511 bright wm thresholded. 1915 bright non-wm voxels segmented. reading original surface position from /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/rh.orig... computing class statistics... border white: 246839 voxels (1.47%) border gray 281365 voxels (1.68%) WM (95.0): 96.1 +- 7.9 [70.0 --> 110.0] GM (83.0) : 81.2 +- 11.4 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 58.6 (was 70) setting MAX_BORDER_WHITE to 111.9 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 47.3 (was 40) setting MAX_GRAY to 96.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.3 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 35.9 (was 40) repositioning cortical surface to gray/white boundary reading volume /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.04-->5.38) (max @ vno 116218 --> 133585) face area 0.28 +- 0.12 (0.00-->4.92) mean absolute distance = 0.76 +- 0.92 3945 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=104, GM=70 mean inside = 95.5, mean outside = 77.8 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group mean border=80.7, 38 (38) missing vertices, mean dist 0.4 [0.6 (%31.3)->0.8 (%68.7))] %62 local maxima, %33 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=biosr, 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 0.92 +- 0.26 (0.09-->5.75) (max @ vno 49088 --> 49087) face area 0.28 +- 0.14 (0.00-->4.73) mean absolute distance = 0.37 +- 0.60 3073 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5383983.0, rms=10.78 001: dt: 0.5000, sse=5731259.0, rms=7.867 (0.000%) 002: dt: 0.5000, sse=5960316.0, rms=6.018 (0.000%) 003: dt: 0.5000, sse=6207681.5, rms=4.800 (0.000%) 004: dt: 0.5000, sse=6375355.5, rms=4.018 (0.000%) 005: dt: 0.5000, sse=6554167.0, rms=3.563 (0.000%) 006: dt: 0.5000, sse=6638873.0, rms=3.308 (0.000%) 007: dt: 0.5000, sse=6726084.5, rms=3.181 (0.000%) 008: dt: 0.5000, sse=6714110.5, rms=3.095 (0.000%) rms = 3.05, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=6746147.5, rms=3.055 (0.000%) 010: dt: 0.2500, sse=4051521.5, rms=2.061 (0.000%) 011: dt: 0.2500, sse=3721497.5, rms=1.834 (0.000%) 012: dt: 0.2500, sse=3595581.8, rms=1.780 (0.000%) rms = 1.75, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=3557403.5, rms=1.753 (0.000%) rms = 1.72, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=3507322.8, rms=1.722 (0.000%) positioning took 2.4 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group mean border=84.1, 60 (11) missing vertices, mean dist -0.2 [0.4 (%74.9)->0.3 (%25.1))] %74 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=biosr, 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 0.91 +- 0.25 (0.11-->5.98) (max @ vno 49088 --> 49087) face area 0.35 +- 0.17 (0.00-->6.70) mean absolute distance = 0.26 +- 0.37 3021 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4156103.5, rms=4.82 015: dt: 0.5000, sse=4446804.0, rms=2.961 (0.000%) 016: dt: 0.5000, sse=4818767.0, rms=2.782 (0.000%) 017: dt: 0.5000, sse=5281498.5, rms=2.629 (0.000%) rms = 2.89, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=4321357.0, rms=1.908 (0.000%) 019: dt: 0.2500, sse=3983290.0, rms=1.576 (0.000%) 020: dt: 0.2500, sse=3858499.5, rms=1.468 (0.000%) rms = 1.44, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=3800422.2, rms=1.439 (0.000%) rms = 1.41, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=3760975.5, rms=1.407 (0.000%) positioning took 1.4 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=86.7, 51 (3) missing vertices, mean dist -0.2 [0.3 (%74.4)->0.2 (%25.6))] %84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=biosr, 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 0.90 +- 0.25 (0.06-->6.08) (max @ vno 49088 --> 49087) face area 0.34 +- 0.16 (0.00-->6.59) mean absolute distance = 0.20 +- 0.30 2680 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3992312.5, rms=3.46 023: dt: 0.5000, sse=4283659.0, rms=2.351 (0.000%) rms = 2.54, time step reduction 1 of 3 to 0.250... 024: dt: 0.2500, sse=4019741.0, rms=1.697 (0.000%) 025: dt: 0.2500, sse=3908269.8, rms=1.359 (0.000%) 026: dt: 0.2500, sse=3874333.8, rms=1.273 (0.000%) rms = 1.28, time step reduction 2 of 3 to 0.125... rms = 1.26, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=3854177.5, rms=1.259 (0.000%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group mean border=87.6, 57 (2) missing vertices, mean dist -0.0 [0.2 (%58.1)->0.2 (%41.9))] %88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=biosr, 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 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=3871363.0, rms=1.67 rms = 1.63, time step reduction 1 of 3 to 0.250... 028: dt: 0.5000, sse=4770623.5, rms=1.632 (0.000%) 029: dt: 0.2500, sse=4186594.0, rms=1.191 (0.000%) 030: dt: 0.2500, sse=4300061.5, rms=1.050 (0.000%) rms = 1.08, time step reduction 2 of 3 to 0.125... rms = 1.02, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=4275306.0, rms=1.022 (0.000%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 11 non-cortical segments detected only using segment with 1931 vertices erasing segment 1 (vno[0] = 55169) erasing segment 2 (vno[0] = 57576) erasing segment 3 (vno[0] = 59686) erasing segment 4 (vno[0] = 78061) erasing segment 5 (vno[0] = 86381) erasing segment 6 (vno[0] = 93703) erasing segment 7 (vno[0] = 94723) erasing segment 8 (vno[0] = 96831) erasing segment 9 (vno[0] = 103430) erasing segment 10 (vno[0] = 103454) writing cortex label to /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/label/rh.cortex.label... writing curvature file /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/rh.curv writing smoothed area to rh.area writing curvature file /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/rh.area vertex spacing 0.90 +- 0.25 (0.05-->6.11) (max @ vno 49088 --> 49087) face area 0.34 +- 0.16 (0.00-->6.30) refinement took 9.0 minutes #-------------------------------------------- #@# Smooth2 rh Sat Nov 14 03:19:41 CET 2015 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/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 Sat Nov 14 03:19:48 CET 2015 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 46.3 mm, total surface area = 81962 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.114 (target=0.015) step 005: RMS=0.079 (target=0.015) step 010: RMS=0.058 (target=0.015) step 015: RMS=0.047 (target=0.015) step 020: RMS=0.039 (target=0.015) step 025: RMS=0.033 (target=0.015) step 030: RMS=0.027 (target=0.015) step 035: RMS=0.023 (target=0.015) step 040: RMS=0.020 (target=0.015) step 045: RMS=0.018 (target=0.015) step 050: RMS=0.016 (target=0.015) inflation complete. inflation took 0.8 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 142 vertices thresholded to be in k1 ~ [-0.22 0.32], k2 ~ [-0.09 0.10] total integrated curvature = 0.590*4pi (7.417) --> 0 handles ICI = 1.7, FI = 11.4, variation=191.099 116 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 = 0.001 136 vertices thresholded to be in [-0.13 0.16] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.017, std = 0.025 done. #----------------------------------------- #@# Curvature Stats rh Sat Nov 14 03:22:46 CET 2015 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm B_LU_02_MRI_E_T0 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 [ B_LU_02_MRI_E_T0/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 [ 218 ] Gb_filter = 0 WARN: S lookup min: -0.517653 WARN: S explicit min: 0.000000 vertex = 661 #-------------------------------------------- #@# Sphere rh Sat Nov 14 03:22:53 CET 2015 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/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=biosr, 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 %19.12 pass 1: epoch 2 of 3 starting distance error %19.05 unfolding complete - removing small folds... starting distance error %18.97 removing remaining folds... final distance error %18.99 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/rh.sphere spherical transformation took 0.99 hours #-------------------------------------------- #@# Surf Reg rh Sat Nov 14 04:22:04 CET 2015 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/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=biosr, 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=biosr, 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 = 0.585 curvature mean = 0.019, std = 0.934 curvature mean = 0.022, std = 0.855 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 0.00, 0.00) sse = 345052.2, tmin=1.4294 d=32.00 min @ (-8.00, 0.00, 8.00) sse = 265375.2, tmin=2.5971 d=16.00 min @ (0.00, 0.00, -4.00) sse = 246551.1, tmin=3.8744 d=4.00 min @ (0.00, 0.00, 1.00) sse = 245199.3, tmin=7.2365 d=1.00 min @ (0.00, 0.00, -0.25) sse = 245054.5, tmin=10.5586 d=0.50 min @ (-0.12, 0.00, 0.00) sse = 245029.7, tmin=12.0637 tol=1.0e+00, sigma=0.5, host=biosr, 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 12.06 min curvature mean = 0.002, std = 0.948 curvature mean = 0.011, std = 0.940 curvature mean = 0.000, std = 0.959 curvature mean = 0.005, std = 0.974 curvature mean = -0.002, std = 0.960 curvature mean = 0.002, std = 0.989 2 Reading smoothwm curvature mean = -0.028, std = 0.288 curvature mean = 0.004, std = 0.070 curvature mean = 0.069, std = 0.354 curvature mean = 0.005, std = 0.084 curvature mean = 0.035, std = 0.547 curvature mean = 0.005, std = 0.090 curvature mean = 0.019, std = 0.688 curvature mean = 0.006, std = 0.092 curvature mean = 0.006, std = 0.799 MRISregister() return, current seed 0 writing registered surface to ../surf/rh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white rh Sat Nov 14 05:02:39 CET 2015 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 Sat Nov 14 05:02:42 CET 2015 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/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 Sat Nov 14 05:02:45 CET 2015 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 B_LU_02_MRI_E_T0 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... 1067 labels changed using aseg relabeling using gibbs priors... 000: 2823 changed, 133676 examined... 001: 656 changed, 12262 examined... 002: 174 changed, 3569 examined... 003: 55 changed, 1088 examined... 004: 22 changed, 330 examined... 005: 14 changed, 137 examined... 006: 5 changed, 72 examined... 007: 3 changed, 23 examined... 008: 3 changed, 15 examined... 009: 1 changed, 13 examined... 010: 0 changed, 5 examined... 202 labels changed using aseg 000: 93 total segments, 56 labels (328 vertices) changed 001: 38 total segments, 1 labels (1 vertices) changed 002: 37 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 30 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1760 vertices marked for relabeling... 1760 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 1 minutes and 25 seconds. #-------------------------------------------- #@# Make Pial Surf rh Sat Nov 14 05:04:11 CET 2015 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs B_LU_02_MRI_E_T0 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 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/filled.mgz... reading volume /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/brain.finalsurfs.mgz... reading volume /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/wm.mgz... 12511 bright wm thresholded. 1915 bright non-wm voxels segmented. reading original surface position from /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/rh.orig... computing class statistics... border white: 246839 voxels (1.47%) border gray 281365 voxels (1.68%) WM (95.0): 96.1 +- 7.9 [70.0 --> 110.0] GM (83.0) : 81.2 +- 11.4 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 58.6 (was 70) setting MAX_BORDER_WHITE to 111.9 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 47.3 (was 40) setting MAX_GRAY to 96.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.3 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 35.9 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=104, GM=70 mean inside = 95.5, mean outside = 77.8 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 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.04-->5.38) (max @ vno 116218 --> 133585) face area 0.28 +- 0.12 (0.00-->4.92) mean absolute distance = 0.76 +- 0.92 3994 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 2 with 319 points - only 0.00% unknown deleting segment 6 with 85 points - only 0.00% unknown deleting segment 7 with 16 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown mean border=80.7, 39 (39) missing vertices, mean dist 0.4 [0.6 (%31.3)->0.8 (%68.7))] %63 local maxima, %33 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=biosr, 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 0.92 +- 0.26 (0.09-->5.75) (max @ vno 49088 --> 49087) face area 0.28 +- 0.13 (0.00-->4.73) mean absolute distance = 0.38 +- 0.60 3105 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5391273.0, rms=10.76 001: dt: 0.5000, sse=5743182.0, rms=7.857 (0.000%) 002: dt: 0.5000, sse=5975386.0, rms=6.010 (0.000%) 003: dt: 0.5000, sse=6223704.5, rms=4.794 (0.000%) 004: dt: 0.5000, sse=6392990.5, rms=4.014 (0.000%) 005: dt: 0.5000, sse=6574286.5, rms=3.560 (0.000%) 006: dt: 0.5000, sse=6658433.0, rms=3.306 (0.000%) 007: dt: 0.5000, sse=6745777.0, rms=3.179 (0.000%) 008: dt: 0.5000, sse=6732655.5, rms=3.093 (0.000%) rms = 3.05, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=6767111.0, rms=3.053 (0.000%) 010: dt: 0.2500, sse=4064140.8, rms=2.060 (0.000%) 011: dt: 0.2500, sse=3733632.2, rms=1.834 (0.000%) 012: dt: 0.2500, sse=3607709.0, rms=1.780 (0.000%) rms = 1.75, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=3570027.8, rms=1.753 (0.000%) rms = 1.72, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=3519326.2, rms=1.722 (0.000%) positioning took 2.4 minutes inhibiting deformation at non-cortical midline structures... deleting segment 3 with 6 points - only 0.00% unknown deleting segment 4 with 254 points - only 0.00% unknown deleting segment 8 with 38 points - only 0.00% unknown deleting segment 9 with 18 points - only 0.00% unknown deleting segment 10 with 19 points - only 0.00% unknown deleting segment 11 with 11 points - only 0.00% unknown mean border=84.1, 62 (12) missing vertices, mean dist -0.2 [0.4 (%74.9)->0.3 (%25.1))] %74 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=biosr, 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 0.91 +- 0.25 (0.11-->5.98) (max @ vno 49088 --> 49087) face area 0.35 +- 0.17 (0.00-->6.70) mean absolute distance = 0.26 +- 0.37 3060 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4170992.5, rms=4.82 015: dt: 0.5000, sse=4461503.0, rms=2.960 (0.000%) 016: dt: 0.5000, sse=4836114.0, rms=2.780 (0.000%) 017: dt: 0.5000, sse=5298210.0, rms=2.627 (0.000%) rms = 2.89, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=4336335.0, rms=1.907 (0.000%) 019: dt: 0.2500, sse=3998087.5, rms=1.575 (0.000%) 020: dt: 0.2500, sse=3872799.0, rms=1.467 (0.000%) rms = 1.44, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=3814942.5, rms=1.439 (0.000%) rms = 1.41, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=3775681.0, rms=1.407 (0.000%) positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 334 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 84 points - only 0.00% unknown deleting segment 4 with 19 points - only 0.00% unknown mean border=86.7, 57 (4) missing vertices, mean dist -0.2 [0.3 (%74.4)->0.2 (%25.6))] %85 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=biosr, 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 0.90 +- 0.25 (0.06-->6.08) (max @ vno 49088 --> 49087) face area 0.34 +- 0.16 (0.00-->6.59) mean absolute distance = 0.21 +- 0.30 2736 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4007404.0, rms=3.46 023: dt: 0.5000, sse=4298775.5, rms=2.350 (0.000%) rms = 2.54, time step reduction 1 of 3 to 0.250... 024: dt: 0.2500, sse=4035073.5, rms=1.697 (0.000%) 025: dt: 0.2500, sse=3923714.0, rms=1.359 (0.000%) 026: dt: 0.2500, sse=3891191.0, rms=1.273 (0.000%) rms = 1.28, time step reduction 2 of 3 to 0.125... rms = 1.26, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=3870873.5, rms=1.259 (0.000%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... deleting segment 1 with 340 points - only 0.00% unknown deleting segment 2 with 87 points - only 0.00% unknown deleting segment 3 with 19 points - only 0.00% unknown mean border=87.6, 63 (2) missing vertices, mean dist -0.0 [0.2 (%58.1)->0.2 (%41.9))] %88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=biosr, 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=3888356.5, rms=1.67 rms = 1.63, time step reduction 1 of 3 to 0.250... 028: dt: 0.5000, sse=4791097.5, rms=1.631 (0.000%) 029: dt: 0.2500, sse=4206568.0, rms=1.191 (0.000%) 030: dt: 0.2500, sse=4320825.5, rms=1.051 (0.000%) rms = 1.09, time step reduction 2 of 3 to 0.125... rms = 1.02, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=4296048.5, rms=1.023 (0.000%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... smoothing surface for 5 iterations... mean border=60.0, 48 (48) missing vertices, mean dist 1.7 [0.1 (%0.0)->2.4 (%100.0))] %23 local maxima, %47 large gradients and %26 min vals, 1703 gradients ignored tol=1.0e-04, sigma=2.0, host=biosr, 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=22410104.0, rms=27.77 001: dt: 0.5000, sse=17204470.0, rms=23.826 (0.000%) 002: dt: 0.5000, sse=13341022.0, rms=20.444 (0.000%) 003: dt: 0.5000, sse=10654898.0, rms=17.648 (0.000%) 004: dt: 0.5000, sse=8936058.0, rms=15.359 (0.000%) 005: dt: 0.5000, sse=7814808.5, rms=13.491 (0.000%) 006: dt: 0.5000, sse=7109762.5, rms=11.970 (0.000%) 007: dt: 0.5000, sse=6638663.5, rms=10.641 (0.000%) 008: dt: 0.5000, sse=6350850.5, rms=9.407 (0.000%) 009: dt: 0.5000, sse=6126020.5, rms=8.255 (0.000%) 010: dt: 0.5000, sse=6015264.0, rms=7.194 (0.000%) 011: dt: 0.5000, sse=5980158.5, rms=6.240 (0.000%) 012: dt: 0.5000, sse=6019770.0, rms=5.442 (0.000%) 013: dt: 0.5000, sse=6102534.0, rms=4.833 (0.000%) 014: dt: 0.5000, sse=6232331.0, rms=4.454 (0.000%) 015: dt: 0.5000, sse=6269312.0, rms=4.192 (0.000%) 016: dt: 0.5000, sse=6370833.5, rms=4.042 (0.000%) 017: dt: 0.5000, sse=6367376.5, rms=3.914 (0.000%) rms = 3.86, time step reduction 1 of 3 to 0.250... 018: dt: 0.5000, sse=6401126.5, rms=3.865 (0.000%) 019: dt: 0.2500, sse=4468090.5, rms=3.139 (0.000%) 020: dt: 0.2500, sse=4269997.0, rms=2.947 (0.000%) rms = 2.91, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=4172123.8, rms=2.915 (0.000%) 022: dt: 0.1250, sse=3994470.0, rms=2.820 (0.000%) rms = 2.81, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=3969822.0, rms=2.809 (0.000%) positioning took 3.9 minutes mean border=57.4, 862 (5) missing vertices, mean dist 0.2 [0.2 (%43.1)->0.5 (%56.9))] %43 local maxima, %32 large gradients and %20 min vals, 520 gradients ignored tol=1.0e-04, sigma=1.0, host=biosr, 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=4692883.0, rms=5.24 024: dt: 0.5000, sse=4777996.5, rms=3.987 (0.000%) 025: dt: 0.5000, sse=6029823.0, rms=3.882 (0.000%) rms = 3.92, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=5036544.5, rms=3.210 (0.000%) 027: dt: 0.2500, sse=4641854.5, rms=2.921 (0.000%) 028: dt: 0.2500, sse=4604134.5, rms=2.860 (0.000%) rms = 2.83, time step reduction 2 of 3 to 0.125... 029: dt: 0.2500, sse=4566439.0, rms=2.826 (0.000%) 030: dt: 0.1250, sse=4425478.0, rms=2.725 (0.000%) rms = 2.71, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=4418564.5, rms=2.708 (0.000%) positioning took 1.5 minutes mean border=55.7, 1101 (4) missing vertices, mean dist 0.1 [0.2 (%38.1)->0.3 (%61.9))] %57 local maxima, %19 large gradients and %20 min vals, 630 gradients ignored tol=1.0e-04, sigma=0.5, host=biosr, 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=4589696.5, rms=3.62 rms = 3.62, time step reduction 1 of 3 to 0.250... 032: dt: 0.5000, sse=4850070.0, rms=3.617 (0.000%) 033: dt: 0.2500, sse=4780177.5, rms=2.852 (0.000%) 034: dt: 0.2500, sse=4789834.0, rms=2.683 (0.000%) rms = 2.67, time step reduction 2 of 3 to 0.125... 035: dt: 0.2500, sse=4766687.5, rms=2.671 (0.000%) 036: dt: 0.1250, sse=4637701.5, rms=2.514 (0.000%) rms = 2.49, time step reduction 3 of 3 to 0.062... 037: dt: 0.1250, sse=4628155.5, rms=2.489 (0.000%) positioning took 1.0 minutes mean border=54.8, 2451 (4) missing vertices, mean dist 0.1 [0.2 (%44.7)->0.3 (%55.3))] %61 local maxima, %14 large gradients and %19 min vals, 498 gradients ignored tol=1.0e-04, sigma=0.2, host=biosr, 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 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=4662207.5, rms=2.74 rms = 3.18, time step reduction 1 of 3 to 0.250... 038: dt: 0.2500, sse=4575343.5, rms=2.549 (0.000%) 039: dt: 0.2500, sse=4703253.0, rms=2.480 (0.000%) rms = 2.46, time step reduction 2 of 3 to 0.125... 040: dt: 0.2500, sse=4749090.0, rms=2.459 (0.000%) 041: dt: 0.1250, sse=4671294.0, rms=2.385 (0.000%) rms = 2.37, time step reduction 3 of 3 to 0.062... 042: dt: 0.1250, sse=4682193.0, rms=2.367 (0.000%) positioning took 1.0 minutes writing curvature file /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/rh.area.pial vertex spacing 1.01 +- 0.42 (0.04-->6.37) (max @ vno 86442 --> 86441) face area 0.41 +- 0.30 (0.00-->7.40) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 133676 vertices processed 25000 of 133676 vertices processed 50000 of 133676 vertices processed 75000 of 133676 vertices processed 100000 of 133676 vertices processed 125000 of 133676 vertices processed 0 of 133676 vertices processed 25000 of 133676 vertices processed 50000 of 133676 vertices processed 75000 of 133676 vertices processed 100000 of 133676 vertices processed 125000 of 133676 vertices processed thickness calculation complete, 403:633 truncations. 32336 vertices at 0 distance 89188 vertices at 1 distance 82313 vertices at 2 distance 35953 vertices at 3 distance 11172 vertices at 4 distance 3446 vertices at 5 distance 1169 vertices at 6 distance 392 vertices at 7 distance 155 vertices at 8 distance 83 vertices at 9 distance 48 vertices at 10 distance 29 vertices at 11 distance 17 vertices at 12 distance 22 vertices at 13 distance 17 vertices at 14 distance 10 vertices at 15 distance 15 vertices at 16 distance 7 vertices at 17 distance 15 vertices at 18 distance 19 vertices at 19 distance 12 vertices at 20 distance writing curvature file /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/rh.thickness positioning took 19.1 minutes #-------------------------------------------- #@# Surf Volume rh Sat Nov 14 05:23:15 CET 2015 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.volume rh.area.mid mul rh.thickness Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# WM/GM Contrast rh Sat Nov 14 05:23:16 CET 2015 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/scripts pctsurfcon --s B_LU_02_MRI_E_T0 --rh-only Log file is /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/scripts/pctsurfcon.log Sat Nov 14 05:23:16 CET 2015 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects cd /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/scripts /usr/local//freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux biosrv1 2.6.32-573.7.1.el6.x86_64 #1 SMP Tue Sep 22 22:00:00 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local//freesurfer mri_vol2surf --mov /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/tmp.pctsurfcon.8702/rh.wm.mgh --regheader B_LU_02_MRI_E_T0 --cortex srcvol = /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/orig.mgz as target reference. Loading label /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/label/rh.cortex.label Reading surface /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/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 = 72969 Masking with /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/label/rh.cortex.label Writing to /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/tmp.pctsurfcon.8702/rh.wm.mgh Dim: 133676 1 1 mri_vol2surf --mov /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/tmp.pctsurfcon.8702/rh.gm.mgh --projfrac 0.3 --regheader B_LU_02_MRI_E_T0 --cortex srcvol = /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/orig.mgz as target reference. Loading label /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/label/rh.cortex.label Reading surface /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/rh.white Done reading source surface Reading thickness /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/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 = 88508 Masking with /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/label/rh.cortex.label Writing to /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/tmp.pctsurfcon.8702/rh.gm.mgh Dim: 133676 1 1 mri_concat /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/tmp.pctsurfcon.8702/rh.wm.mgh /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/tmp.pctsurfcon.8702/rh.gm.mgh --paired-diff-norm --mul 100 --o /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/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 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/rh.w-g.pct.mgh mri_segstats --in /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/rh.w-g.pct.mgh --annot B_LU_02_MRI_E_T0 rh aparc --sum /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/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 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/rh.w-g.pct.mgh --annot B_LU_02_MRI_E_T0 rh aparc --sum /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/stats/rh.w-g.pct.stats --snr sysname Linux hostname biosrv1 machine x86_64 user root 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 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/rh.w-g.pct.mgh Vertex Area is 0.668866 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 2000 unknown 0 0.000 1 2001 bankssts 1522 1051.977 2 2002 caudalanteriorcingulate 1056 701.147 3 2003 caudalmiddlefrontal 3722 2554.960 4 2004 corpuscallosum 0 0.000 5 2005 cuneus 2019 1287.991 6 2006 entorhinal 488 345.394 7 2007 fusiform 4647 3143.718 8 2008 inferiorparietal 8054 5460.723 9 2009 inferiortemporal 4478 3043.860 10 2010 isthmuscingulate 1237 782.874 11 2011 lateraloccipital 5749 3770.276 12 2012 lateralorbitofrontal 3898 2573.655 13 2013 lingual 4038 2673.963 14 2014 medialorbitofrontal 2754 1894.734 15 2015 middletemporal 5033 3392.055 16 2016 parahippocampal 938 638.307 17 2017 paracentral 2870 1813.841 18 2018 parsopercularis 1911 1317.873 19 2019 parsorbitalis 1042 701.442 20 2020 parstriangularis 1823 1248.721 21 2021 pericalcarine 2006 1292.619 22 2022 postcentral 6193 4049.092 23 2023 posteriorcingulate 1971 1349.496 24 2024 precentral 8058 5131.126 25 2025 precuneus 5683 3832.667 26 2026 rostralanteriorcingulate 1385 907.206 27 2027 rostralmiddlefrontal 8671 5996.673 28 2028 superiorfrontal 10832 7377.152 29 2029 superiorparietal 8620 5719.217 30 2030 superiortemporal 5298 3582.649 31 2031 supramarginal 5066 3398.752 32 2032 frontalpole 435 304.309 33 2033 temporalpole 564 406.232 34 2034 transversetemporal 461 276.730 35 2035 insula 3391 2298.018 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats rh Sat Nov 14 05:23:29 CET 2015 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/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 B_LU_02_MRI_E_T0 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/rh.white... reading input pial surface /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/rh.pial... reading input white surface /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/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 1522 1052 2517 2.551 0.479 0.101 0.025 11 1.6 bankssts 1056 701 1965 2.700 0.541 0.148 0.045 18 2.1 caudalanteriorcingulate 3722 2555 7244 2.641 0.472 0.129 0.042 46 6.2 caudalmiddlefrontal 2019 1288 2505 1.681 0.467 0.157 0.048 33 4.1 cuneus 488 345 1742 3.279 0.838 0.169 0.133 14 3.0 entorhinal 4647 3144 9808 2.675 0.607 0.138 0.057 191 12.8 fusiform 8054 5461 15557 2.471 0.556 0.143 0.065 129 14.4 inferiorparietal 4478 3044 9989 2.695 0.654 0.145 0.054 77 9.9 inferiortemporal 1237 783 2228 2.584 0.827 0.155 0.070 23 2.8 isthmuscingulate 5749 3770 9324 2.224 0.579 0.159 0.057 107 12.2 lateraloccipital 3898 2574 7315 2.639 0.799 0.163 0.079 85 12.9 lateralorbitofrontal 4038 2674 5919 2.064 0.627 0.161 0.064 93 11.3 lingual 2754 1895 5062 2.398 0.704 0.170 0.271 130 9.5 medialorbitofrontal 5033 3392 11781 2.911 0.567 0.145 0.051 91 10.2 middletemporal 938 638 2193 2.906 0.642 0.104 0.026 7 0.9 parahippocampal 2870 1814 4546 2.276 0.570 0.117 0.034 29 4.1 paracentral 1911 1318 3656 2.637 0.517 0.132 0.037 22 2.7 parsopercularis 1042 701 2373 2.589 0.599 0.169 0.073 29 3.1 parsorbitalis 1823 1249 3848 2.678 0.588 0.142 0.040 22 3.1 parstriangularis 2006 1293 1906 1.523 0.406 0.139 0.052 34 4.4 pericalcarine 6193 4049 8668 1.946 0.655 0.124 0.036 67 9.2 postcentral 1971 1349 3858 2.549 0.676 0.158 0.062 39 4.1 posteriorcingulate 8058 5131 15131 2.631 0.542 0.116 0.039 111 14.5 precentral 5683 3833 9877 2.408 0.540 0.148 0.048 95 10.9 precuneus 1385 907 2917 2.985 0.529 0.143 0.048 22 3.0 rostralanteriorcingulate 8671 5997 16084 2.276 0.604 0.163 0.066 194 24.4 rostralmiddlefrontal 10832 7377 22626 2.769 0.589 0.144 0.057 223 26.1 superiorfrontal 8620 5719 13311 2.075 0.493 0.139 0.040 118 14.0 superiorparietal 5298 3583 11403 2.787 0.597 0.113 0.031 56 6.4 superiortemporal 5066 3399 9432 2.526 0.549 0.152 0.058 95 11.2 supramarginal 435 304 954 2.469 0.679 0.208 0.102 14 1.8 frontalpole 564 406 2322 3.825 0.573 0.159 0.059 9 1.3 temporalpole 461 277 835 2.668 0.320 0.130 0.038 6 0.7 transversetemporal 3391 2298 6769 3.037 0.908 0.124 0.062 58 7.7 insula #----------------------------------------- #@# Cortical Parc 2 rh Sat Nov 14 05:24:10 CET 2015 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 B_LU_02_MRI_E_T0 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... 17 labels changed using aseg relabeling using gibbs priors... 000: 9480 changed, 133676 examined... 001: 2206 changed, 36486 examined... 002: 703 changed, 11400 examined... 003: 297 changed, 3930 examined... 004: 135 changed, 1668 examined... 005: 72 changed, 805 examined... 006: 47 changed, 413 examined... 007: 23 changed, 245 examined... 008: 16 changed, 145 examined... 009: 8 changed, 96 examined... 010: 6 changed, 37 examined... 011: 4 changed, 35 examined... 012: 6 changed, 26 examined... 013: 4 changed, 34 examined... 014: 5 changed, 25 examined... 015: 3 changed, 28 examined... 016: 1 changed, 23 examined... 017: 0 changed, 5 examined... 9 labels changed using aseg 000: 299 total segments, 216 labels (2485 vertices) changed 001: 104 total segments, 21 labels (80 vertices) changed 002: 83 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 123 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 928 vertices marked for relabeling... 928 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 1 minutes and 55 seconds. #----------------------------------------- #@# Parcellation Stats 2 rh Sat Nov 14 05:26:06 CET 2015 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/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 B_LU_02_MRI_E_T0 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/rh.white... reading input pial surface /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/rh.pial... reading input white surface /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/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 819 558 1696 2.374 0.706 0.186 0.095 46 3.7 G_and_S_frontomargin 849 576 1520 2.457 0.543 0.153 0.058 14 1.4 G_and_S_occipital_inf 1754 1001 2747 2.295 0.583 0.130 0.051 36 3.9 G_and_S_paracentral 1186 836 2240 2.517 0.469 0.160 0.048 19 2.3 G_and_S_subcentral 1192 818 2458 2.386 0.628 0.196 0.094 34 4.8 G_and_S_transv_frontopol 2861 1937 5390 2.711 0.528 0.136 0.047 37 5.6 G_and_S_cingul-Ant 1836 1270 3872 2.890 0.514 0.143 0.044 26 3.2 G_and_S_cingul-Mid-Ant 1829 1272 3361 2.647 0.494 0.145 0.079 94 7.1 G_and_S_cingul-Mid-Post 592 368 1412 2.863 0.566 0.193 0.081 16 2.2 G_cingul-Post-dorsal 189 113 407 3.270 0.623 0.165 0.078 4 0.5 G_cingul-Post-ventral 1992 1227 2440 1.667 0.464 0.151 0.049 36 4.2 G_cuneus 1193 832 3128 2.870 0.431 0.160 0.051 23 2.5 G_front_inf-Opercular 313 205 832 3.043 0.554 0.167 0.047 5 0.6 G_front_inf-Orbital 871 603 2247 2.796 0.556 0.170 0.054 16 1.9 G_front_inf-Triangul 5225 3586 11543 2.523 0.569 0.162 0.066 112 14.0 G_front_middle 6664 4438 15860 2.874 0.584 0.162 0.095 171 18.0 G_front_sup 442 311 1236 3.941 0.817 0.137 0.112 18 2.0 G_Ins_lg_and_S_cent_ins 603 366 1643 3.399 0.615 0.171 0.106 20 2.7 G_insular_short 2219 1431 5046 2.742 0.470 0.172 0.067 52 5.5 G_occipital_middle 1806 1162 3105 2.165 0.500 0.158 0.045 31 3.4 G_occipital_sup 1817 1156 4307 2.788 0.583 0.152 0.089 162 8.5 G_oc-temp_lat-fusifor 2551 1652 3824 2.017 0.665 0.171 0.066 50 6.7 G_oc-temp_med-Lingual 1299 879 3596 3.078 0.898 0.134 0.074 20 4.1 G_oc-temp_med-Parahip 2556 1695 5848 2.634 0.799 0.181 0.095 77 10.4 G_orbital 3062 2097 7561 2.746 0.570 0.178 0.123 84 8.1 G_pariet_inf-Angular 2411 1619 5450 2.694 0.519 0.176 0.071 61 6.8 G_pariet_inf-Supramar 2697 1807 5171 2.256 0.492 0.148 0.046 47 5.0 G_parietal_sup 2206 1402 3591 2.028 0.549 0.123 0.036 25 3.2 G_postcentral 3122 1815 6846 2.858 0.486 0.113 0.040 42 5.2 G_precentral 2737 1852 5841 2.562 0.521 0.166 0.060 65 6.8 G_precuneus 577 477 1397 2.175 0.627 0.245 0.748 51 3.4 G_rectus 604 371 886 2.264 0.839 0.124 0.068 11 1.4 G_subcallosal 360 209 680 2.675 0.395 0.134 0.039 5 0.6 G_temp_sup-G_T_transv 1907 1244 4878 2.834 0.579 0.138 0.046 34 3.4 G_temp_sup-Lateral 890 624 2305 3.196 0.668 0.101 0.026 5 1.0 G_temp_sup-Plan_polar 791 539 1442 2.487 0.485 0.120 0.032 8 1.0 G_temp_sup-Plan_tempo 2357 1626 6089 2.810 0.673 0.163 0.069 54 6.7 G_temporal_inf 3196 2139 8228 2.910 0.563 0.152 0.057 70 7.3 G_temporal_middle 305 216 521 2.611 0.516 0.108 0.024 2 0.2 Lat_Fis-ant-Horizont 191 139 276 2.050 0.544 0.115 0.026 1 0.2 Lat_Fis-ant-Vertical 1323 896 1889 2.612 0.487 0.122 0.032 11 1.6 Lat_Fis-post 2943 1921 4178 1.875 0.504 0.168 0.063 65 7.2 Pole_occipital 1695 1171 5765 3.441 0.602 0.153 0.056 30 3.8 Pole_temporal 2029 1343 2243 1.838 0.679 0.144 0.060 53 5.8 S_calcarine 3203 2119 3533 1.835 0.638 0.102 0.034 29 5.5 S_central 1537 1051 2043 2.006 0.492 0.102 0.026 10 1.7 S_cingul-Marginalis 473 314 780 3.006 0.680 0.115 0.073 3 0.8 S_circular_insula_ant 1110 745 1955 3.038 0.691 0.077 0.016 4 0.8 S_circular_insula_inf 1431 955 2291 2.775 0.459 0.114 0.031 10 1.7 S_circular_insula_sup 797 576 1619 2.444 0.598 0.126 0.038 10 1.3 S_collat_transv_ant 566 376 694 1.845 0.364 0.136 0.036 6 0.9 S_collat_transv_post 1803 1246 2836 2.283 0.513 0.121 0.033 16 2.3 S_front_inf 2101 1464 2979 2.061 0.578 0.144 0.046 24 4.0 S_front_middle 3266 2285 5333 2.393 0.501 0.124 0.038 37 5.5 S_front_sup 655 435 846 2.172 0.381 0.113 0.030 5 0.8 S_interm_prim-Jensen 3160 2113 4012 1.987 0.480 0.121 0.033 31 4.0 S_intrapariet_and_P_trans 705 491 918 2.174 0.409 0.121 0.029 5 0.8 S_oc_middle_and_Lunatus 1714 1158 2266 2.041 0.496 0.125 0.031 15 2.2 S_oc_sup_and_transversal 416 286 705 2.411 0.505 0.139 0.040 5 0.6 S_occipital_ant 1160 804 1924 2.518 0.503 0.127 0.031 11 1.6 S_oc-temp_lat 2134 1499 3294 2.425 0.503 0.111 0.028 13 2.5 S_oc-temp_med_and_Lingual 359 248 574 2.351 0.600 0.147 0.051 5 0.8 S_orbital_lateral 1108 751 1505 2.217 0.800 0.117 0.050 15 2.2 S_orbital_med-olfact 1412 948 2480 2.606 0.723 0.155 0.052 21 3.1 S_orbital-H_Shaped 2062 1396 2820 2.200 0.559 0.150 0.044 27 3.6 S_parieto_occipital 1603 1024 2144 2.458 0.905 0.147 0.052 27 3.0 S_pericallosal 2679 1806 3281 1.983 0.480 0.123 0.036 31 3.6 S_postcentral 2115 1434 3402 2.674 0.463 0.121 0.029 17 2.6 S_precentral-inf-part 1167 790 1828 2.412 0.489 0.099 0.022 7 1.2 S_precentral-sup-part 347 232 528 2.326 0.674 0.150 0.040 4 0.6 S_suborbital 1178 800 1916 2.366 0.511 0.143 0.062 16 2.1 S_subparietal 1402 944 1999 2.558 0.471 0.122 0.032 12 1.8 S_temporal_inf 5958 4051 9731 2.490 0.535 0.106 0.027 40 6.4 S_temporal_sup 231 178 432 2.469 0.312 0.104 0.020 1 0.2 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 rh Sat Nov 14 05:26:47 CET 2015 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 B_LU_02_MRI_E_T0 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... 1098 labels changed using aseg relabeling using gibbs priors... 000: 2731 changed, 133676 examined... 001: 618 changed, 11661 examined... 002: 157 changed, 3383 examined... 003: 53 changed, 973 examined... 004: 19 changed, 302 examined... 005: 9 changed, 134 examined... 006: 7 changed, 56 examined... 007: 6 changed, 40 examined... 008: 5 changed, 35 examined... 009: 6 changed, 28 examined... 010: 5 changed, 34 examined... 011: 5 changed, 33 examined... 012: 2 changed, 26 examined... 013: 3 changed, 12 examined... 014: 1 changed, 17 examined... 015: 0 changed, 6 examined... 175 labels changed using aseg 000: 69 total segments, 36 labels (188 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 51 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 792 vertices marked for relabeling... 792 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas40.annot... classification took 1 minutes and 17 seconds. #----------------------------------------- #@# Parcellation Stats 3 rh Sat Nov 14 05:28:04 CET 2015 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/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 B_LU_02_MRI_E_T0 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot. reading volume /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/rh.white... reading input pial surface /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/rh.pial... reading input white surface /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/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 1069 709 2026 2.731 0.540 0.152 0.049 19 2.2 caudalanteriorcingulate 3736 2555 7261 2.645 0.473 0.129 0.042 46 6.3 caudalmiddlefrontal 2633 1683 3251 1.750 0.479 0.154 0.047 41 5.2 cuneus 525 363 1717 3.211 0.807 0.158 0.120 12 2.8 entorhinal 4177 2825 8656 2.655 0.603 0.139 0.060 187 12.2 fusiform 7607 5155 14733 2.482 0.558 0.145 0.067 126 13.9 inferiorparietal 4940 3367 11188 2.706 0.658 0.143 0.052 81 10.4 inferiortemporal 1258 796 2272 2.597 0.815 0.154 0.070 23 2.8 isthmuscingulate 5839 3832 9392 2.215 0.581 0.159 0.057 108 12.3 lateraloccipital 4418 2929 8435 2.554 0.815 0.165 0.083 124 15.4 lateralorbitofrontal 4058 2689 5953 2.066 0.625 0.162 0.064 93 11.3 lingual 2402 1676 4394 2.299 0.762 0.169 0.232 86 8.1 medialorbitofrontal 6289 4245 13843 2.834 0.579 0.136 0.046 99 11.6 middletemporal 909 618 2060 2.882 0.639 0.103 0.025 7 0.9 parahippocampal 2988 1886 4708 2.287 0.565 0.117 0.034 29 4.2 paracentral 2072 1427 3923 2.619 0.513 0.134 0.039 25 3.4 parsopercularis 1012 696 2138 2.563 0.605 0.149 0.050 22 2.1 parsorbitalis 1913 1311 3937 2.622 0.577 0.146 0.043 26 3.4 parstriangularis 1980 1274 1877 1.522 0.406 0.140 0.052 34 4.4 pericalcarine 6746 4420 9636 1.984 0.657 0.126 0.037 77 10.4 postcentral 2134 1456 4088 2.546 0.665 0.166 0.089 110 8.7 posteriorcingulate 7805 4953 14655 2.640 0.540 0.118 0.040 110 14.2 precentral 5838 3923 10163 2.389 0.548 0.150 0.049 100 11.5 precuneus 1598 1042 3314 2.968 0.526 0.144 0.049 26 3.3 rostralanteriorcingulate 5920 4104 10895 2.260 0.581 0.159 0.059 103 14.6 rostralmiddlefrontal 13741 9401 28326 2.676 0.624 0.148 0.070 264 32.0 superiorfrontal 7306 4876 11438 2.076 0.489 0.135 0.038 96 11.0 superiorparietal 7016 4790 16022 2.861 0.667 0.120 0.036 82 10.2 superiortemporal 4743 3187 8690 2.501 0.553 0.150 0.057 86 10.1 supramarginal 439 260 786 2.664 0.313 0.131 0.039 6 0.7 transversetemporal 2802 1872 5881 3.247 0.753 0.126 0.059 49 6.7 insula #-------------------------------------------- #@# Cortical ribbon mask Sat Nov 14 05:28:35 CET 2015 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon B_LU_02_MRI_E_T0 SUBJECTS_DIR is /usr/local/freesurfer/subjects loading input data... computing distance to left white surface computing distance to left pial surface computing distance to right white surface computing distance to right pial surface hemi masks overlap voxels = 40 writing volume /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/ribbon.mgz writing ribbon files #-------------------------------------------- #@# ASeg Stats Sat Nov 14 05:52:51 CET 2015 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0 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 B_LU_02_MRI_E_T0 $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 B_LU_02_MRI_E_T0 sysname Linux hostname biosrv1 machine x86_64 user root UseRobust 0 atlas_icv (eTIV) = 1285784 mm^3 (det: 1.515111 ) Computing euler number orig.nofix lheno = -42, rheno = -40 orig.nofix lhholes = 22, rhholes = 21 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 234828.432 234529.000 diff= 299.4 pctdiff= 0.128 rhCtxGM: 233441.035 233289.000 diff= 152.0 pctdiff= 0.065 lhCtxWM: 219579.428 220212.000 diff= -632.6 pctdiff=-0.288 rhCtxWM: 218204.831 217754.000 diff= 450.8 pctdiff= 0.207 SubCortGMVol 61400.000 SupraTentVol 986510.726 (984960.000) diff=1550.726 pctdiff=0.157 SupraTentVolNotVent 968894.726 (967344.000) diff=1550.726 pctdiff=0.160 BrainSegVol 1134684.000 (1132263.000) diff=2421.000 pctdiff=0.213 BrainSegVolNotVent 1113472.000 (1113531.726) diff=-59.726 pctdiff=-0.005 BrainSegVolNotVent 1113472.000 CerebellumVol 145918.000 VentChorVol 17616.000 3rd4th5thCSF 3596.000 CSFVol 1195.000, OptChiasmVol 190.000 MaskVol 1695143.000 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 7244 7244.014 4 5 Left-Inf-Lat-Vent 516 515.917 5 7 Left-Cerebellum-White-Matter 17286 17285.709 6 8 Left-Cerebellum-Cortex 56598 56597.914 7 10 Left-Thalamus-Proper 8462 8461.579 8 11 Left-Caudate 3987 3986.883 9 12 Left-Putamen 6070 6070.230 10 13 Left-Pallidum 1373 1372.814 11 14 3rd-Ventricle 1170 1170.397 12 15 4th-Ventricle 1463 1462.666 13 16 Brain-Stem 22220 22219.805 14 17 Left-Hippocampus 4179 4179.109 15 18 Left-Amygdala 1456 1455.988 16 24 CSF 1151 1151.167 17 26 Left-Accumbens-area 580 579.991 18 28 Left-VentralDC 4073 4073.121 19 30 Left-vessel 89 89.018 20 31 Left-choroid-plexus 1124 1124.299 23 43 Right-Lateral-Ventricle 7218 7217.524 24 44 Right-Inf-Lat-Vent 367 367.475 25 46 Right-Cerebellum-White-Matter 17730 17729.814 26 47 Right-Cerebellum-Cortex 56691 56690.746 27 49 Right-Thalamus-Proper 7255 7254.675 28 50 Right-Caudate 3998 3998.086 29 51 Right-Putamen 5816 5815.995 30 52 Right-Pallidum 1707 1707.329 31 53 Right-Hippocampus 4387 4386.803 32 54 Right-Amygdala 1694 1693.917 33 58 Right-Accumbens-area 690 690.345 34 60 Right-VentralDC 4163 4162.838 35 62 Right-vessel 92 92.309 36 63 Right-choroid-plexus 1395 1395.424 37 72 5th-Ventricle 0 0.000 38 77 WM-hypointensities 1108 1107.999 39 78 Left-WM-hypointensities 0 0.000 40 79 Right-WM-hypointensities 0 0.000 41 80 non-WM-hypointensities 21 21.257 42 81 Left-non-WM-hypointensities 0 0.000 43 82 Right-non-WM-hypointensities 0 0.000 44 85 Optic-Chiasm 178 178.395 45 251 CC_Posterior 822 821.907 46 252 CC_Mid_Posterior 329 329.062 47 253 CC_Central 334 333.880 48 254 CC_Mid_Anterior 444 443.805 49 255 CC_Anterior 700 700.430 Reporting on 45 segmentations mri_segstats done #----------------------------------------- #@# AParc-to-ASeg Sat Nov 14 05:59:48 CET 2015 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0 mri_aparc2aseg --s B_LU_02_MRI_E_T0 --volmask SUBJECTS_DIR /usr/local/freesurfer/subjects subject B_LU_02_MRI_E_T0 outvol /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/lh.white Reading lh pial surface /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/lh.pial Loading lh annotations from /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/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 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/rh.white Reading rh pial surface /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/rh.pial Loading rh annotations from /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/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 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/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 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/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 = 466296 Used brute-force search on 0 voxels Writing output aseg to /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/aparc+aseg.mgz /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0 mri_aparc2aseg --s B_LU_02_MRI_E_T0 --volmask --a2009s SUBJECTS_DIR /usr/local/freesurfer/subjects subject B_LU_02_MRI_E_T0 outvol /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/lh.white Reading lh pial surface /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/lh.pial Loading lh annotations from /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/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 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/rh.white Reading rh pial surface /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/rh.pial Loading rh annotations from /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/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 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/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 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/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 = 466296 Used brute-force search on 0 voxels Writing output aseg to /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# WMParc Sat Nov 14 06:10:21 CET 2015 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0 mri_aparc2aseg --s B_LU_02_MRI_E_T0 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /usr/local/freesurfer/subjects subject B_LU_02_MRI_E_T0 outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/aparc+aseg.mgz Reading lh white surface /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/lh.white Reading lh pial surface /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/lh.pial Loading lh annotations from /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/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 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/rh.white Reading rh pial surface /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/surf/rh.pial Loading rh annotations from /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/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 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/ribbon.mgz Loading filled from /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/filled.mgz Ripping vertices labeled as unkown Ripped 7136 vertices from left hemi Ripped 7763 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 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/mri/aseg.mgz Loading Ctx Seg File /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/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 = 903028 Used brute-force search on 533 voxels Fixing Parahip LH WM Found 8 clusters 0 k 1.000000 1 k 1.000000 2 k 1.000000 3 k 1.000000 4 k 1502.000000 5 k 3.000000 6 k 2.000000 7 k 1.000000 Fixing Parahip RH WM Found 10 clusters 0 k 1.000000 1 k 1.000000 2 k 1.000000 3 k 1506.000000 4 k 1.000000 5 k 2.000000 6 k 2.000000 7 k 1.000000 8 k 2.000000 9 k 1.000000 Writing output aseg to mri/wmparc.mgz /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0 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 B_LU_02_MRI_E_T0 --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 B_LU_02_MRI_E_T0 --surf-wm-vol --ctab /usr/local//freesurfer/WMParcStatsLUT.txt --etiv sysname Linux hostname biosrv1 machine x86_64 user root UseRobust 0 atlas_icv (eTIV) = 1285784 mm^3 (det: 1.515111 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 234828.432 234529.000 diff= 299.4 pctdiff= 0.128 rhCtxGM: 233441.035 233289.000 diff= 152.0 pctdiff= 0.065 lhCtxWM: 219579.428 220212.000 diff= -632.6 pctdiff=-0.288 rhCtxWM: 218204.831 217754.000 diff= 450.8 pctdiff= 0.207 SubCortGMVol 61400.000 SupraTentVol 986510.726 (984960.000) diff=1550.726 pctdiff=0.157 SupraTentVolNotVent 968894.726 (967344.000) diff=1550.726 pctdiff=0.160 BrainSegVol 1134684.000 (1132263.000) diff=2421.000 pctdiff=0.213 BrainSegVolNotVent 1113472.000 (1113531.726) diff=-59.726 pctdiff=-0.005 BrainSegVolNotVent 1113472.000 CerebellumVol 145918.000 VentChorVol 17616.000 3rd4th5thCSF 3596.000 CSFVol 1195.000, OptChiasmVol 190.000 MaskVol 1695143.000 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 2795 2794.665 2 3002 wm-lh-caudalanteriorcingulate 2463 2462.736 3 3003 wm-lh-caudalmiddlefrontal 7900 7899.857 4 3004 wm-lh-corpuscallosum 0 0.000 5 3005 wm-lh-cuneus 2037 2037.158 6 3006 wm-lh-entorhinal 940 940.097 7 3007 wm-lh-fusiform 7085 7085.028 8 3008 wm-lh-inferiorparietal 9906 9905.920 9 3009 wm-lh-inferiortemporal 5681 5681.335 10 3010 wm-lh-isthmuscingulate 3572 3571.942 11 3011 wm-lh-lateraloccipital 7983 7983.345 12 3012 wm-lh-lateralorbitofrontal 6472 6472.335 13 3013 wm-lh-lingual 5360 5359.716 14 3014 wm-lh-medialorbitofrontal 3161 3160.646 15 3015 wm-lh-middletemporal 4892 4891.864 16 3016 wm-lh-parahippocampal 1573 1572.862 17 3017 wm-lh-paracentral 4534 4534.095 18 3018 wm-lh-parsopercularis 3486 3485.988 19 3019 wm-lh-parsorbitalis 858 858.227 20 3020 wm-lh-parstriangularis 2943 2942.944 21 3021 wm-lh-pericalcarine 2466 2466.499 22 3022 wm-lh-postcentral 7938 7937.728 23 3023 wm-lh-posteriorcingulate 4577 4577.468 24 3024 wm-lh-precentral 13703 13702.606 25 3025 wm-lh-precuneus 9761 9761.215 26 3026 wm-lh-rostralanteriorcingulate 2736 2736.206 27 3027 wm-lh-rostralmiddlefrontal 13114 13114.465 28 3028 wm-lh-superiorfrontal 16233 16233.181 29 3029 wm-lh-superiorparietal 11262 11262.220 30 3030 wm-lh-superiortemporal 6620 6619.606 31 3031 wm-lh-supramarginal 7708 7707.711 32 3032 wm-lh-frontalpole 203 203.303 33 3033 wm-lh-temporalpole 513 513.142 34 3034 wm-lh-transversetemporal 874 874.286 35 3035 wm-lh-insula 8134 8134.024 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 3434 3433.863 120 4002 wm-rh-caudalanteriorcingulate 2891 2890.563 121 4003 wm-rh-caudalmiddlefrontal 7472 7472.208 122 4004 wm-rh-corpuscallosum 0 0.000 123 4005 wm-rh-cuneus 1695 1694.525 124 4006 wm-rh-entorhinal 544 544.302 125 4007 wm-rh-fusiform 6482 6481.740 126 4008 wm-rh-inferiorparietal 11177 11176.732 127 4009 wm-rh-inferiortemporal 5735 5735.139 128 4010 wm-rh-isthmuscingulate 2882 2881.927 129 4011 wm-rh-lateraloccipital 6883 6883.232 130 4012 wm-rh-lateralorbitofrontal 6554 6554.179 131 4013 wm-rh-lingual 4427 4427.264 132 4014 wm-rh-medialorbitofrontal 3489 3488.845 133 4015 wm-rh-middletemporal 5955 5955.043 134 4016 wm-rh-parahippocampal 1569 1569.108 135 4017 wm-rh-paracentral 5185 5184.676 136 4018 wm-rh-parsopercularis 3492 3491.963 137 4019 wm-rh-parsorbitalis 970 969.674 138 4020 wm-rh-parstriangularis 2935 2935.031 139 4021 wm-rh-pericalcarine 2428 2427.510 140 4022 wm-rh-postcentral 7520 7520.153 141 4023 wm-rh-posteriorcingulate 4022 4022.247 142 4024 wm-rh-precentral 13727 13726.800 143 4025 wm-rh-precuneus 8442 8441.839 144 4026 wm-rh-rostralanteriorcingulate 2141 2140.961 145 4027 wm-rh-rostralmiddlefrontal 12145 12144.841 146 4028 wm-rh-superiorfrontal 18202 18202.398 147 4029 wm-rh-superiorparietal 12249 12249.331 148 4030 wm-rh-superiortemporal 6060 6059.819 149 4031 wm-rh-supramarginal 7207 7206.956 150 4032 wm-rh-frontalpole 321 321.409 151 4033 wm-rh-temporalpole 526 526.305 152 4034 wm-rh-transversetemporal 540 540.163 153 4035 wm-rh-insula 8450 8450.405 154 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 30276 30275.807 237 5002 Right-UnsegmentedWhiteMatter 29932 29932.461 238 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 /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/label #-------------------------------------------- #@# BA Labels lh Sat Nov 14 06:33:30 CET 2015 INFO: fsaverage subject does not exist in SUBJECTS_DIR INFO: Creating symlink to fsaverage subject... cd /usr/local/freesurfer/subjects; ln -s /usr/local//freesurfer/subjects/fsaverage; cd - ln: creating symbolic link `./fsaverage': File exists mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label --trgsubject B_LU_02_MRI_E_T0 --trglabel ./lh.BA1.label --hemi lh --regmethod surface Too many levels of symbolic links mri_label2label: could not open label file /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = B_LU_02_MRI_E_T0 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 /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local//freesurfer Loading source label. Invalid argument ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label Linux biosrv1 2.6.32-573.7.1.el6.x86_64 #1 SMP Tue Sep 22 22:00:00 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux recon-all -s B_LU_02_MRI_E_T0 exited with ERRORS at Sat Nov 14 06:33:30 CET 2015 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting