lun 4 gen 2016, 21.30.30, CET /home/salvatore/freesurfer/subjects/T1-1 /home/salvatore/freesurfer/bin/recon-all -s T1-1 -i /home/salvatore/TIrocinio/Dati/TDL-T1/001.mgz -all subjid T1-1 setenv SUBJECTS_DIR /home/salvatore/freesurfer/subjects FREESURFER_HOME /home/salvatore/freesurfer Actual FREESURFER_HOME /home/salvatore/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-dev-20151230 Linux salvatore-SATELLITE-P50-B-11M 3.19.0-42-generic #48~14.04.1-Ubuntu SMP Fri Dec 18 10:24:49 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 63495 maxlocks unlimited maxsignal 63495 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 16342168 2378820 13963348 408172 129940 1338672 -/+ buffers/cache: 910208 15431960 Swap: 16686076 0 16686076 ######################################## program versions used $Id: recon-all,v 1.560 2015/12/30 03:06:56 greve Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/04-20:30:30-GMT BuildTimeStamp: Dec 30 2015 21:02:43 CVS: $Id: mri_convert.c,v 1.225 2015/10/19 18:48:26 fischl Exp $ User: salvatore Machine: salvatore-SATELLITE-P50-B-11M Platform: Linux PlatformVersion: 3.19.0-42-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 6.0 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert --version dev build (use --all-info flag for full version info) ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/04-20:30:30-GMT BuildTimeStamp: Dec 30 2015 21:02:43 CVS: $Id: tkregister2.c,v 1.129 2014/02/26 21:31:58 greve Exp $ User: salvatore Machine: salvatore-SATELLITE-P50-B-11M Platform: Linux PlatformVersion: 3.19.0-42-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/04-20:30:30-GMT BuildTimeStamp: Dec 30 2015 21:02:43 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: salvatore Machine: salvatore-SATELLITE-P50-B-11M Platform: Linux PlatformVersion: 3.19.0-42-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/04-20:30:30-GMT BuildTimeStamp: Dec 30 2015 21:02:43 CVS: $Id: mri_normalize.c,v 1.88 2015/12/23 17:30:35 fischl Exp $ User: salvatore Machine: salvatore-SATELLITE-P50-B-11M Platform: Linux PlatformVersion: 3.19.0-42-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/04-20:30:30-GMT BuildTimeStamp: Dec 30 2015 21:02:43 CVS: $Id: mri_watershed.cpp,v 1.101 2015/07/10 18:57:33 greve Exp $ User: salvatore Machine: salvatore-SATELLITE-P50-B-11M Platform: Linux PlatformVersion: 3.19.0-42-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/04-20:30:30-GMT BuildTimeStamp: Dec 30 2015 21:02:43 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: salvatore Machine: salvatore-SATELLITE-P50-B-11M Platform: Linux PlatformVersion: 3.19.0-42-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/04-20:30:30-GMT BuildTimeStamp: Dec 30 2015 21:02:43 CVS: $Id: mri_segment.c,v 1.43 2015/02/05 23:34:40 zkaufman Exp $ User: salvatore Machine: salvatore-SATELLITE-P50-B-11M Platform: Linux PlatformVersion: 3.19.0-42-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/04-20:30:30-GMT BuildTimeStamp: Dec 30 2015 21:02:43 CVS: $Id: mri_label2label.c,v 1.47 2014/12/22 19:59:18 greve Exp $ User: salvatore Machine: salvatore-SATELLITE-P50-B-11M Platform: Linux PlatformVersion: 3.19.0-42-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/04-20:30:30-GMT BuildTimeStamp: Dec 30 2015 21:02:43 CVS: $Id: mri_em_register.c,v 1.103 2015/08/26 16:51:09 fischl Exp $ User: salvatore Machine: salvatore-SATELLITE-P50-B-11M Platform: Linux PlatformVersion: 3.19.0-42-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/04-20:30:30-GMT BuildTimeStamp: Dec 30 2015 21:02:43 CVS: $Id: mri_ca_normalize.c,v 1.65 2015/10/10 17:28:19 fischl Exp $ User: salvatore Machine: salvatore-SATELLITE-P50-B-11M Platform: Linux PlatformVersion: 3.19.0-42-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/04-20:30:30-GMT BuildTimeStamp: Dec 30 2015 21:02:43 CVS: $Id: mri_ca_register.c,v 1.94 2015/11/24 20:36:25 greve Exp $ User: salvatore Machine: salvatore-SATELLITE-P50-B-11M Platform: Linux PlatformVersion: 3.19.0-42-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/04-20:30:30-GMT BuildTimeStamp: Dec 30 2015 21:02:43 CVS: $Id: mri_ca_label.c,v 1.109 2015/08/26 16:46:38 fischl Exp $ User: salvatore Machine: salvatore-SATELLITE-P50-B-11M Platform: Linux PlatformVersion: 3.19.0-42-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/04-20:30:30-GMT BuildTimeStamp: Dec 30 2015 21:02:43 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: salvatore Machine: salvatore-SATELLITE-P50-B-11M Platform: Linux PlatformVersion: 3.19.0-42-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/04-20:30:31-GMT BuildTimeStamp: Dec 30 2015 21:02:43 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: salvatore Machine: salvatore-SATELLITE-P50-B-11M Platform: Linux PlatformVersion: 3.19.0-42-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/04-20:30:31-GMT BuildTimeStamp: Dec 30 2015 21:02:43 CVS: $Id: mri_tessellate.c,v 1.38 2014/03/22 00:41:04 greve Exp $ User: salvatore Machine: salvatore-SATELLITE-P50-B-11M Platform: Linux PlatformVersion: 3.19.0-42-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/04-20:30:31-GMT BuildTimeStamp: Dec 30 2015 21:02:43 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: salvatore Machine: salvatore-SATELLITE-P50-B-11M Platform: Linux PlatformVersion: 3.19.0-42-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/04-20:30:31-GMT BuildTimeStamp: Dec 30 2015 21:02:43 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: salvatore Machine: salvatore-SATELLITE-P50-B-11M Platform: Linux PlatformVersion: 3.19.0-42-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/04-20:30:31-GMT BuildTimeStamp: Dec 30 2015 21:02:43 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: salvatore Machine: salvatore-SATELLITE-P50-B-11M Platform: Linux PlatformVersion: 3.19.0-42-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/04-20:30:32-GMT BuildTimeStamp: Dec 30 2015 21:02:43 CVS: $Id: mris_inflate.c,v 1.44 2012/01/05 18:36:17 greve Exp $ User: salvatore Machine: salvatore-SATELLITE-P50-B-11M Platform: Linux PlatformVersion: 3.19.0-42-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/04-20:30:32-GMT BuildTimeStamp: Dec 30 2015 21:02:43 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: salvatore Machine: salvatore-SATELLITE-P50-B-11M Platform: Linux PlatformVersion: 3.19.0-42-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/04-20:30:32-GMT BuildTimeStamp: Dec 30 2015 21:02:43 CVS: $Id: mris_sphere.c,v 1.60 2015/11/24 20:36:25 greve Exp $ User: salvatore Machine: salvatore-SATELLITE-P50-B-11M Platform: Linux PlatformVersion: 3.19.0-42-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/04-20:30:32-GMT BuildTimeStamp: Dec 30 2015 21:02:43 CVS: $Id: mris_fix_topology.c,v 1.49 2015/11/24 20:36:25 greve Exp $ User: salvatore Machine: salvatore-SATELLITE-P50-B-11M Platform: Linux PlatformVersion: 3.19.0-42-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/04-20:30:33-GMT BuildTimeStamp: Dec 30 2015 21:02:43 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: salvatore Machine: salvatore-SATELLITE-P50-B-11M Platform: Linux PlatformVersion: 3.19.0-42-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/04-20:30:33-GMT BuildTimeStamp: Dec 30 2015 21:02:43 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: salvatore Machine: salvatore-SATELLITE-P50-B-11M Platform: Linux PlatformVersion: 3.19.0-42-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/04-20:30:33-GMT BuildTimeStamp: Dec 30 2015 21:02:43 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: salvatore Machine: salvatore-SATELLITE-P50-B-11M Platform: Linux PlatformVersion: 3.19.0-42-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/04-20:30:33-GMT BuildTimeStamp: Dec 30 2015 21:02:43 CVS: $Id: mris_make_surfaces.c,v 1.162 2015/12/10 21:15:02 fischl Exp $ User: salvatore Machine: salvatore-SATELLITE-P50-B-11M Platform: Linux PlatformVersion: 3.19.0-42-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/04-20:30:33-GMT BuildTimeStamp: Dec 30 2015 21:02:43 CVS: $Id: mris_register.c,v 1.62 2015/11/24 20:36:25 greve Exp $ User: salvatore Machine: salvatore-SATELLITE-P50-B-11M Platform: Linux PlatformVersion: 3.19.0-42-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/04-20:30:34-GMT BuildTimeStamp: Dec 30 2015 21:02:43 CVS: $Id: mris_volmask.cpp,v 1.26 2014/11/06 03:40:22 nicks Exp $ User: salvatore Machine: salvatore-SATELLITE-P50-B-11M Platform: Linux PlatformVersion: 3.19.0-42-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/04-20:30:34-GMT BuildTimeStamp: Dec 30 2015 21:02:43 CVS: $Id: mris_anatomical_stats.c,v 1.78 2015/07/06 21:58:51 greve Exp $ User: salvatore Machine: salvatore-SATELLITE-P50-B-11M Platform: Linux PlatformVersion: 3.19.0-42-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/04-20:30:34-GMT BuildTimeStamp: Dec 30 2015 21:02:43 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: salvatore Machine: salvatore-SATELLITE-P50-B-11M Platform: Linux PlatformVersion: 3.19.0-42-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/04-20:30:34-GMT BuildTimeStamp: Dec 30 2015 21:02:43 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: salvatore Machine: salvatore-SATELLITE-P50-B-11M Platform: Linux PlatformVersion: 3.19.0-42-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/04-20:30:35-GMT BuildTimeStamp: Dec 30 2015 21:02:43 CVS: $Id: mris_calc.c,v 1.54 2015/12/14 23:18:58 greve Exp $ User: salvatore Machine: salvatore-SATELLITE-P50-B-11M Platform: Linux PlatformVersion: 3.19.0-42-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.76 2015/09/22 19:55:12 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/04-20:30:35-GMT BuildTimeStamp: Dec 30 2015 21:02:43 CVS: $Id: mri_robust_register.cpp,v 1.76 2015/09/22 19:55:12 mreuter Exp $ User: salvatore Machine: salvatore-SATELLITE-P50-B-11M Platform: Linux PlatformVersion: 3.19.0-42-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.52 2015/12/15 21:20:46 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/04-20:30:35-GMT BuildTimeStamp: Dec 30 2015 21:02:43 CVS: $Id: mri_robust_template.cpp,v 1.52 2015/12/15 21:20:46 mreuter Exp $ User: salvatore Machine: salvatore-SATELLITE-P50-B-11M Platform: Linux PlatformVersion: 3.19.0-42-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/04-20:30:35-GMT BuildTimeStamp: Dec 30 2015 21:02:43 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: salvatore Machine: salvatore-SATELLITE-P50-B-11M Platform: Linux PlatformVersion: 3.19.0-42-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/04-20:30:36-GMT BuildTimeStamp: Dec 30 2015 21:02:43 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: salvatore Machine: salvatore-SATELLITE-P50-B-11M Platform: Linux PlatformVersion: 3.19.0-42-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/04-20:30:36-GMT BuildTimeStamp: Dec 30 2015 21:02:43 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: salvatore Machine: salvatore-SATELLITE-P50-B-11M Platform: Linux PlatformVersion: 3.19.0-42-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/04-20:30:36-GMT BuildTimeStamp: Dec 30 2015 21:02:43 CVS: $Id: mri_segstats.c,v 1.119 2015/10/06 18:46:12 greve Exp $ User: salvatore Machine: salvatore-SATELLITE-P50-B-11M Platform: Linux PlatformVersion: 3.19.0-42-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/04-20:30:36-GMT BuildTimeStamp: Dec 30 2015 21:02:43 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: salvatore Machine: salvatore-SATELLITE-P50-B-11M Platform: Linux PlatformVersion: 3.19.0-42-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /home/salvatore/freesurfer/average GCA RB_all_2015-08-04.gca GCASkull RB_all_withskull_2014-08-21.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /home/salvatore/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /home/salvatore/freesurfer/subjects/T1-1 mri_convert /home/salvatore/TIrocinio/Dati/TDL-T1/001.mgz /home/salvatore/freesurfer/subjects/T1-1/mri/orig/001.mgz mri_convert /home/salvatore/TIrocinio/Dati/TDL-T1/001.mgz /home/salvatore/freesurfer/subjects/T1-1/mri/orig/001.mgz $Id: mri_convert.c,v 1.225 2015/10/19 18:48:26 fischl Exp $ reading from /home/salvatore/TIrocinio/Dati/TDL-T1/001.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.995936, -0.0850198, 0.029719) j_ras = (0.0813559, 0.990805, 0.108105) k_ras = (-0.0386368, -0.105248, 0.993695) writing to /home/salvatore/freesurfer/subjects/T1-1/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor lun 4 gen 2016, 21.30.40, CET Found 1 runs /home/salvatore/freesurfer/subjects/T1-1/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /home/salvatore/freesurfer/subjects/T1-1/mri/orig/001.mgz /home/salvatore/freesurfer/subjects/T1-1/mri/rawavg.mgz /home/salvatore/freesurfer/subjects/T1-1 mri_convert /home/salvatore/freesurfer/subjects/T1-1/mri/rawavg.mgz /home/salvatore/freesurfer/subjects/T1-1/mri/orig.mgz --conform mri_convert /home/salvatore/freesurfer/subjects/T1-1/mri/rawavg.mgz /home/salvatore/freesurfer/subjects/T1-1/mri/orig.mgz --conform $Id: mri_convert.c,v 1.225 2015/10/19 18:48:26 fischl Exp $ reading from /home/salvatore/freesurfer/subjects/T1-1/mri/rawavg.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.995936, -0.0850198, 0.029719) j_ras = (0.0813559, 0.990805, 0.108105) k_ras = (-0.0386368, -0.105248, 0.993695) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /home/salvatore/freesurfer/subjects/T1-1/mri/orig.mgz... mri_add_xform_to_header -c /home/salvatore/freesurfer/subjects/T1-1/mri/transforms/talairach.xfm /home/salvatore/freesurfer/subjects/T1-1/mri/orig.mgz /home/salvatore/freesurfer/subjects/T1-1/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach lun 4 gen 2016, 21.30.47, CET /home/salvatore/freesurfer/subjects/T1-1/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /home/salvatore/freesurfer/subjects/T1-1/mri /home/salvatore/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.25 2015/12/09 20:02:53 zkaufman Exp $ Linux salvatore-SATELLITE-P50-B-11M 3.19.0-42-generic #48~14.04.1-Ubuntu SMP Fri Dec 18 10:24:49 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux lun 4 gen 2016, 21.30.47, CET Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 tmpdir is ./tmp.mri_nu_correct.mni.4626 /home/salvatore/freesurfer/subjects/T1-1/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.4626/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.4626/nu0.mnc -odt float $Id: mri_convert.c,v 1.225 2015/10/19 18:48:26 fischl Exp $ reading from orig.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -4.65661e-10, 3.72529e-09) j_ras = (0, 0, -1) k_ras = (7.45058e-09, 1, 7.45058e-09) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.4626/nu0.mnc... -------------------------------------------------------- Iteration 1 lun 4 gen 2016, 21.30.48, CET nu_correct -clobber ./tmp.mri_nu_correct.mni.4626/nu0.mnc ./tmp.mri_nu_correct.mni.4626/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.4626/0/ -iterations 1000 -distance 50 [salvatore@salvatore-SATELLITE-P50-B-11M:/home/salvatore/freesurfer/subjects/T1-1/mri/] [2016-01-04 21:30:48] running: /home/salvatore/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.4626/0/ ./tmp.mri_nu_correct.mni.4626/nu0.mnc ./tmp.mri_nu_correct.mni.4626/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done 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TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -4.65661e-10, 3.72529e-09) j_ras = (0, 0, -1) k_ras = (7.45058e-09, 1, 7.45058e-09) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz... lun 4 gen 2016, 21.31.34, CET mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at lun 4 gen 2016, 21.31.34, CET Ended at lun 4 gen 2016, 21.32.01, CET talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection lun 4 gen 2016, 21.32.03, CET /home/salvatore/freesurfer/subjects/T1-1/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.5547, pval=0.2115 >= threshold=0.0050) awk -f /home/salvatore/freesurfer/bin/extract_talairach_avi_QA.awk /home/salvatore/freesurfer/subjects/T1-1/mri/transforms/talairach_avi.log tal_QC_AZS /home/salvatore/freesurfer/subjects/T1-1/mri/transforms/talairach_avi.log TalAviQA: 0.96589 z-score: -2 #-------------------------------------------- #@# Nu Intensity Correction lun 4 gen 2016, 21.32.04, CET mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /home/salvatore/freesurfer/subjects/T1-1/mri /home/salvatore/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 1.25 2015/12/09 20:02:53 zkaufman Exp $ Linux salvatore-SATELLITE-P50-B-11M 3.19.0-42-generic #48~14.04.1-Ubuntu SMP Fri Dec 18 10:24:49 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux lun 4 gen 2016, 21.32.04, CET Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 tmpdir is ./tmp.mri_nu_correct.mni.5652 /home/salvatore/freesurfer/subjects/T1-1/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.5652/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.5652/nu0.mnc -odt float $Id: mri_convert.c,v 1.225 2015/10/19 18:48:26 fischl Exp $ reading from orig.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -4.65661e-10, 3.72529e-09) j_ras = (0, 0, -1) k_ras = (7.45058e-09, 1, 7.45058e-09) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.5652/nu0.mnc... -------------------------------------------------------- Iteration 1 lun 4 gen 2016, 21.32.05, CET nu_correct -clobber ./tmp.mri_nu_correct.mni.5652/nu0.mnc ./tmp.mri_nu_correct.mni.5652/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.5652/0/ [salvatore@salvatore-SATELLITE-P50-B-11M:/home/salvatore/freesurfer/subjects/T1-1/mri/] [2016-01-04 21:32:05] running: /home/salvatore/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 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.5652/0/ ./tmp.mri_nu_correct.mni.5652/nu0.mnc ./tmp.mri_nu_correct.mni.5652/nu1.imp 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./tmp.mri_nu_correct.mni.5652/nu1.mnc ./tmp.mri_nu_correct.mni.5652/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.5652/1/ [salvatore@salvatore-SATELLITE-P50-B-11M:/home/salvatore/freesurfer/subjects/T1-1/mri/] [2016-01-04 21:32:31] running: /home/salvatore/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 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.5652/1/ ./tmp.mri_nu_correct.mni.5652/nu1.mnc ./tmp.mri_nu_correct.mni.5652/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done 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Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 23 CV of field change: 0.000991859 mri_binarize --i ./tmp.mri_nu_correct.mni.5652/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.5652/ones.mgz $Id: mri_binarize.c,v 1.41 2014/08/17 17:47:29 greve Exp $ cwd /home/salvatore/freesurfer/subjects/T1-1/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.5652/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.5652/ones.mgz sysname Linux hostname salvatore-SATELLITE-P50-B-11M machine x86_64 user salvatore input ./tmp.mri_nu_correct.mni.5652/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.5652/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 16777216 values in range Counting number of voxels in first frame Found 16777216 voxels in final mask Count: 16777216 16777216.000000 16777216 100.000000 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.5652/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.5652/sum.junk --avgwf ./tmp.mri_nu_correct.mni.5652/input.mean.dat $Id: mri_segstats.c,v 1.119 2015/10/06 18:46:12 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.5652/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.5652/sum.junk --avgwf ./tmp.mri_nu_correct.mni.5652/input.mean.dat sysname Linux hostname salvatore-SATELLITE-P50-B-11M machine x86_64 user salvatore UseRobust 0 Loading ./tmp.mri_nu_correct.mni.5652/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.5652/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.5652/ones.mgz --i ./tmp.mri_nu_correct.mni.5652/nu2.mnc --sum ./tmp.mri_nu_correct.mni.5652/sum.junk --avgwf ./tmp.mri_nu_correct.mni.5652/output.mean.dat $Id: mri_segstats.c,v 1.119 2015/10/06 18:46:12 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.5652/ones.mgz --i ./tmp.mri_nu_correct.mni.5652/nu2.mnc --sum ./tmp.mri_nu_correct.mni.5652/sum.junk --avgwf ./tmp.mri_nu_correct.mni.5652/output.mean.dat sysname Linux hostname salvatore-SATELLITE-P50-B-11M machine x86_64 user salvatore UseRobust 0 Loading ./tmp.mri_nu_correct.mni.5652/ones.mgz Loading ./tmp.mri_nu_correct.mni.5652/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.5652/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.5652/nu2.mnc ./tmp.mri_nu_correct.mni.5652/nu2.mnc mul 1.02798836992795657342 Saving result to './tmp.mri_nu_correct.mni.5652/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.5652/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.5652/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.225 2015/10/19 18:48:26 fischl Exp $ reading from ./tmp.mri_nu_correct.mni.5652/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -4.65661e-10, 3.72529e-09) j_ras = (0, 0, -1) k_ras = (7.45058e-09, 1, 7.45058e-09) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 5 seconds. mapping ( 8, 118) to ( 3, 110) lun 4 gen 2016, 21.33.16, CET mri_nu_correct.mni done mri_add_xform_to_header -c /home/salvatore/freesurfer/subjects/T1-1/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization lun 4 gen 2016, 21.33.16, CET /home/salvatore/freesurfer/subjects/T1-1/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.08305 -0.09602 0.01702 -2.72818; 0.08470 0.96256 0.39107 0.44635; -0.07549 -0.36277 0.99433 12.91113; 0.00000 0.00000 0.00000 1.00000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 15 Starting OpenSpline(): npoints = 15 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 109 gm peak at 84 (84), valley at 36 (36) csf peak at 42, setting threshold to 70 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 85 (85), valley at 35 (35) csf peak at 42, setting threshold to 70 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 31 seconds. #-------------------------------------------- #@# Skull Stripping lun 4 gen 2016, 21.34.47, CET /home/salvatore/freesurfer/subjects/T1-1/mri mri_em_register -skull nu.mgz /home/salvatore/freesurfer/average/RB_all_withskull_2014-08-21.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach_with_skull.log reading '/home/salvatore/freesurfer/average/RB_all_withskull_2014-08-21.gca'... average std = 23.5 using min determinant for regularization = 55.2 0 singular and 5018 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 15.9 or > 1063.6 total sample mean = 86.3 (1445 zeros) ************************************************ spacing=8, using 3388 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3388, passno 0, spacing 8 resetting wm mean[0]: 110 --> 118 resetting gm mean[0]: 70 --> 70 input volume #1 is the most T1-like using real data threshold=13.0 skull bounding box = (49, 51, 20) --> (211, 209, 217) using (103, 104, 119) as brain centroid... mean wm in atlas = 118, using box (83,85,95) --> (122, 123,143) to find MRI wm before smoothing, mri peak at 106 robust fit to distribution - 105 +- 14.2 distribution too broad for accurate scaling - disabling after smoothing, mri peak at 118, scaling input intensities by 1.000 scaling channel 0 by 1 initial log_p = -4.616 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.532342 @ (9.091, -9.091, -9.091) max log p = -4.497181 @ (-4.545, -4.545, 4.545) max log p = -4.452760 @ (-2.273, -6.818, -6.818) max log p = -4.446340 @ (-1.136, 1.136, 3.409) max log p = -4.437193 @ (0.568, -0.568, -1.705) max log p = -4.437193 @ (0.000, 0.000, 0.000) Found translation: (1.7, -19.9, -9.7): log p = -4.437 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.135, old_max_log_p =-4.437 (thresh=-4.4) 1.13041 0.08173 0.19494 -48.02423; -0.13766 0.98130 0.38685 -32.01011; -0.15011 -0.43632 1.05337 72.66406; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.128, old_max_log_p =-4.135 (thresh=-4.1) 1.13041 0.08173 0.19494 -48.02423; -0.14798 1.05490 0.41587 -43.97282; -0.15011 -0.43632 1.05337 72.66406; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.128, old_max_log_p =-4.128 (thresh=-4.1) 1.13041 0.08173 0.19494 -48.02423; -0.14798 1.05490 0.41587 -43.97282; -0.15011 -0.43632 1.05337 72.66406; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.053, old_max_log_p =-4.128 (thresh=-4.1) 1.09929 0.02361 0.12698 -32.35003; -0.06137 1.04360 0.34449 -45.30691; -0.11078 -0.34528 1.02378 54.65086; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.045, old_max_log_p =-4.053 (thresh=-4.0) 1.11713 0.05843 0.14188 -41.06248; -0.10089 1.03042 0.37345 -41.68113; -0.10668 -0.37213 0.99298 61.23942; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.039, old_max_log_p =-4.045 (thresh=-4.0) 1.10167 0.03467 0.09589 -30.66255; -0.06065 1.04376 0.34414 -45.38176; -0.07331 -0.33612 1.00877 50.26640; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.039, old_max_log_p =-4.039 (thresh=-4.0) 1.10167 0.03467 0.09589 -30.66255; -0.06065 1.04376 0.34414 -45.38176; -0.07331 -0.33612 1.00877 50.26640; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.029, old_max_log_p =-4.039 (thresh=-4.0) 1.10232 0.03195 0.10428 -30.85228; -0.06072 1.04498 0.34455 -45.58434; -0.08240 -0.33679 1.00914 51.48662; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 8 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.029, old_max_log_p =-4.029 (thresh=-4.0) 1.10425 0.03475 0.09614 -30.56356; -0.06072 1.04498 0.34455 -45.58434; -0.07329 -0.33612 1.00877 50.26745; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3388 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.10425 0.03475 0.09614 -30.56356; -0.06072 1.04498 0.34455 -45.58434; -0.07329 -0.33612 1.00877 50.26745; 0.00000 0.00000 0.00000 1.00000; nsamples 3388 Quasinewton: input matrix 1.10425 0.03475 0.09614 -30.56356; -0.06072 1.04498 0.34455 -45.58434; -0.07329 -0.33612 1.00877 50.26745; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.10425 0.03475 0.09614 -30.56356; -0.06072 1.04498 0.34455 -45.58434; -0.07329 -0.33612 1.00877 50.26745; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -4.029 (old=-4.616) transform before final EM align: 1.10425 0.03475 0.09614 -30.56356; -0.06072 1.04498 0.34455 -45.58434; -0.07329 -0.33612 1.00877 50.26745; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 380366 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.10425 0.03475 0.09614 -30.56356; -0.06072 1.04498 0.34455 -45.58434; -0.07329 -0.33612 1.00877 50.26745; 0.00000 0.00000 0.00000 1.00000; nsamples 380366 Quasinewton: input matrix 1.10425 0.03475 0.09614 -30.56356; -0.06072 1.04498 0.34455 -45.58434; -0.07329 -0.33612 1.00877 50.26745; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 013: -log(p) = 4.3 tol 0.000000 final transform: 1.10425 0.03475 0.09614 -30.56356; -0.06072 1.04498 0.34455 -45.58434; -0.07329 -0.33612 1.00877 50.26745; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... registration took 16 minutes and 3 seconds. mri_watershed -T1 -brain_atlas /home/salvatore/freesurfer/average/RB_all_withskull_2014-08-21.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=126 y=133 z=104 r=74 first estimation of the main basin volume: 1750584 voxels Looking for seedpoints 2 found in the cerebellum 18 found in the rest of the brain global maximum in x=113, y=115, z=69, Imax=255 CSF=18, 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=22121812740 voxels, voxel volume =1.000 = 22121812740 mmm3 = 22121811.968 cm3 done. PostAnalyze...Basin Prior 460 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=130,y=130, z=108, r=9958 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=4, CSF_MAX=20 , nb = 41826 RIGHT_CER CSF_MIN=0, CSF_intensity=4, CSF_MAX=34 , nb = -1028190481 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=43 , nb = -1049054540 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=4, CSF_MAX=18 , nb = 1037131934 LEFT_BRAIN CSF_MIN=0, CSF_intensity=4, CSF_MAX=22 , nb = 1078543370 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1080428638 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 20, 42, 64, 80 after analyzing : 20, 56, 64, 62 RIGHT_CER before analyzing : 34, 49, 63, 91 after analyzing : 34, 58, 63, 66 LEFT_CER before analyzing : 43, 54, 63, 92 after analyzing : 43, 60, 63, 68 RIGHT_BRAIN before analyzing : 18, 39, 65, 81 after analyzing : 18, 56, 65, 62 LEFT_BRAIN before analyzing : 22, 42, 62, 80 after analyzing : 22, 55, 62, 61 OTHER before analyzing : 4, 6, 55, 95 after analyzing : 4, 38, 55, 52 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...61 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.009 curvature mean = 69.073, std = 6.318 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 3.30, sigma = 5.45 after rotation: sse = 3.30, sigma = 5.45 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 4.54, its var is 7.57 before Erosion-Dilatation 3.50% of inacurate vertices after Erosion-Dilatation 4.70% 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...36 iterations mri_strip_skull: done peeling brain Brain Size = 1586233 voxels, voxel volume = 1.000 mm3 = 1586233 mmm3 = 1586.233 cm3 ****************************** Saving brainmask.auto.mgz done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration lun 4 gen 2016, 21.51.06, CET /home/salvatore/freesurfer/subjects/T1-1/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /home/salvatore/freesurfer/average/RB_all_2015-08-04.gca transforms/talairach.lta setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading '/home/salvatore/freesurfer/average/RB_all_2015-08-04.gca'... average std = 7.4 using min determinant for regularization = 5.4 0 singular and 937 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 6.2 or > 452.2 total sample mean = 78.8 (1019 zeros) ************************************************ spacing=8, using 2854 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2854, passno 0, spacing 8 resetting wm mean[0]: 97 --> 105 resetting gm mean[0]: 60 --> 60 input volume #1 is the most T1-like using real data threshold=16.0 skull bounding box = (65, 65, 35) --> (195, 208, 193) using (108, 113, 114) as brain centroid... mean wm in atlas = 105, using box (92,95,95) --> (123, 130,133) to find MRI wm before smoothing, mri peak at 104 robust fit to distribution - 104 +- 10.3 distribution too broad for accurate scaling - disabling after smoothing, mri peak at 116, scaling input intensities by 0.905 scaling channel 0 by 0.905172 initial log_p = -4.184 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.127555 @ (-9.091, -9.091, -9.091) max log p = -4.102374 @ (4.545, -4.545, -4.545) max log p = -4.076101 @ (2.273, 2.273, 2.273) max log p = -4.049582 @ (-1.136, -1.136, -1.136) max log p = -4.041231 @ (1.705, 3.977, 5.114) max log p = -4.041231 @ (0.000, 0.000, 0.000) Found translation: (-1.7, -8.5, -7.4): log p = -4.041 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.887, old_max_log_p =-4.041 (thresh=-4.0) 1.05465 -0.03125 0.11662 -18.01052; 0.00000 1.03837 0.27823 -45.11765; -0.15011 -0.25660 0.95766 49.96105; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.887, old_max_log_p =-3.887 (thresh=-3.9) 1.05465 -0.03125 0.11662 -18.01052; 0.00000 1.03837 0.27823 -45.11765; -0.15011 -0.25660 0.95766 49.96105; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.791, old_max_log_p =-3.887 (thresh=-3.9) 1.07812 0.01337 0.09762 -26.64465; -0.04363 1.00037 0.33099 -40.56395; -0.12081 -0.33696 0.97586 58.21386; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.784, old_max_log_p =-3.791 (thresh=-3.8) 1.08150 0.02439 0.06564 -24.98704; -0.04282 0.98161 0.32478 -37.54426; -0.08387 -0.33003 0.96019 54.18562; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.782, old_max_log_p =-3.784 (thresh=-3.8) 1.07620 0.04569 0.10760 -31.70001; -0.07807 0.98064 0.32143 -32.40993; -0.12144 -0.33686 0.97548 58.32624; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.750, old_max_log_p =-3.782 (thresh=-3.8) 1.07603 0.02952 0.10247 -28.06730; -0.05832 0.98432 0.30643 -33.82927; -0.12227 -0.31964 0.97716 56.00848; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.745, old_max_log_p =-3.750 (thresh=-3.7) 1.07477 0.02948 0.10235 -27.88473; -0.05852 0.98779 0.30751 -34.37221; -0.12227 -0.31964 0.97716 56.00848; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.745, old_max_log_p =-3.745 (thresh=-3.7) 1.07477 0.02948 0.10235 -27.88473; -0.05852 0.98779 0.30751 -34.37221; -0.12227 -0.31964 0.97716 56.00848; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2854 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.07477 0.02948 0.10235 -27.88473; -0.05852 0.98779 0.30751 -34.37221; -0.12227 -0.31964 0.97716 56.00848; 0.00000 0.00000 0.00000 1.00000; nsamples 2854 Quasinewton: input matrix 1.07477 0.02948 0.10235 -27.88473; -0.05852 0.98779 0.30751 -34.37221; -0.12227 -0.31964 0.97716 56.00848; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.07477 0.02948 0.10235 -27.88473; -0.05852 0.98779 0.30751 -34.37221; -0.12227 -0.31964 0.97716 56.00848; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.745 (old=-4.184) transform before final EM align: 1.07477 0.02948 0.10235 -27.88473; -0.05852 0.98779 0.30751 -34.37221; -0.12227 -0.31964 0.97716 56.00848; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 314792 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.07477 0.02948 0.10235 -27.88473; -0.05852 0.98779 0.30751 -34.37221; -0.12227 -0.31964 0.97716 56.00848; 0.00000 0.00000 0.00000 1.00000; nsamples 314792 Quasinewton: input matrix 1.07477 0.02948 0.10235 -27.88473; -0.05852 0.98779 0.30751 -34.37221; -0.12227 -0.31964 0.97716 56.00848; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 012: -log(p) = 4.0 tol 0.000000 final transform: 1.07477 0.02948 0.10235 -27.88473; -0.05852 0.98779 0.30751 -34.37221; -0.12227 -0.31964 0.97716 56.00848; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... registration took 11 minutes and 39 seconds. #-------------------------------------- #@# CA Normalize lun 4 gen 2016, 22.02.44, CET /home/salvatore/freesurfer/subjects/T1-1/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /home/salvatore/freesurfer/average/RB_all_2015-08-04.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 '/home/salvatore/freesurfer/average/RB_all_2015-08-04.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 97 --> 105 resetting gm mean[0]: 60 --> 60 input volume #1 is the most T1-like using real data threshold=15.0 skull bounding box = (64, 65, 35) --> (195, 209, 193) using (108, 113, 114) as brain centroid... mean wm in atlas = 105, using box (92,95,95) --> (124, 130,133) to find MRI wm before smoothing, mri peak at 104 robust fit to distribution - 104 +- 10.7 distribution too broad for accurate scaling - disabling after smoothing, mri peak at 116, scaling input intensities by 0.905 scaling channel 0 by 0.905172 using 245868 sample points... INFO: compute sample coordinates transform 1.07477 0.02948 0.10235 -27.88473; -0.05852 0.98779 0.30751 -34.37221; -0.12227 -0.31964 0.97716 56.00848; 0.00000 0.00000 0.00000 1.00000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 39361 control points for structure... bounding box (126, 67, 39) --> (191, 180, 195) Left_Cerebral_White_Matter: limiting intensities to 86.0 --> 230.0 237 of 1470 (16.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39033 control points for structure... bounding box (69, 66, 35) --> (132, 172, 194) Right_Cerebral_White_Matter: limiting intensities to 76.0 --> 230.0 0 of 4159 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 2873 control points for structure... bounding box (131, 155, 72) --> (175, 196, 122) Left_Cerebellum_White_Matter: limiting intensities to 87.0 --> 230.0 0 of 85 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2551 control points for structure... bounding box (88, 156, 65) --> (131, 195, 119) Right_Cerebellum_White_Matter: limiting intensities to 87.0 --> 230.0 0 of 86 (0.0%) samples deleted finding control points in Brain_Stem.... found 3424 control points for structure... bounding box (112, 139, 100) --> (145, 207, 131) Brain_Stem: limiting intensities to 78.0 --> 230.0 0 of 172 (0.0%) samples deleted using 5972 total control points for intensity normalization... bias field = 1.115 +- 0.089 3 of 5735 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39361 control points for structure... bounding box (126, 67, 39) --> (191, 180, 195) Left_Cerebral_White_Matter: limiting intensities to 85.0 --> 253.0 235 of 1500 (15.7%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39033 control points for structure... bounding box (69, 66, 35) --> (132, 172, 194) Right_Cerebral_White_Matter: limiting intensities to 87.0 --> 253.0 3 of 3772 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 2873 control points for structure... bounding box (131, 155, 72) --> (175, 196, 122) Left_Cerebellum_White_Matter: limiting intensities to 98.0 --> 253.0 26 of 98 (26.5%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2551 control points for structure... bounding box (88, 156, 65) --> (131, 195, 119) Right_Cerebellum_White_Matter: limiting intensities to 87.0 --> 253.0 0 of 119 (0.0%) samples deleted finding control points in Brain_Stem.... found 3424 control points for structure... bounding box (112, 139, 100) --> (145, 207, 131) Brain_Stem: limiting intensities to 81.0 --> 253.0 0 of 184 (0.0%) samples deleted using 5673 total control points for intensity normalization... bias field = 1.014 +- 0.063 10 of 5360 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39361 control points for structure... bounding box (126, 67, 39) --> (191, 180, 195) Left_Cerebral_White_Matter: limiting intensities to 84.0 --> 255.0 140 of 1399 (10.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39033 control points for structure... bounding box (69, 66, 35) --> (132, 172, 194) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 255.0 9 of 3814 (0.2%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 2873 control points for structure... bounding box (131, 155, 72) --> (175, 196, 122) Left_Cerebellum_White_Matter: limiting intensities to 73.0 --> 255.0 0 of 156 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2551 control points for structure... bounding box (88, 156, 65) --> (131, 195, 119) Right_Cerebellum_White_Matter: limiting intensities to 93.0 --> 255.0 48 of 148 (32.4%) samples deleted finding control points in Brain_Stem.... found 3424 control points for structure... bounding box (112, 139, 100) --> (145, 207, 131) Brain_Stem: limiting intensities to 77.0 --> 255.0 0 of 254 (0.0%) samples deleted using 5771 total control points for intensity normalization... bias field = 1.010 +- 0.051 15 of 5474 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 7 seconds. #-------------------------------------- #@# CA Reg lun 4 gen 2016, 22.03.52, CET /home/salvatore/freesurfer/subjects/T1-1/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /home/salvatore/freesurfer/average/RB_all_2015-08-04.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_ca_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/home/salvatore/freesurfer/average/RB_all_2015-08-04.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.16 (predicted orig area = 6.9) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.993, neg=0, invalid=3294 0001: dt=207.680000, rms=0.959 (3.392%), neg=0, invalid=3294 0002: dt=453.916927, rms=0.912 (4.970%), neg=0, invalid=3294 0003: dt=63.394322, rms=0.909 (0.298%), neg=0, invalid=3294 0004: dt=32.368000, rms=0.909 (0.046%), neg=0, invalid=3294 0005: dt=32.368000, rms=0.908 (0.034%), neg=0, invalid=3294 0006: dt=32.368000, rms=0.908 (0.017%), neg=0, invalid=3294 0007: dt=32.368000, rms=0.908 (-0.013%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.909, neg=0, invalid=3294 0008: dt=240.484848, rms=0.898 (1.177%), neg=0, invalid=3294 0009: dt=295.936000, rms=0.895 (0.304%), neg=0, invalid=3294 0010: dt=369.920000, rms=0.893 (0.245%), neg=0, invalid=3294 0011: dt=369.920000, rms=0.893 (0.008%), neg=0, invalid=3294 0012: dt=369.920000, rms=0.889 (0.445%), neg=0, invalid=3294 0013: dt=369.920000, rms=0.889 (0.009%), neg=0, invalid=3294 0014: dt=369.920000, rms=0.888 (0.104%), neg=0, invalid=3294 0015: dt=369.920000, rms=0.885 (0.293%), neg=0, invalid=3294 0016: dt=369.920000, rms=0.883 (0.226%), neg=0, invalid=3294 0017: dt=369.920000, rms=0.880 (0.342%), neg=0, invalid=3294 0018: dt=369.920000, rms=0.878 (0.218%), neg=0, invalid=3294 0019: dt=369.920000, rms=0.876 (0.243%), neg=0, invalid=3294 0020: dt=369.920000, rms=0.876 (-2.222%), neg=0, invalid=3294 0021: dt=66.921739, rms=0.872 (0.495%), neg=0, invalid=3294 0022: dt=295.936000, rms=0.871 (0.100%), neg=0, invalid=3294 0023: dt=295.936000, rms=0.870 (0.083%), neg=0, invalid=3294 0024: dt=295.936000, rms=0.870 (-0.220%), neg=0, invalid=3294 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.883, neg=0, invalid=3294 0025: dt=31.104000, rms=0.879 (0.404%), neg=0, invalid=3294 0026: dt=128.810127, rms=0.870 (1.057%), neg=0, invalid=3294 0027: dt=141.490725, rms=0.850 (2.349%), neg=0, invalid=3294 0028: dt=9.072000, rms=0.848 (0.205%), neg=0, invalid=3294 0029: dt=9.072000, rms=0.848 (0.043%), neg=0, invalid=3294 0030: dt=9.072000, rms=0.848 (-0.101%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.848, neg=0, invalid=3294 0031: dt=36.288000, rms=0.845 (0.331%), neg=0, invalid=3294 0032: dt=36.288000, rms=0.844 (0.123%), neg=0, invalid=3294 0033: dt=36.288000, rms=0.843 (0.109%), neg=0, invalid=3294 0034: dt=36.288000, rms=0.843 (0.102%), neg=0, invalid=3294 0035: dt=36.288000, rms=0.842 (0.105%), neg=0, invalid=3294 0036: dt=36.288000, rms=0.841 (0.107%), neg=0, invalid=3294 0037: dt=36.288000, rms=0.839 (0.170%), neg=0, invalid=3294 0038: dt=36.288000, rms=0.837 (0.248%), neg=0, invalid=3294 0039: dt=36.288000, rms=0.835 (0.310%), neg=0, invalid=3294 0040: dt=36.288000, rms=0.832 (0.343%), neg=0, invalid=3294 0041: dt=36.288000, rms=0.829 (0.366%), neg=0, invalid=3294 0042: dt=36.288000, rms=0.826 (0.378%), neg=0, invalid=3294 0043: dt=36.288000, rms=0.823 (0.325%), neg=0, invalid=3294 0044: dt=36.288000, rms=0.821 (0.278%), neg=0, invalid=3294 0045: dt=36.288000, rms=0.819 (0.259%), neg=0, invalid=3294 0046: dt=36.288000, rms=0.817 (0.255%), neg=0, invalid=3294 0047: dt=36.288000, rms=0.814 (0.254%), neg=0, invalid=3294 0048: dt=36.288000, rms=0.813 (0.234%), neg=0, invalid=3294 0049: dt=36.288000, rms=0.811 (0.186%), neg=0, invalid=3294 0050: dt=36.288000, rms=0.810 (0.136%), neg=0, invalid=3294 0051: dt=36.288000, rms=0.809 (0.101%), neg=0, invalid=3294 0052: dt=36.288000, rms=0.809 (0.074%), neg=0, invalid=3294 0053: dt=103.680000, rms=0.808 (0.050%), neg=0, invalid=3294 0054: dt=3.240000, rms=0.808 (0.003%), neg=0, invalid=3294 0055: dt=1.620000, rms=0.808 (0.001%), neg=0, invalid=3294 0056: dt=0.405000, rms=0.808 (0.000%), neg=0, invalid=3294 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.846, neg=0, invalid=3294 0057: dt=2.800000, rms=0.844 (0.231%), neg=0, invalid=3294 0058: dt=0.700000, rms=0.844 (0.040%), neg=0, invalid=3294 0059: dt=0.700000, rms=0.843 (0.037%), neg=0, invalid=3294 0060: dt=0.350000, rms=0.843 (0.018%), neg=0, invalid=3294 0061: dt=0.175000, rms=0.843 (0.008%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.844, neg=0, invalid=3294 0062: dt=0.043750, rms=0.843 (0.059%), neg=0, invalid=3294 0063: dt=0.010937, rms=0.843 (-0.000%), neg=0, invalid=3294 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.951, neg=0, invalid=3294 0064: dt=8.262976, rms=0.912 (4.120%), neg=0, invalid=3294 0065: dt=4.032000, rms=0.903 (0.990%), neg=0, invalid=3294 0066: dt=17.090909, rms=0.892 (1.154%), neg=0, invalid=3294 0067: dt=9.216000, rms=0.890 (0.258%), neg=0, invalid=3294 0068: dt=11.428571, rms=0.887 (0.359%), neg=0, invalid=3294 0069: dt=5.200000, rms=0.885 (0.170%), neg=0, invalid=3294 0070: dt=5.200000, rms=0.884 (0.126%), neg=0, invalid=3294 0071: dt=5.200000, rms=0.882 (0.217%), neg=0, invalid=3294 0072: dt=5.200000, rms=0.880 (0.226%), neg=0, invalid=3294 0073: dt=5.200000, rms=0.879 (0.203%), neg=0, invalid=3294 0074: dt=5.200000, rms=0.877 (0.215%), neg=0, invalid=3294 0075: dt=5.200000, rms=0.875 (0.206%), neg=0, invalid=3294 0076: dt=5.200000, rms=0.874 (0.150%), neg=0, invalid=3294 0077: dt=5.200000, rms=0.873 (0.102%), neg=0, invalid=3294 0078: dt=5.200000, rms=0.872 (0.080%), neg=0, invalid=3294 0079: dt=3.000000, rms=0.872 (0.004%), neg=0, invalid=3294 0080: dt=0.750000, rms=0.872 (0.002%), neg=0, invalid=3294 0081: dt=0.375000, rms=0.872 (0.001%), neg=0, invalid=3294 0082: dt=0.187500, rms=0.872 (-0.001%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.872, neg=0, invalid=3294 0083: dt=0.000000, rms=0.872 (0.058%), neg=0, invalid=3294 0084: dt=0.000000, rms=0.872 (0.000%), neg=0, invalid=3294 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.912, neg=0, invalid=3294 0085: dt=0.000000, rms=0.911 (0.053%), neg=0, invalid=3294 0086: dt=0.000000, rms=0.911 (0.000%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.912, neg=0, invalid=3294 0087: dt=0.000000, rms=0.911 (0.053%), neg=0, invalid=3294 0088: dt=0.000000, rms=0.911 (0.000%), neg=0, invalid=3294 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.845, neg=0, invalid=3294 0089: dt=0.020000, rms=0.844 (0.164%), neg=0, invalid=3294 0090: dt=0.001750, rms=0.844 (0.010%), neg=0, invalid=3294 0091: dt=0.000438, rms=0.844 (0.002%), neg=0, invalid=3294 0092: dt=0.000109, rms=0.844 (0.001%), neg=0, invalid=3294 0093: dt=0.000027, rms=0.844 (0.000%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.844, neg=0, invalid=3294 0094: dt=0.000000, rms=0.844 (0.063%), neg=0, invalid=3294 0095: dt=0.000000, rms=0.844 (0.000%), neg=0, invalid=3294 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.12974 (17) mri peak = 0.18920 (54) Left_Lateral_Ventricle (4): linear fit = 3.10 x + 0.0 (2211 voxels, overlap=0.001) Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (2211 voxels, peak = 53), gca=25.5 gca peak = 0.13808 (16) mri peak = 0.15337 (25) Right_Lateral_Ventricle (43): linear fit = 1.62 x + 0.0 (1309 voxels, overlap=0.273) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (1309 voxels, peak = 26), gca=24.0 gca peak = 0.25042 (96) mri peak = 0.12649 (102) Right_Pallidum (52): linear fit = 1.07 x + 0.0 (962 voxels, overlap=0.839) Right_Pallidum (52): linear fit = 1.07 x + 0.0 (962 voxels, peak = 102), gca=102.2 gca peak = 0.22986 (96) mri peak = 0.10664 (89) Left_Pallidum (13): linear fit = 0.94 x + 0.0 (828 voxels, overlap=0.979) Left_Pallidum (13): linear fit = 0.94 x + 0.0 (828 voxels, peak = 91), gca=90.7 gca peak = 0.21624 (56) mri peak = 0.06414 (75) Right_Hippocampus (53): linear fit = 1.32 x + 0.0 (999 voxels, overlap=0.019) Right_Hippocampus (53): linear fit = 1.32 x + 0.0 (999 voxels, peak = 74), gca=73.6 gca peak = 0.29672 (58) mri peak = 0.10292 (68) Left_Hippocampus (17): linear fit = 1.15 x + 0.0 (865 voxels, overlap=0.022) Left_Hippocampus (17): linear fit = 1.15 x + 0.0 (865 voxels, peak = 67), gca=67.0 gca peak = 0.11066 (101) mri peak = 0.09984 (104) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (73204 voxels, overlap=0.688) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (73204 voxels, peak = 106), gca=105.5 gca peak = 0.10944 (101) mri peak = 0.06758 (107) Left_Cerebral_White_Matter (2): linear fit = 1.08 x + 0.0 (77108 voxels, overlap=0.682) Left_Cerebral_White_Matter (2): linear fit = 1.08 x + 0.0 (77108 voxels, peak = 109), gca=108.6 gca peak = 0.14864 (59) mri peak = 0.03700 (78) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (57744 voxels, overlap=0.000) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (57744 voxels, peak = 79), gca=79.4 gca peak = 0.16234 (58) mri peak = 0.05646 (78) Right_Cerebral_Cortex (42): linear fit = 1.35 x + 0.0 (53142 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.35 x + 0.0 (53142 voxels, peak = 78), gca=78.0 gca peak = 0.14764 (67) mri peak = 0.12883 (91) Right_Caudate (50): linear fit = 1.40 x + 0.0 (817 voxels, overlap=0.020) Right_Caudate (50): linear fit = 1.40 x + 0.0 (817 voxels, peak = 94), gca=94.1 gca peak = 0.15152 (71) mri peak = 0.06798 (70) Left_Caudate (11): linear fit = 0.77 x + 0.0 (894 voxels, overlap=0.253) Left_Caudate (11): linear fit = 0.77 x + 0.0 (894 voxels, peak = 55), gca=55.0 gca peak = 0.12476 (59) mri peak = 0.04921 (78) Left_Cerebellum_Cortex (8): linear fit = 1.41 x + 0.0 (23680 voxels, overlap=0.001) Left_Cerebellum_Cortex (8): linear fit = 1.41 x + 0.0 (23680 voxels, peak = 83), gca=83.5 gca peak = 0.13886 (58) mri peak = 0.05454 (82) Right_Cerebellum_Cortex (47): linear fit = 1.42 x + 0.0 (23322 voxels, overlap=0.001) Right_Cerebellum_Cortex (47): linear fit = 1.42 x + 0.0 (23322 voxels, peak = 83), gca=82.6 gca peak = 0.19332 (88) mri peak = 0.05904 (94) Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (9844 voxels, overlap=0.594) Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (9844 voxels, peak = 95), gca=95.5 gca peak = 0.19182 (87) mri peak = 0.06240 (91) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (8461 voxels, overlap=0.645) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (8461 voxels, peak = 94), gca=93.5 gca peak = 0.19349 (58) mri peak = 0.11204 (79) Left_Amygdala (18): linear fit = 1.25 x + 0.0 (424 voxels, overlap=0.054) Left_Amygdala (18): linear fit = 1.25 x + 0.0 (424 voxels, peak = 72), gca=72.2 gca peak = 0.32581 (57) mri peak = 0.10856 (69) Right_Amygdala (54): linear fit = 1.22 x + 0.0 (502 voxels, overlap=0.034) Right_Amygdala (54): linear fit = 1.22 x + 0.0 (502 voxels, peak = 69), gca=69.3 gca peak = 0.09144 (86) mri peak = 0.08283 (101) Left_Thalamus_Proper (10): linear fit = 1.20 x + 0.0 (5299 voxels, overlap=0.035) Left_Thalamus_Proper (10): linear fit = 1.20 x + 0.0 (5299 voxels, peak = 103), gca=102.8 gca peak = 0.10273 (84) mri peak = 0.07396 (91) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (3396 voxels, overlap=0.576) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (3396 voxels, peak = 94), gca=93.7 gca peak = 0.13860 (78) mri peak = 0.05909 (71) Left_Putamen (12): linear fit = 0.98 x + 0.0 (2514 voxels, overlap=0.997) Left_Putamen (12): linear fit = 0.98 x + 0.0 (2514 voxels, peak = 76), gca=76.1 gca peak = 0.12691 (78) mri peak = 0.09032 (94) Right_Putamen (51): linear fit = 1.25 x + 0.0 (2493 voxels, overlap=0.020) Right_Putamen (51): linear fit = 1.25 x + 0.0 (2493 voxels, peak = 98), gca=97.9 gca peak = 0.11764 (82) mri peak = 0.10005 (88) Brain_Stem (16): linear fit = 1.10 x + 0.0 (13575 voxels, overlap=0.433) Brain_Stem (16): linear fit = 1.10 x + 0.0 (13575 voxels, peak = 90), gca=89.8 gca peak = 0.10015 (86) mri peak = 0.06500 (96) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1495 voxels, overlap=0.555) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1495 voxels, peak = 93), gca=93.3 gca peak = 0.11151 (90) mri peak = 0.10426 (98) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (1879 voxels, overlap=0.534) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (1879 voxels, peak = 99), gca=99.5 gca peak = 0.19608 (23) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13512 (19) mri peak = 0.15142 (23) Fourth_Ventricle (15): linear fit = 1.13 x + 0.0 (229 voxels, overlap=0.743) Fourth_Ventricle (15): linear fit = 1.13 x + 0.0 (229 voxels, peak = 22), gca=21.6 gca peak Unknown = 0.94959 ( 0) gca peak Left_Inf_Lat_Vent = 0.12743 (29) gca peak Left_Thalamus = 0.71074 (95) gca peak Third_Ventricle = 0.19608 (23) gca peak CSF = 0.17789 (37) gca peak Left_Accumbens_area = 0.50032 (62) gca peak Left_undetermined = 0.97690 (28) gca peak Left_vessel = 0.36001 (53) gca peak Left_choroid_plexus = 0.12300 (45) gca peak Right_Inf_Lat_Vent = 0.21149 (25) gca peak Right_Accumbens_area = 0.31737 (65) gca peak Right_vessel = 0.50186 (52) gca peak Right_choroid_plexus = 0.10991 (44) gca peak Fifth_Ventricle = 0.55462 (35) gca peak WM_hypointensities = 0.10555 (76) gca peak non_WM_hypointensities = 0.08508 (48) gca peak Optic_Chiasm = 0.30852 (73) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 1.27 x + 0.0 estimating mean wm scale to be 1.06 x + 0.0 estimating mean csf scale to be 1.38 x + 0.0 Right_Putamen too bright - rescaling by 0.984 (from 1.255) to 96.4 (was 97.9) saving intensity scales to talairach.label_intensities.txt ********************* ALLOWING NEGATIVE NODES IN DEFORMATION******************************** **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.832, neg=0, invalid=3294 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0096: dt=114.651934, rms=0.777 (6.640%), neg=0, invalid=3294 0097: dt=252.761357, rms=0.761 (2.023%), neg=0, invalid=3294 0098: dt=177.523810, rms=0.755 (0.767%), neg=0, invalid=3294 0099: dt=295.936000, rms=0.749 (0.869%), neg=0, invalid=3294 0100: dt=92.480000, rms=0.747 (0.218%), neg=0, invalid=3294 0101: dt=92.480000, rms=0.746 (0.126%), neg=0, invalid=3294 0102: dt=92.480000, rms=0.744 (0.220%), neg=0, invalid=3294 0103: dt=92.480000, rms=0.742 (0.289%), neg=0, invalid=3294 0104: dt=92.480000, rms=0.740 (0.295%), neg=0, invalid=3294 0105: dt=92.480000, rms=0.738 (0.263%), neg=0, invalid=3294 0106: dt=92.480000, rms=0.737 (0.197%), neg=0, invalid=3294 iter 0, gcam->neg = 7 after 4 iterations, nbhd size=0, neg = 0 0107: dt=92.480000, rms=0.735 (0.153%), neg=0, invalid=3294 iter 0, gcam->neg = 97 after 11 iterations, nbhd size=1, neg = 0 0108: dt=92.480000, rms=0.734 (0.154%), neg=0, invalid=3294 iter 0, gcam->neg = 161 after 14 iterations, nbhd size=1, neg = 0 0109: dt=92.480000, rms=0.733 (0.146%), neg=0, invalid=3294 iter 0, gcam->neg = 236 after 16 iterations, nbhd size=1, neg = 0 0110: dt=92.480000, rms=0.733 (0.090%), neg=0, invalid=3294 iter 0, gcam->neg = 266 after 23 iterations, nbhd size=1, neg = 0 0111: dt=92.480000, rms=0.732 (0.019%), neg=0, invalid=3294 iter 0, gcam->neg = 11 after 10 iterations, nbhd size=0, neg = 0 0112: dt=517.888000, rms=0.730 (0.276%), neg=0, invalid=3294 iter 0, gcam->neg = 2 after 5 iterations, nbhd size=0, neg = 0 0113: dt=295.936000, rms=0.729 (0.135%), neg=0, invalid=3294 iter 0, gcam->neg = 18 after 7 iterations, nbhd size=0, neg = 0 0114: dt=295.936000, rms=0.729 (-0.122%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.730, neg=0, invalid=3294 iter 0, gcam->neg = 8 after 2 iterations, nbhd size=0, neg = 0 0115: dt=73.984000, rms=0.729 (0.198%), neg=0, invalid=3294 iter 0, gcam->neg = 8 after 7 iterations, nbhd size=0, neg = 0 0116: dt=73.984000, rms=0.728 (0.024%), neg=0, invalid=3294 iter 0, gcam->neg = 5 after 1 iterations, nbhd size=0, neg = 0 0117: dt=73.984000, rms=0.728 (0.021%), neg=0, invalid=3294 iter 0, gcam->neg = 16 after 9 iterations, nbhd size=0, neg = 0 0118: dt=73.984000, rms=0.728 (0.009%), neg=0, invalid=3294 iter 0, gcam->neg = 19 after 12 iterations, nbhd size=0, neg = 0 0119: dt=73.984000, rms=0.728 (-0.008%), neg=0, invalid=3294 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.733, neg=0, invalid=3294 iter 0, gcam->neg = 5 after 9 iterations, nbhd size=1, neg = 0 0120: dt=93.847534, rms=0.726 (1.063%), neg=0, invalid=3294 iter 0, gcam->neg = 210 after 20 iterations, nbhd size=1, neg = 0 0121: dt=116.869565, rms=0.716 (1.359%), neg=0, invalid=3294 iter 0, gcam->neg = 34 after 14 iterations, nbhd size=1, neg = 0 0122: dt=73.442623, rms=0.712 (0.538%), neg=0, invalid=3294 iter 0, gcam->neg = 163 after 22 iterations, nbhd size=1, neg = 0 0123: dt=91.254753, rms=0.707 (0.623%), neg=0, invalid=3294 iter 0, gcam->neg = 6 after 3 iterations, nbhd size=0, neg = 0 0124: dt=36.288000, rms=0.706 (0.260%), neg=0, invalid=3294 iter 0, gcam->neg = 337 after 29 iterations, nbhd size=1, neg = 0 0125: dt=331.776000, rms=0.700 (0.744%), neg=0, invalid=3294 iter 0, gcam->neg = 62 after 22 iterations, nbhd size=1, neg = 0 0126: dt=53.760000, rms=0.697 (0.443%), neg=0, invalid=3294 iter 0, gcam->neg = 29 after 8 iterations, nbhd size=0, neg = 0 0127: dt=89.234286, rms=0.696 (0.185%), neg=0, invalid=3294 iter 0, gcam->neg = 50 after 24 iterations, nbhd size=1, neg = 0 0128: dt=89.234286, rms=0.695 (0.191%), neg=0, invalid=3294 iter 0, gcam->neg = 86 after 22 iterations, nbhd size=1, neg = 0 0129: dt=89.234286, rms=0.692 (0.441%), neg=0, invalid=3294 iter 0, gcam->neg = 149 after 20 iterations, nbhd size=1, neg = 0 0130: dt=89.234286, rms=0.689 (0.321%), neg=0, invalid=3294 iter 0, gcam->neg = 284 after 29 iterations, nbhd size=1, neg = 0 0131: dt=89.234286, rms=0.686 (0.511%), neg=0, invalid=3294 iter 0, gcam->neg = 260 after 1000 iterations, nbhd size=4, neg = 1 starting rms=0.016, neg=1, removing folds in lattice.... iter 1, dt=0.119772: new neg 11, old_neg 1, delta -10, rms=0.013 (21.363%) iter 2, dt=0.097656: new neg 1, old_neg 11, delta 10, rms=0.011 (12.253%) iter 3, dt=0.088839: new neg 3, old_neg 1, delta -2, rms=0.011 (7.467%) iter 4, dt=0.073438: new neg 1, old_neg 3, delta 2, rms=0.010 (5.966%) iter 5, dt=0.071214: new neg 1, old_neg 1, delta 0, rms=0.009 (3.945%) iter 6, dt=0.059537: new neg 1, old_neg 1, delta 0, rms=0.009 (3.583%) iter 7, dt=0.059896: new neg 1, old_neg 1, delta 0, rms=0.009 (2.410%) iter 8, dt=0.065789: new neg 1, old_neg 1, delta 0, rms=0.009 (2.160%) iter 9, dt=0.059304: new neg 1, old_neg 1, delta 0, rms=0.009 (2.349%) iter 10, dt=0.052344: new neg 1, old_neg 1, delta 0, rms=0.008 (1.681%) iter 11, dt=0.056641: new neg 1, old_neg 1, delta 0, rms=0.008 (1.415%) iter 12, dt=0.049342: new neg 1, old_neg 1, delta 0, rms=0.008 (1.593%) iter 13, dt=0.057943: new neg 1, old_neg 1, delta 0, rms=0.008 (0.837%) iter 14, dt=0.054228: new neg 1, old_neg 1, delta 0, rms=0.008 (1.607%) iter 15, dt=0.044678: new neg 1, old_neg 1, delta 0, rms=0.008 (0.979%) iter 16, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.008 (0.464%) iter 17, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.008 (0.349%) iter 18, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.008 (0.291%) iter 19, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.008 (0.263%) iter 20, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.008 (0.247%) iter 21, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.008 (0.235%) iter 22, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.008 (0.226%) iter 23, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.008 (0.218%) iter 24, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.008 (0.212%) iter 25, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.008 (0.207%) iter 26, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.008 (0.202%) iter 27, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.008 (0.198%) iter 28, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.008 (0.194%) iter 29, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.008 (0.191%) iter 30, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.008 (0.188%) iter 31, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.008 (0.185%) iter 32, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.008 (0.182%) iter 33, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.008 (0.179%) iter 34, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.008 (0.177%) iter 35, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.008 (0.174%) iter 36, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.007 (0.172%) iter 37, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.007 (0.170%) iter 38, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.007 (0.168%) iter 39, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.007 (0.166%) iter 40, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.007 (0.164%) iter 41, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.007 (0.162%) iter 42, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.007 (0.161%) iter 43, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.007 (0.159%) iter 44, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.007 (0.157%) iter 45, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.007 (0.156%) iter 46, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.007 (0.154%) iter 47, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.007 (0.153%) iter 48, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.007 (0.152%) iter 49, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.007 (0.150%) iter 50, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.007 (0.149%) iter 51, dt=0.009175: new neg 0, old_neg 1, delta 1, rms=0.007 (0.148%) 0132: dt=89.234286, rms=0.683 (0.394%), neg=0, invalid=3294 iter 0, gcam->neg = 3 after 5 iterations, nbhd size=0, neg = 0 0133: dt=89.234286, rms=0.682 (0.130%), neg=0, invalid=3294 iter 0, gcam->neg = 138 after 17 iterations, nbhd size=1, neg = 0 0134: dt=89.234286, rms=0.680 (0.305%), neg=0, invalid=3294 iter 0, gcam->neg = 450 after 26 iterations, nbhd size=1, neg = 0 0135: dt=89.234286, rms=0.680 (-0.236%), neg=0, invalid=3294 iter 0, gcam->neg = 4 after 9 iterations, nbhd size=1, neg = 0 0136: dt=17.142857, rms=0.680 (0.024%), neg=0, invalid=3294 0137: dt=6.480000, rms=0.680 (0.002%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.681, neg=0, invalid=3294 0138: dt=31.104000, rms=0.679 (0.191%), neg=0, invalid=3294 0139: dt=36.288000, rms=0.679 (0.049%), neg=0, invalid=3294 0140: dt=36.288000, rms=0.679 (0.069%), neg=0, invalid=3294 0141: dt=36.288000, rms=0.678 (0.044%), neg=0, invalid=3294 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0142: dt=36.288000, rms=0.678 (-0.075%), neg=0, invalid=3294 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.700, neg=0, invalid=3294 iter 0, gcam->neg = 8 after 3 iterations, nbhd size=0, neg = 0 0143: dt=28.753623, rms=0.694 (0.956%), neg=0, invalid=3294 iter 0, gcam->neg = 280 after 21 iterations, nbhd size=1, neg = 0 0144: dt=66.105263, rms=0.684 (1.353%), neg=0, invalid=3294 iter 0, gcam->neg = 4 after 2 iterations, nbhd size=0, neg = 0 0145: dt=17.411765, rms=0.681 (0.431%), neg=0, invalid=3294 iter 0, gcam->neg = 181 after 16 iterations, nbhd size=1, neg = 0 0146: dt=84.737984, rms=0.677 (0.691%), neg=0, invalid=3294 iter 0, gcam->neg = 22 after 11 iterations, nbhd size=0, neg = 0 0147: dt=11.200000, rms=0.675 (0.263%), neg=0, invalid=3294 iter 0, gcam->neg = 32 after 12 iterations, nbhd size=0, neg = 0 0148: dt=38.400000, rms=0.674 (0.135%), neg=0, invalid=3294 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0149: dt=38.400000, rms=0.673 (0.098%), neg=0, invalid=3294 iter 0, gcam->neg = 24 after 12 iterations, nbhd size=1, neg = 0 0150: dt=38.400000, rms=0.672 (0.234%), neg=0, invalid=3294 iter 0, gcam->neg = 114 after 20 iterations, nbhd size=1, neg = 0 0151: dt=38.400000, rms=0.669 (0.458%), neg=0, invalid=3294 iter 0, gcam->neg = 174 after 1000 iterations, nbhd size=6, neg = 1 starting rms=0.010, neg=1, removing folds in lattice.... iter 1, dt=0.125388: new neg 6, old_neg 1, delta -5, rms=0.008 (14.631%) iter 2, dt=0.125521: new neg 3, old_neg 6, delta 3, rms=0.008 (8.546%) iter 3, dt=0.118089: new neg 2, old_neg 3, delta 1, rms=0.007 (6.518%) iter 4, dt=0.100361: new neg 1, old_neg 2, delta 1, rms=0.007 (5.490%) iter 5, dt=0.136161: new neg 1, old_neg 1, delta 0, rms=0.006 (2.808%) iter 6, dt=0.097187: new neg 1, old_neg 1, delta 0, rms=0.006 (5.612%) iter 7, dt=0.093750: new neg 1, old_neg 1, delta 0, rms=0.006 (2.601%) iter 8, dt=0.113636: new neg 1, old_neg 1, delta 0, rms=0.006 (1.146%) iter 9, dt=0.089638: new neg 1, old_neg 1, delta 0, rms=0.006 (3.730%) iter 10, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.006 (0.492%) iter 11, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.006 (0.416%) iter 12, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.006 (0.365%) iter 13, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.006 (0.328%) iter 14, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.006 (0.301%) iter 15, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.006 (0.280%) iter 16, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.006 (0.264%) iter 17, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.251%) iter 18, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.241%) iter 19, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.232%) iter 20, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.225%) iter 21, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.219%) iter 22, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.213%) iter 23, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.208%) iter 24, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.203%) iter 25, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.199%) iter 26, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.195%) iter 27, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.191%) iter 28, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.188%) iter 29, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.184%) iter 30, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.181%) iter 31, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.178%) iter 32, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.176%) iter 33, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.173%) iter 34, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.171%) iter 35, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.168%) iter 36, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.166%) iter 37, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.164%) iter 38, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.162%) iter 39, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.159%) iter 40, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.157%) iter 41, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.155%) iter 42, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.154%) iter 43, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.152%) iter 44, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.150%) iter 45, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.149%) iter 46, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.147%) iter 47, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.146%) iter 48, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.144%) iter 49, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.143%) iter 50, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.141%) iter 51, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.140%) iter 52, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.139%) iter 53, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.137%) iter 54, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.136%) iter 55, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.135%) iter 56, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.134%) iter 57, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.132%) iter 58, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.131%) iter 59, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.130%) iter 60, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.129%) iter 61, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.128%) iter 62, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.127%) iter 63, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.126%) iter 64, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.125%) iter 65, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.124%) iter 66, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.123%) iter 67, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.122%) iter 68, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.121%) iter 69, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.121%) iter 70, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.120%) iter 71, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.119%) iter 72, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.118%) iter 73, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.117%) iter 74, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.116%) iter 75, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.116%) iter 76, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.115%) iter 77, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.114%) iter 78, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.113%) iter 79, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.113%) iter 80, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.112%) iter 81, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.111%) iter 82, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.111%) iter 83, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.110%) iter 84, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.109%) iter 85, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.109%) iter 86, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.108%) iter 87, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.107%) iter 88, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.107%) iter 89, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.106%) iter 90, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.106%) iter 91, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.105%) iter 92, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.104%) iter 93, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.104%) iter 94, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.103%) iter 95, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.103%) iter 96, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.102%) iter 97, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.102%) iter 98, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.101%) iter 99, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.101%) iter 100, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.100%) ---------- unfolding failed - restoring original position -------------------- 0152: dt=38.400000, rms=0.669 (0.001%), neg=0, invalid=3294 iter 0, gcam->neg = 45 after 18 iterations, nbhd size=1, neg = 0 0153: dt=38.400000, rms=0.669 (-0.004%), neg=0, invalid=3294 iter 0, gcam->neg = 10 after 7 iterations, nbhd size=0, neg = 0 0154: dt=11.200000, rms=0.668 (0.047%), neg=0, invalid=3294 iter 0, gcam->neg = 66 after 17 iterations, nbhd size=1, neg = 0 0155: dt=44.800000, rms=0.668 (0.094%), neg=0, invalid=3294 iter 0, gcam->neg = 16 after 1000 iterations, nbhd size=6, neg = 1 starting rms=0.009, neg=1, removing folds in lattice.... iter 1, dt=0.169657: new neg 2, old_neg 1, delta -1, rms=0.007 (15.801%) iter 2, dt=0.144531: new neg 1, old_neg 2, delta 1, rms=0.007 (7.822%) iter 3, dt=0.143029: new neg 1, old_neg 1, delta 0, rms=0.006 (4.689%) iter 4, dt=0.123884: new neg 1, old_neg 1, delta 0, rms=0.006 (4.225%) iter 5, dt=0.139757: new neg 1, old_neg 1, delta 0, rms=0.006 (2.512%) iter 6, dt=0.157118: new neg 1, old_neg 1, delta 0, rms=0.006 (2.414%) iter 7, dt=0.110491: new neg 1, old_neg 1, delta 0, rms=0.006 (4.337%) iter 8, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.006 (0.348%) iter 9, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.006 (0.304%) iter 10, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.269%) iter 11, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.242%) iter 12, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.222%) iter 13, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.207%) iter 14, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.196%) iter 15, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.187%) iter 16, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.180%) iter 17, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.174%) iter 18, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.169%) iter 19, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.165%) iter 20, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.161%) iter 21, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.158%) iter 22, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.155%) iter 23, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.153%) iter 24, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.150%) iter 25, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.148%) iter 26, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.146%) iter 27, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.145%) iter 28, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.143%) iter 29, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.141%) iter 30, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.140%) iter 31, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.138%) iter 32, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.137%) iter 33, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.136%) iter 34, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.135%) iter 35, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.133%) iter 36, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.132%) iter 37, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.131%) iter 38, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.130%) iter 39, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.129%) iter 40, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.128%) iter 41, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.127%) iter 42, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.126%) iter 43, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.125%) iter 44, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.124%) iter 45, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.123%) iter 46, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.122%) iter 47, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.121%) iter 48, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.120%) iter 49, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.120%) iter 50, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.119%) iter 51, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.118%) iter 52, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.117%) iter 53, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.117%) iter 54, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.116%) iter 55, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.115%) iter 56, dt=0.009175: new 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dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.106%) iter 71, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.105%) iter 72, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.105%) iter 73, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.104%) iter 74, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.104%) iter 75, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.103%) iter 76, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.102%) iter 77, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.102%) iter 78, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.101%) iter 79, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.101%) iter 80, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.100%) iter 81, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.100%) iter 82, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.100%) iter 83, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.099%) iter 84, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.099%) iter 85, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.098%) iter 86, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.098%) iter 87, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.097%) iter 88, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.097%) iter 89, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.096%) iter 90, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.096%) iter 91, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.095%) iter 92, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.095%) iter 93, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.095%) iter 94, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.094%) iter 95, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.094%) iter 96, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.093%) iter 97, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.093%) iter 98, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.093%) iter 99, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.092%) iter 100, dt=0.009175: new neg 1, old_neg 1, delta 0, rms=0.005 (0.092%) ---------- unfolding failed - restoring original position -------------------- 0156: dt=32.000000, rms=0.668 (-0.000%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.668, neg=0, invalid=3294 0157: dt=-0.001465, rms=0.668 (0.084%), neg=0, invalid=3294 0158: dt=0.000000, rms=0.668 (0.000%), neg=0, invalid=3294 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.707, neg=0, invalid=3294 0159: dt=0.000000, rms=0.706 (0.075%), neg=0, invalid=3294 0160: dt=0.000000, rms=0.706 (0.000%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.707, neg=0, invalid=3294 0161: dt=0.000000, rms=0.706 (0.075%), neg=0, invalid=3294 0162: dt=0.000000, rms=0.706 (0.000%), neg=0, invalid=3294 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.782, neg=0, invalid=3294 iter 0, gcam->neg = 4 after 4 iterations, nbhd size=0, neg = 0 0163: dt=1.146830, rms=0.772 (1.303%), neg=0, invalid=3294 iter 0, gcam->neg = 5 after 3 iterations, nbhd size=0, neg = 0 0164: dt=1.280000, rms=0.768 (0.425%), neg=0, invalid=3294 iter 0, gcam->neg = 4 after 7 iterations, nbhd size=0, neg = 0 0165: dt=1.792000, rms=0.764 (0.510%), neg=0, invalid=3294 iter 0, gcam->neg = 2 after 4 iterations, nbhd size=0, neg = 0 0166: dt=1.536000, rms=0.763 (0.252%), neg=0, invalid=3294 iter 0, gcam->neg = 1 after 4 iterations, nbhd size=0, neg = 0 0167: dt=1.792000, rms=0.759 (0.497%), neg=0, invalid=3294 0168: dt=0.448000, rms=0.758 (0.091%), neg=0, invalid=3294 0169: dt=0.448000, rms=0.758 (0.052%), neg=0, invalid=3294 0170: dt=0.448000, rms=0.757 (0.081%), neg=0, invalid=3294 0171: dt=0.448000, rms=0.756 (0.126%), neg=0, invalid=3294 0172: dt=0.448000, rms=0.755 (0.190%), neg=0, invalid=3294 0173: dt=0.448000, rms=0.753 (0.201%), neg=0, invalid=3294 0174: dt=0.448000, rms=0.752 (0.159%), neg=0, invalid=3294 0175: dt=0.448000, rms=0.751 (0.101%), neg=0, invalid=3294 0176: dt=0.448000, rms=0.751 (0.046%), neg=0, invalid=3294 0177: dt=3.072000, rms=0.750 (0.143%), neg=0, invalid=3294 0178: dt=1.792000, rms=0.748 (0.246%), neg=0, invalid=3294 0179: dt=0.384000, rms=0.748 (0.024%), neg=0, invalid=3294 0180: dt=0.384000, rms=0.748 (0.002%), neg=0, invalid=3294 0181: dt=0.384000, rms=0.748 (-0.005%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.748, neg=0, invalid=3294 0182: dt=1.536000, rms=0.747 (0.191%), neg=0, invalid=3294 0183: dt=1.280000, rms=0.746 (0.069%), neg=0, invalid=3294 0184: dt=1.280000, rms=0.746 (0.065%), neg=0, invalid=3294 0185: dt=1.280000, rms=0.745 (0.093%), neg=0, invalid=3294 0186: dt=1.280000, rms=0.744 (0.094%), neg=0, invalid=3294 0187: dt=1.280000, rms=0.744 (0.057%), neg=0, invalid=3294 0188: dt=1.280000, rms=0.744 (0.034%), neg=0, invalid=3294 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.731, neg=0, invalid=3294 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0189: dt=1.130811, rms=0.702 (3.969%), neg=0, invalid=3294 0190: dt=0.112000, rms=0.700 (0.286%), neg=0, invalid=3294 0191: dt=0.024000, rms=0.700 (0.007%), neg=0, invalid=3294 0192: dt=0.024000, rms=0.700 (-0.007%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.701, neg=0, invalid=3294 0193: dt=0.028000, rms=0.700 (0.082%), neg=0, invalid=3294 0194: dt=0.007000, rms=0.700 (0.002%), neg=0, invalid=3294 0195: dt=0.007000, rms=0.700 (-0.000%), neg=0, invalid=3294 label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.687, neg=0, invalid=3294 0196: dt=38.400000, rms=0.685 (0.351%), neg=0, invalid=3294 0197: dt=32.368000, rms=0.684 (0.114%), neg=0, invalid=3294 0198: dt=32.368000, rms=0.684 (0.073%), neg=0, invalid=3294 0199: dt=32.368000, rms=0.683 (0.031%), neg=0, invalid=3294 0200: dt=32.368000, rms=0.683 (-0.083%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.683, neg=0, invalid=3294 0201: dt=92.480000, rms=0.682 (0.135%), neg=0, invalid=3294 0202: dt=221.952000, rms=0.681 (0.174%), neg=0, invalid=3294 0203: dt=369.920000, rms=0.680 (0.113%), neg=0, invalid=3294 0204: dt=369.920000, rms=0.679 (0.157%), neg=0, invalid=3294 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0205: dt=369.920000, rms=0.679 (-0.435%), neg=0, invalid=3294 0206: dt=27.744000, rms=0.679 (0.006%), neg=0, invalid=3294 0207: dt=18.496000, rms=0.679 (0.002%), neg=0, invalid=3294 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.680, neg=0, invalid=3294 iter 0, gcam->neg = 16 after 8 iterations, nbhd size=1, neg = 0 0208: dt=63.881262, rms=0.671 (1.300%), neg=0, invalid=3294 iter 0, gcam->neg = 482 after 21 iterations, nbhd size=1, neg = 0 0209: dt=117.415008, rms=0.662 (1.274%), neg=0, invalid=3294 iter 0, gcam->neg = 143 after 25 iterations, nbhd size=1, neg = 0 0210: dt=36.288000, rms=0.660 (0.318%), neg=0, invalid=3294 iter 0, gcam->neg = 819 after 25 iterations, nbhd size=1, neg = 0 0211: dt=124.416000, rms=0.658 (0.361%), neg=0, invalid=3294 iter 0, gcam->neg = 535 after 31 iterations, nbhd size=1, neg = 0 0212: dt=145.152000, rms=0.655 (0.399%), neg=0, invalid=3294 iter 0, gcam->neg = 74 after 27 iterations, nbhd size=1, neg = 0 0213: dt=36.288000, rms=0.655 (0.067%), neg=0, invalid=3294 iter 0, gcam->neg = 78 after 23 iterations, nbhd size=1, neg = 0 0214: dt=36.288000, rms=0.655 (0.032%), neg=0, invalid=3294 iter 0, gcam->neg = 134 after 29 iterations, nbhd size=1, neg = 0 0215: dt=36.288000, rms=0.654 (0.056%), neg=0, invalid=3294 iter 0, gcam->neg = 196 after 31 iterations, nbhd size=1, neg = 0 0216: dt=36.288000, rms=0.653 (0.113%), neg=0, invalid=3294 iter 0, gcam->neg = 250 after 30 iterations, nbhd size=1, neg = 0 0217: dt=36.288000, rms=0.653 (0.145%), neg=0, invalid=3294 iter 0, gcam->neg = 457 after 32 iterations, nbhd size=1, neg = 0 0218: dt=36.288000, rms=0.652 (0.079%), neg=0, invalid=3294 iter 0, gcam->neg = 613 after 32 iterations, nbhd size=1, neg = 0 0219: dt=36.288000, rms=0.652 (-0.028%), neg=0, invalid=3294 0220: dt=0.000000, rms=0.652 (0.000%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.652, neg=0, invalid=3294 iter 0, gcam->neg = 42 after 21 iterations, nbhd size=0, neg = 0 0221: dt=36.288000, rms=0.651 (0.156%), neg=0, invalid=3294 iter 0, gcam->neg = 77 after 13 iterations, nbhd size=0, neg = 0 0222: dt=95.604938, rms=0.650 (0.207%), neg=0, invalid=3294 iter 0, gcam->neg = 52 after 13 iterations, nbhd size=1, neg = 0 0223: dt=145.152000, rms=0.647 (0.370%), neg=0, invalid=3294 iter 0, gcam->neg = 29 after 12 iterations, nbhd size=1, neg = 0 0224: dt=145.152000, rms=0.646 (0.235%), neg=0, invalid=3294 iter 0, gcam->neg = 35 after 13 iterations, nbhd size=1, neg = 0 0225: dt=145.152000, rms=0.643 (0.438%), neg=0, invalid=3294 iter 0, gcam->neg = 206 after 23 iterations, nbhd size=1, neg = 0 0226: dt=145.152000, rms=0.643 (-0.069%), neg=0, invalid=3294 iter 0, gcam->neg = 7 after 9 iterations, nbhd size=1, neg = 0 0227: dt=25.920000, rms=0.643 (0.051%), neg=0, invalid=3294 iter 0, gcam->neg = 10 after 8 iterations, nbhd size=0, neg = 0 0228: dt=31.104000, rms=0.642 (0.018%), neg=0, invalid=3294 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.654, neg=0, invalid=3294 iter 0, gcam->neg = 84 after 10 iterations, nbhd size=0, neg = 0 0229: dt=31.619802, rms=0.647 (1.086%), neg=0, invalid=3294 iter 0, gcam->neg = 202 after 23 iterations, nbhd size=1, neg = 0 0230: dt=56.483221, rms=0.641 (0.945%), neg=0, invalid=3294 iter 0, gcam->neg = 9 after 12 iterations, nbhd size=1, neg = 0 0231: dt=11.200000, rms=0.639 (0.313%), neg=0, invalid=3294 iter 0, gcam->neg = 8 after 11 iterations, nbhd size=1, neg = 0 0232: dt=25.600000, rms=0.638 (0.132%), neg=0, invalid=3294 iter 0, gcam->neg = 48 after 10 iterations, nbhd size=0, neg = 0 0233: dt=25.600000, rms=0.637 (0.201%), neg=0, invalid=3294 iter 0, gcam->neg = 129 after 21 iterations, nbhd size=1, neg = 0 0234: dt=25.600000, rms=0.635 (0.264%), neg=0, invalid=3294 iter 0, gcam->neg = 170 after 20 iterations, nbhd size=1, neg = 0 0235: dt=25.600000, rms=0.634 (0.270%), neg=0, invalid=3294 iter 0, gcam->neg = 138 after 18 iterations, nbhd size=0, neg = 0 0236: dt=25.600000, rms=0.632 (0.247%), neg=0, invalid=3294 iter 0, gcam->neg = 211 after 17 iterations, nbhd size=0, neg = 0 0237: dt=25.600000, rms=0.631 (0.245%), neg=0, invalid=3294 iter 0, gcam->neg = 288 after 17 iterations, nbhd size=0, neg = 0 0238: dt=25.600000, rms=0.630 (0.168%), neg=0, invalid=3294 iter 0, gcam->neg = 263 after 24 iterations, nbhd size=1, neg = 0 0239: dt=25.600000, rms=0.629 (0.066%), neg=0, invalid=3294 iter 0, gcam->neg = 229 after 23 iterations, nbhd size=1, neg = 0 0240: dt=25.600000, rms=0.629 (0.028%), neg=0, invalid=3294 iter 0, gcam->neg = 44 after 13 iterations, nbhd size=1, neg = 0 0241: dt=44.800000, rms=0.628 (0.161%), neg=0, invalid=3294 iter 0, gcam->neg = 13 after 5 iterations, nbhd size=0, neg = 0 0242: dt=11.200000, rms=0.628 (0.033%), neg=0, invalid=3294 iter 0, gcam->neg = 19 after 5 iterations, nbhd size=0, neg = 0 0243: dt=11.200000, rms=0.628 (0.013%), neg=0, invalid=3294 iter 0, gcam->neg = 95 after 10 iterations, nbhd size=0, neg = 0 0244: dt=11.200000, rms=0.628 (0.018%), neg=0, invalid=3294 iter 0, gcam->neg = 202 after 13 iterations, nbhd size=0, neg = 0 0245: dt=11.200000, rms=0.627 (0.004%), neg=0, invalid=3294 iter 0, gcam->neg = 330 after 12 iterations, nbhd size=0, neg = 0 0246: dt=11.200000, rms=0.627 (-0.007%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.627, neg=0, invalid=3294 iter 0, gcam->neg = 3 after 4 iterations, nbhd size=0, neg = 0 0247: dt=11.200000, rms=0.627 (0.110%), neg=0, invalid=3294 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0248: dt=6.400000, rms=0.627 (0.012%), neg=0, invalid=3294 0249: dt=6.400000, rms=0.627 (-0.007%), neg=0, invalid=3294 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.657, neg=0, invalid=3294 0250: dt=0.000039, rms=0.657 (0.000%), neg=0, invalid=3294 0251: dt=0.000000, rms=0.657 (0.000%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.657, neg=0, invalid=3294 0252: dt=0.144000, rms=0.657 (0.001%), neg=0, invalid=3294 0253: dt=0.015750, rms=0.657 (0.000%), neg=0, invalid=3294 0254: dt=0.015750, rms=0.657 (0.000%), neg=0, invalid=3294 0255: dt=0.015750, rms=0.657 (-0.000%), neg=0, invalid=3294 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.715, neg=0, invalid=3294 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0256: dt=1.024000, rms=0.708 (0.942%), neg=0, invalid=3294 0257: dt=0.448000, rms=0.707 (0.098%), neg=0, invalid=3294 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0258: dt=0.448000, rms=0.707 (0.024%), neg=0, invalid=3294 0259: dt=0.448000, rms=0.707 (-0.159%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.707, neg=0, invalid=3294 0260: dt=0.448000, rms=0.706 (0.083%), neg=0, invalid=3294 0261: dt=0.448000, rms=0.706 (0.050%), neg=0, invalid=3294 0262: dt=0.448000, rms=0.706 (0.037%), neg=0, invalid=3294 0263: dt=0.448000, rms=0.706 (-0.017%), neg=0, invalid=3294 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.657, neg=0, invalid=3294 iter 0, gcam->neg = 251 after 16 iterations, nbhd size=1, neg = 0 0264: dt=0.954477, rms=0.636 (3.228%), neg=0, invalid=3294 0265: dt=0.096000, rms=0.635 (0.177%), neg=0, invalid=3294 0266: dt=0.096000, rms=0.635 (-0.134%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.635, neg=0, invalid=3294 0267: dt=0.028000, rms=0.635 (0.014%), neg=0, invalid=3294 0268: dt=0.001750, rms=0.635 (0.000%), neg=0, invalid=3294 0269: dt=0.001750, rms=0.635 (-0.000%), neg=0, invalid=3294 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 2 hours, 17 minutes and 7 seconds. FSRUNTIME@ mri_ca_register 2.2852 hours 1 threads #-------------------------------------- #@# Remove Neck mar 5 gen 2016, 00.20.58, CET mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /home/salvatore/freesurfer/average/RB_all_2015-08-04.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/home/salvatore/freesurfer/average/RB_all_2015-08-04.gca'... reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... setting orig areas to linear transform determinant scaled 6.91 removing structures at least 25 mm from brain... 11186716 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 0 minutes and 34 seconds. #-------------------------------------- #@# SubCort Seg mar 5 gen 2016, 00.21.32, CET mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /home/salvatore/freesurfer/average/RB_all_2015-08-04.gca aseg.auto_noCCseg.mgz sysname Linux hostname salvatore-SATELLITE-P50-B-11M machine x86_64 setenv SUBJECTS_DIR /home/salvatore/freesurfer/subjects cd /home/salvatore/freesurfer/subjects/T1-1/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /home/salvatore/freesurfer/average/RB_all_2015-08-04.gca aseg.auto_noCCseg.mgz == Number of threads available to mri_ca_label for OpenMP = 1 == relabeling unlikely voxels with window_size = 9 and prior threshold 0.30 using Gibbs prior factor = 0.500 renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes... reading classifier array from /home/salvatore/freesurfer/average/RB_all_2015-08-04.gca... reading input volume from norm.mgz... average std[0] = 7.4 reading transform from transforms/talairach.m3z... setting orig areas to linear transform determinant scaled 6.91 Atlas used for the 3D morph was /home/salvatore/freesurfer/average/RB_all_2015-08-04.gca average std = 7.4 using min determinant for regularization = 5.4 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.16337 (20) mri peak = 0.13136 (28) Left_Lateral_Ventricle (4): linear fit = 1.27 x + 0.0 (281 voxels, overlap=0.729) Left_Lateral_Ventricle (4): linear fit = 1.27 x + 0.0 (281 voxels, peak = 26), gca=25.5 gca peak = 0.19190 (13) mri peak = 0.12279 (24) Right_Lateral_Ventricle (43): linear fit = 1.74 x + 0.0 (831 voxels, overlap=0.255) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (831 voxels, peak = 23), gca=19.5 gca peak = 0.24200 (96) mri peak = 0.11964 (102) Right_Pallidum (52): linear fit = 1.09 x + 0.0 (763 voxels, overlap=0.382) Right_Pallidum (52): linear fit = 1.09 x + 0.0 (763 voxels, peak = 104), gca=104.2 gca peak = 0.14904 (91) mri peak = 0.08094 (89) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (678 voxels, overlap=1.014) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (678 voxels, peak = 92), gca=92.4 gca peak = 0.25211 (57) mri peak = 0.08856 (71) Right_Hippocampus (53): linear fit = 1.25 x + 0.0 (954 voxels, overlap=0.022) Right_Hippocampus (53): linear fit = 1.25 x + 0.0 (954 voxels, peak = 72), gca=71.5 gca peak = 0.31987 (57) mri peak = 0.08270 (75) Left_Hippocampus (17): linear fit = 1.25 x + 0.0 (477 voxels, overlap=0.024) Left_Hippocampus (17): linear fit = 1.25 x + 0.0 (477 voxels, peak = 72), gca=71.5 gca peak = 0.08094 (102) mri peak = 0.10662 (104) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (65745 voxels, overlap=0.649) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (65745 voxels, peak = 104), gca=103.5 gca peak = 0.08600 (104) mri peak = 0.07203 (107) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (82355 voxels, overlap=0.588) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (82355 voxels, peak = 110), gca=109.7 gca peak = 0.09612 (57) mri peak = 0.03508 (76) Left_Cerebral_Cortex (3): linear fit = 1.29 x + 0.0 (72768 voxels, overlap=0.000) Left_Cerebral_Cortex (3): linear fit = 1.29 x + 0.0 (72768 voxels, peak = 74), gca=73.8 gca peak = 0.11462 (58) mri peak = 0.05881 (78) Right_Cerebral_Cortex (42): linear fit = 1.35 x + 0.0 (45723 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.35 x + 0.0 (45723 voxels, peak = 78), gca=78.0 gca peak = 0.25255 (66) mri peak = 0.16443 (91) Right_Caudate (50): linear fit = 1.33 x + 0.0 (93 voxels, overlap=0.025) Right_Caudate (50): linear fit = 1.33 x + 0.0 (93 voxels, peak = 87), gca=87.5 gca peak = 0.18480 (77) mri peak = 0.16505 (90) Left_Caudate (11): linear fit = 1.15 x + 0.0 (306 voxels, overlap=0.019) Left_Caudate (11): linear fit = 1.15 x + 0.0 (306 voxels, peak = 89), gca=88.9 gca peak = 0.12729 (58) mri peak = 0.06038 (83) Left_Cerebellum_Cortex (8): linear fit = 1.40 x + 0.0 (23966 voxels, overlap=0.001) Left_Cerebellum_Cortex (8): linear fit = 1.40 x + 0.0 (23966 voxels, peak = 81), gca=81.5 gca peak = 0.12622 (58) mri peak = 0.06251 (82) Right_Cerebellum_Cortex (47): linear fit = 1.40 x + 0.0 (24483 voxels, overlap=0.001) Right_Cerebellum_Cortex (47): linear fit = 1.40 x + 0.0 (24483 voxels, peak = 81), gca=81.5 gca peak = 0.15410 (88) mri peak = 0.07170 (101) Left_Cerebellum_White_Matter (7): linear fit = 1.12 x + 0.0 (9191 voxels, overlap=0.488) Left_Cerebellum_White_Matter (7): linear fit = 1.12 x + 0.0 (9191 voxels, peak = 99), gca=99.0 gca peak = 0.15661 (88) mri peak = 0.07628 (97) Right_Cerebellum_White_Matter (46): linear fit = 1.12 x + 0.0 (8086 voxels, overlap=0.446) Right_Cerebellum_White_Matter (46): linear fit = 1.12 x + 0.0 (8086 voxels, peak = 98), gca=98.1 gca peak = 0.30376 (59) mri peak = 0.11577 (68) Left_Amygdala (18): linear fit = 1.20 x + 0.0 (241 voxels, overlap=0.050) Left_Amygdala (18): linear fit = 1.20 x + 0.0 (241 voxels, peak = 71), gca=70.5 gca peak = 0.35132 (58) mri peak = 0.10795 (70) Right_Amygdala (54): linear fit = 1.26 x + 0.0 (352 voxels, overlap=0.053) Right_Amygdala (54): linear fit = 1.26 x + 0.0 (352 voxels, peak = 73), gca=73.4 gca peak = 0.10548 (89) mri peak = 0.08841 (101) Left_Thalamus_Proper (10): linear fit = 1.12 x + 0.0 (4836 voxels, overlap=0.329) Left_Thalamus_Proper (10): linear fit = 1.12 x + 0.0 (4836 voxels, peak = 99), gca=99.2 gca peak = 0.10706 (82) mri peak = 0.08242 (95) Right_Thalamus_Proper (49): linear fit = 1.14 x + 0.0 (4105 voxels, overlap=0.255) Right_Thalamus_Proper (49): linear fit = 1.14 x + 0.0 (4105 voxels, peak = 94), gca=93.9 gca peak = 0.08512 (74) mri peak = 0.06295 (89) Left_Putamen (12): linear fit = 1.15 x + 0.0 (1237 voxels, overlap=0.417) Left_Putamen (12): linear fit = 1.15 x + 0.0 (1237 voxels, peak = 85), gca=85.5 gca peak = 0.08440 (78) mri peak = 0.08516 (94) Right_Putamen (51): linear fit = 1.21 x + 0.0 (1641 voxels, overlap=0.102) Right_Putamen (51): linear fit = 1.21 x + 0.0 (1641 voxels, peak = 94), gca=94.0 gca peak = 0.07263 (80) mri peak = 0.10243 (88) Brain_Stem (16): linear fit = 1.08 x + 0.0 (12497 voxels, overlap=0.562) Brain_Stem (16): linear fit = 1.08 x + 0.0 (12497 voxels, peak = 86), gca=86.0 gca peak = 0.13309 (90) mri peak = 0.08313 (92) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (1464 voxels, overlap=0.649) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (1464 voxels, peak = 97), gca=96.8 gca peak = 0.15558 (86) mri peak = 0.08277 (98) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1705 voxels, overlap=0.795) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1705 voxels, peak = 92), gca=92.5 gca peak = 0.17913 (26) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.17310 (16) mri peak = 0.14493 (23) Fourth_Ventricle (15): linear fit = 1.41 x + 0.0 (204 voxels, overlap=0.488) Fourth_Ventricle (15): linear fit = 1.41 x + 0.0 (204 voxels, peak = 23), gca=22.6 gca peak Unknown = 0.94959 ( 0) gca peak Left_Inf_Lat_Vent = 0.21424 (27) gca peak Left_Thalamus = 1.00000 (95) gca peak Third_Ventricle = 0.17913 (26) gca peak CSF = 0.22008 (37) gca peak Left_Accumbens_area = 0.78455 (62) gca peak Left_undetermined = 1.00000 (28) gca peak Left_vessel = 0.87251 (52) gca peak Left_choroid_plexus = 0.09096 (57) gca peak Right_Inf_Lat_Vent = 0.24233 (28) gca peak Right_Accumbens_area = 0.41783 (64) gca peak Right_vessel = 0.68147 (52) gca peak Right_choroid_plexus = 0.11536 (37) gca peak Fifth_Ventricle = 0.55384 (33) gca peak WM_hypointensities = 0.10945 (75) gca peak non_WM_hypointensities = 0.07381 (29) gca peak Optic_Chiasm = 0.66945 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.27 x + 0.0 estimating mean wm scale to be 1.03 x + 0.0 estimating mean csf scale to be 1.40 x + 0.0 Right_Putamen too bright - rescaling by 1.021 (from 1.205) to 96.0 (was 94.0) Right_Pallidum too bright - rescaling by 0.993 (from 1.085) to 103.4 (was 104.2) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15038 (25) mri peak = 0.13136 (28) Left_Lateral_Ventricle (4): linear fit = 1.05 x + 0.0 (281 voxels, overlap=0.863) Left_Lateral_Ventricle (4): linear fit = 1.05 x + 0.0 (281 voxels, peak = 26), gca=26.4 gca peak = 0.14274 (19) mri peak = 0.12279 (24) Right_Lateral_Ventricle (43): linear fit = 1.18 x + 0.0 (831 voxels, overlap=0.481) Right_Lateral_Ventricle (43): linear fit = 1.18 x + 0.0 (831 voxels, peak = 23), gca=22.5 gca peak = 0.20469 (101) mri peak = 0.11964 (102) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (763 voxels, overlap=1.004) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (763 voxels, peak = 102), gca=101.5 gca peak = 0.16196 (97) mri peak = 0.08094 (89) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (678 voxels, overlap=1.011) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (678 voxels, peak = 97), gca=97.5 gca peak = 0.23998 (71) mri peak = 0.08856 (71) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (954 voxels, overlap=1.005) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (954 voxels, peak = 70), gca=69.9 gca peak = 0.27799 (72) mri peak = 0.08270 (75) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (477 voxels, overlap=1.004) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (477 voxels, peak = 72), gca=72.0 gca peak = 0.08174 (105) mri peak = 0.10662 (104) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (65745 voxels, overlap=0.717) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (65745 voxels, peak = 105), gca=105.0 gca peak = 0.08120 (109) mri peak = 0.07203 (107) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (82355 voxels, overlap=0.818) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (82355 voxels, peak = 109), gca=109.0 gca peak = 0.07556 (75) mri peak = 0.03508 (76) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (72768 voxels, overlap=0.768) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (72768 voxels, peak = 75), gca=75.0 gca peak = 0.08281 (78) mri peak = 0.05881 (78) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (45723 voxels, overlap=0.943) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (45723 voxels, peak = 78), gca=78.0 gca peak = 0.18633 (88) mri peak = 0.16443 (91) Right_Caudate (50): linear fit = 1.00 x + 0.0 (93 voxels, overlap=0.982) Right_Caudate (50): linear fit = 1.00 x + 0.0 (93 voxels, peak = 88), gca=88.0 gca peak = 0.17326 (89) mri peak = 0.16505 (90) Left_Caudate (11): linear fit = 1.00 x + 0.0 (306 voxels, overlap=0.957) Left_Caudate (11): linear fit = 1.00 x + 0.0 (306 voxels, peak = 89), gca=89.0 gca peak = 0.09279 (80) mri peak = 0.06038 (83) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (23966 voxels, overlap=0.903) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (23966 voxels, peak = 80), gca=79.6 gca peak = 0.09335 (81) mri peak = 0.06251 (82) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (24483 voxels, overlap=0.947) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (24483 voxels, peak = 81), gca=80.6 gca peak = 0.13620 (99) mri peak = 0.07170 (101) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (9191 voxels, overlap=0.980) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (9191 voxels, peak = 99), gca=99.5 gca peak = 0.13910 (98) mri peak = 0.07628 (97) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (8086 voxels, overlap=0.970) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (8086 voxels, peak = 98), gca=98.5 gca peak = 0.28271 (70) mri peak = 0.11577 (68) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (241 voxels, overlap=0.998) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (241 voxels, peak = 70), gca=70.0 gca peak = 0.27422 (73) mri peak = 0.10795 (70) Right_Amygdala (54): linear fit = 0.98 x + 0.0 (352 voxels, overlap=0.991) Right_Amygdala (54): linear fit = 0.98 x + 0.0 (352 voxels, peak = 71), gca=71.2 gca peak = 0.10438 (99) mri peak = 0.08841 (101) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (4836 voxels, overlap=0.910) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (4836 voxels, peak = 100), gca=100.5 gca peak = 0.09687 (94) mri peak = 0.08242 (95) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4105 voxels, overlap=0.912) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4105 voxels, peak = 94), gca=94.0 gca peak = 0.07664 (93) mri peak = 0.06295 (89) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1237 voxels, overlap=0.951) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1237 voxels, peak = 93), gca=92.5 gca peak = 0.06795 (96) mri peak = 0.08516 (94) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1641 voxels, overlap=0.843) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1641 voxels, peak = 95), gca=94.6 gca peak = 0.06963 (87) mri peak = 0.10243 (88) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12497 voxels, overlap=0.781) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12497 voxels, peak = 87), gca=86.6 gca peak = 0.13420 (91) mri peak = 0.08313 (92) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1464 voxels, overlap=0.827) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1464 voxels, peak = 91), gca=91.5 gca peak = 0.14819 (93) mri peak = 0.08277 (98) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1705 voxels, overlap=0.916) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1705 voxels, peak = 93), gca=93.5 gca peak = 0.14872 (36) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.12670 (23) mri peak = 0.14493 (23) Fourth_Ventricle (15): linear fit = 0.94 x + 0.0 (204 voxels, overlap=0.611) Fourth_Ventricle (15): linear fit = 0.94 x + 0.0 (204 voxels, peak = 22), gca=21.7 gca peak Unknown = 0.94960 ( 0) gca peak Left_Inf_Lat_Vent = 0.17508 (34) gca peak Left_Thalamus = 0.35898 (121) gca peak Third_Ventricle = 0.14872 (36) gca peak CSF = 0.19284 (52) gca peak Left_Accumbens_area = 0.69763 (72) gca peak Left_undetermined = 0.97908 (30) gca peak Left_vessel = 0.87251 (52) gca peak Left_choroid_plexus = 0.09970 (44) gca peak Right_Inf_Lat_Vent = 0.18199 (29) gca peak Right_Accumbens_area = 0.29426 (85) gca peak Right_vessel = 0.68147 (52) gca peak Right_choroid_plexus = 0.11438 (37) gca peak Fifth_Ventricle = 0.55145 (44) gca peak WM_hypointensities = 0.11169 (77) gca peak non_WM_hypointensities = 0.08334 (45) gca peak Optic_Chiasm = 0.66471 (76) not using caudate to estimate GM means estimating mean gm scale to be 0.99 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.06 x + 0.0 Right_Putamen too bright - rescaling by 1.018 (from 0.985) to 96.3 (was 94.6) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 117153 voxels changed in iteration 0 of unlikely voxel relabeling 297 voxels changed in iteration 1 of unlikely voxel relabeling 35 voxels changed in iteration 2 of unlikely voxel relabeling 12 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 125912 gm and wm labels changed (%36 to gray, %64 to white out of all changed labels) 719 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 94197 changed. image ll: -2.207, PF=0.500 pass 2: 26912 changed. image ll: -2.204, PF=0.500 pass 3: 9974 changed. pass 4: 4353 changed. MRItoUCHAR: min=0, max=85 MRItoUCHAR: converting to UCHAR writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 32 minutes and 40 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/salvatore/freesurfer/subjects/T1-1/mri/transforms/cc_up.lta T1-1 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /home/salvatore/freesurfer/subjects/T1-1/mri/transforms/cc_up.lta reading aseg from /home/salvatore/freesurfer/subjects/T1-1/mri/aseg.auto_noCCseg.mgz reading norm from /home/salvatore/freesurfer/subjects/T1-1/mri/norm.mgz 110487 voxels in left wm, 121229 in right wm, xrange [116, 137] searching rotation angles z=[-8 6], y=[-1 13] searching scale 1 Z rot -8.0 searching scale 1 Z rot -7.8 searching scale 1 Z rot -7.5 searching scale 1 Z rot -7.3 searching scale 1 Z rot -7.0 searching scale 1 Z rot -6.8 searching scale 1 Z rot -6.5 searching scale 1 Z rot -6.3 searching scale 1 Z rot -6.0 searching scale 1 Z rot -5.8 searching scale 1 Z rot -5.5 searching scale 1 Z rot -5.3 searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.8 searching scale 1 Z rot -4.5 searching scale 1 Z rot -4.3 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.8 searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.3 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.8 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.3 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.8 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.3 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.8 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.3 searching scale 1 Z rot -0.0 searching scale 1 Z rot 0.2 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.7 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.2 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.7 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.2 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.7 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.2 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.7 searching scale 1 Z rot 4.0 searching scale 1 Z rot 4.2 searching scale 1 Z rot 4.5 searching scale 1 Z rot 4.7 global minimum found at slice 126.0, rotations (6.88, -2.01) final transformation (x=126.0, yr=6.875, zr=-2.007): 0.99220 0.03503 0.11963 -14.26883; -0.03477 0.99939 -0.00419 22.91866; -0.11970 0.00000 0.99281 31.88811; 0.00000 0.00000 0.00000 1.00000; updating x range to be [122, 133] in xformed coordinates best xformed slice 126 cc center is found at 126 110 112 eigenvectors: 0.00723 -0.00892 0.99993; 0.01148 -0.99989 -0.00900; 0.99991 0.01154 -0.00712; writing aseg with callosum to /home/salvatore/freesurfer/subjects/T1-1/mri/aseg.auto.mgz... corpus callosum segmentation took 1.9 minutes #-------------------------------------- #@# Merge ASeg mar 5 gen 2016, 00.56.07, CET cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 mar 5 gen 2016, 00.56.07, CET /home/salvatore/freesurfer/subjects/T1-1/mri mri_normalize -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.presurf.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 1708 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 107 gm peak at 83 (83), valley at 34 (34) csf peak at 41, setting threshold to 69 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 109 gm peak at 83 (83), valley at 34 (34) csf peak at 41, setting threshold to 69 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 2 minutes and 14 seconds. #-------------------------------------------- #@# Mask BFS mar 5 gen 2016, 00.58.22, CET /home/salvatore/freesurfer/subjects/T1-1/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1542914 voxels in mask (pct= 9.20) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation mar 5 gen 2016, 00.58.24, CET mri_segment brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (103.0): 104.2 +- 7.3 [80.0 --> 125.0] GM (77.0) : 74.2 +- 14.0 [30.0 --> 96.0] setting bottom of white matter range to 88.1 setting top of gray matter range to 102.1 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 17228 sparsely connected voxels removed... thickening thin strands.... 20 segments, 6542 filled 19583 bright non-wm voxels segmented. 7708 diagonally connected voxels added... white matter segmentation took 1.4 minutes writing output to wm.seg.mgz... mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.35 minutes reading wm segmentation from wm.seg.mgz... 299 voxels added to wm to prevent paths from MTL structures to cortex 11262 additional wm voxels added 0 additional wm voxels added SEG EDIT: 63160 voxels turned on, 3858 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 0 new 0 115,126,128 old 0 new 0 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 116 found - 116 modified | TOTAL: 116 pass 2 (xy+): 0 found - 116 modified | TOTAL: 116 pass 1 (xy-): 93 found - 93 modified | TOTAL: 209 pass 2 (xy-): 0 found - 93 modified | TOTAL: 209 pass 1 (yz+): 124 found - 124 modified | TOTAL: 333 pass 2 (yz+): 0 found - 124 modified | TOTAL: 333 pass 1 (yz-): 129 found - 129 modified | TOTAL: 462 pass 2 (yz-): 0 found - 129 modified | TOTAL: 462 pass 1 (xz+): 84 found - 84 modified | TOTAL: 546 pass 2 (xz+): 0 found - 84 modified | TOTAL: 546 pass 1 (xz-): 59 found - 59 modified | TOTAL: 605 pass 2 (xz-): 0 found - 59 modified | TOTAL: 605 Iteration Number : 1 pass 1 (+++): 121 found - 121 modified | TOTAL: 121 pass 2 (+++): 0 found - 121 modified | TOTAL: 121 pass 1 (+++): 139 found - 139 modified | TOTAL: 260 pass 2 (+++): 0 found - 139 modified | TOTAL: 260 pass 1 (+++): 122 found - 122 modified | TOTAL: 382 pass 2 (+++): 0 found - 122 modified | TOTAL: 382 pass 1 (+++): 183 found - 183 modified | TOTAL: 565 pass 2 (+++): 0 found - 183 modified | TOTAL: 565 Iteration Number : 1 pass 1 (++): 273 found - 273 modified | TOTAL: 273 pass 2 (++): 0 found - 273 modified | TOTAL: 273 pass 1 (+-): 204 found - 204 modified | TOTAL: 477 pass 2 (+-): 0 found - 204 modified | TOTAL: 477 pass 1 (--): 241 found - 241 modified | TOTAL: 718 pass 2 (--): 0 found - 241 modified | TOTAL: 718 pass 1 (-+): 227 found - 227 modified | TOTAL: 945 pass 2 (-+): 0 found - 227 modified | TOTAL: 945 Iteration Number : 2 pass 1 (xy+): 32 found - 32 modified | TOTAL: 32 pass 2 (xy+): 0 found - 32 modified | TOTAL: 32 pass 1 (xy-): 27 found - 27 modified | TOTAL: 59 pass 2 (xy-): 0 found - 27 modified | TOTAL: 59 pass 1 (yz+): 31 found - 31 modified | TOTAL: 90 pass 2 (yz+): 0 found - 31 modified | TOTAL: 90 pass 1 (yz-): 35 found - 35 modified | TOTAL: 125 pass 2 (yz-): 0 found - 35 modified | TOTAL: 125 pass 1 (xz+): 30 found - 30 modified | TOTAL: 155 pass 2 (xz+): 0 found - 30 modified | TOTAL: 155 pass 1 (xz-): 32 found - 32 modified | TOTAL: 187 pass 2 (xz-): 0 found - 32 modified | TOTAL: 187 Iteration Number : 2 pass 1 (+++): 13 found - 13 modified | TOTAL: 13 pass 2 (+++): 0 found - 13 modified | TOTAL: 13 pass 1 (+++): 13 found - 13 modified | TOTAL: 26 pass 2 (+++): 0 found - 13 modified | TOTAL: 26 pass 1 (+++): 12 found - 12 modified | TOTAL: 38 pass 2 (+++): 0 found - 12 modified | TOTAL: 38 pass 1 (+++): 4 found - 4 modified | TOTAL: 42 pass 2 (+++): 0 found - 4 modified | TOTAL: 42 Iteration Number : 2 pass 1 (++): 17 found - 17 modified | TOTAL: 17 pass 2 (++): 0 found - 17 modified | TOTAL: 17 pass 1 (+-): 15 found - 15 modified | TOTAL: 32 pass 2 (+-): 0 found - 15 modified | TOTAL: 32 pass 1 (--): 13 found - 13 modified | TOTAL: 45 pass 2 (--): 0 found - 13 modified | TOTAL: 45 pass 1 (-+): 18 found - 18 modified | TOTAL: 63 pass 2 (-+): 0 found - 18 modified | TOTAL: 63 Iteration Number : 3 pass 1 (xy+): 4 found - 4 modified | TOTAL: 4 pass 2 (xy+): 0 found - 4 modified | TOTAL: 4 pass 1 (xy-): 5 found - 5 modified | TOTAL: 9 pass 2 (xy-): 0 found - 5 modified | TOTAL: 9 pass 1 (yz+): 6 found - 6 modified | TOTAL: 15 pass 2 (yz+): 0 found - 6 modified | TOTAL: 15 pass 1 (yz-): 3 found - 3 modified | TOTAL: 18 pass 2 (yz-): 0 found - 3 modified | TOTAL: 18 pass 1 (xz+): 4 found - 4 modified | TOTAL: 22 pass 2 (xz+): 0 found - 4 modified | TOTAL: 22 pass 1 (xz-): 2 found - 2 modified | TOTAL: 24 pass 2 (xz-): 0 found - 2 modified | TOTAL: 24 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 4 pass 2 (+++): 0 found - 2 modified | TOTAL: 4 Iteration Number : 3 pass 1 (++): 2 found - 2 modified | TOTAL: 2 pass 2 (++): 0 found - 2 modified | TOTAL: 2 pass 1 (+-): 3 found - 3 modified | TOTAL: 5 pass 2 (+-): 0 found - 3 modified | TOTAL: 5 pass 1 (--): 1 found - 1 modified | TOTAL: 6 pass 2 (--): 0 found - 1 modified | TOTAL: 6 pass 1 (-+): 1 found - 1 modified | TOTAL: 7 pass 2 (-+): 0 found - 1 modified | TOTAL: 7 Iteration Number : 4 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 0 found - 0 modified | TOTAL: 2 pass 1 (yz+): 0 found - 0 modified | TOTAL: 2 pass 1 (yz-): 0 found - 0 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 1 found - 1 modified | TOTAL: 3 pass 2 (xz-): 0 found - 1 modified | TOTAL: 3 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 1 found - 1 modified | TOTAL: 1 pass 2 (+++): 0 found - 1 modified | TOTAL: 1 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 5 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 5 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 5 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 6 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 6 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 6 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 2447 (out of 491515: 0.497848) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill mar 5 gen 2016, 01.00.15, CET /home/salvatore/freesurfer/subjects/T1-1/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 1.07477 0.02948 0.10235 -27.88472; -0.05852 0.98778 0.30751 -34.37221; -0.12227 -0.31964 0.97716 56.00847; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.07477 0.02948 0.10235 -27.88472; -0.05852 0.98778 0.30751 -34.37221; -0.12227 -0.31964 0.97716 56.00847; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 2534 (min = 350, max = 1400), aspect = 0.84 (min = 0.10, max = 0.75) need search nearby using seed (124, 109, 91), TAL = (4.0, -37.0, 19.0) talairach voxel to voxel transform 0.91849 -0.05313 -0.07948 28.23716; 0.01691 0.91782 -0.29061 48.29572; 0.12047 0.29358 0.91837 -37.98613; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (124, 109, 91) --> (4.0, -37.0, 19.0) done. writing output to filled.mgz... filling took 0.5 minutes talairach cc position changed to (4.00, -37.00, 19.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(22.00, -37.00, 19.00) SRC: (112.57, 123.69, 90.35) search lh wm seed point around talairach space (-14.00, -37.00, 19.00), SRC: (145.64, 124.29, 94.69) 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 mar 5 gen 2016, 01.00.43, CET /home/salvatore/freesurfer/subjects/T1-1/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 13 found - 13 modified | TOTAL: 13 pass 2 (xy+): 0 found - 13 modified | TOTAL: 13 pass 1 (xy-): 3 found - 3 modified | TOTAL: 16 pass 2 (xy-): 0 found - 3 modified | TOTAL: 16 pass 1 (yz+): 8 found - 8 modified | TOTAL: 24 pass 2 (yz+): 0 found - 8 modified | TOTAL: 24 pass 1 (yz-): 5 found - 5 modified | TOTAL: 29 pass 2 (yz-): 0 found - 5 modified | TOTAL: 29 pass 1 (xz+): 1 found - 1 modified | TOTAL: 30 pass 2 (xz+): 0 found - 1 modified | TOTAL: 30 pass 1 (xz-): 9 found - 9 modified | TOTAL: 39 pass 2 (xz-): 0 found - 9 modified | TOTAL: 39 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 3 found - 3 modified | TOTAL: 3 pass 2 (++): 0 found - 3 modified | TOTAL: 3 pass 1 (+-): 3 found - 3 modified | TOTAL: 6 pass 2 (+-): 0 found - 3 modified | TOTAL: 6 pass 1 (--): 4 found - 4 modified | TOTAL: 10 pass 2 (--): 0 found - 4 modified | TOTAL: 10 pass 1 (-+): 9 found - 9 modified | TOTAL: 19 pass 2 (-+): 0 found - 9 modified | TOTAL: 19 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-): 1 found - 1 modified | TOTAL: 1 pass 2 (yz-): 0 found - 1 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 59 (out of 228289: 0.025844) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.38 2014/03/22 00:41:04 greve Exp $ $Id: mrisurf.c,v 1.776 2015/12/17 18:09:34 fischl Exp $ slice 40: 184 vertices, 243 faces slice 50: 5491 vertices, 5825 faces slice 60: 15284 vertices, 15761 faces slice 70: 26228 vertices, 26872 faces slice 80: 39333 vertices, 39958 faces slice 90: 52660 vertices, 53452 faces slice 100: 67971 vertices, 68866 faces slice 110: 83273 vertices, 84250 faces slice 120: 98649 vertices, 99681 faces slice 130: 112770 vertices, 113816 faces slice 140: 123412 vertices, 124354 faces slice 150: 131256 vertices, 132174 faces slice 160: 138058 vertices, 138949 faces slice 170: 144045 vertices, 144926 faces slice 180: 148647 vertices, 149473 faces slice 190: 151080 vertices, 151820 faces slice 200: 151256 vertices, 151966 faces slice 210: 151256 vertices, 151966 faces slice 220: 151256 vertices, 151966 faces slice 230: 151256 vertices, 151966 faces slice 240: 151256 vertices, 151966 faces slice 250: 151256 vertices, 151966 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 151256 voxel in cpt #1: X=-710 [v=151256,e=455898,f=303932] located at (-26.712111, -22.492191, 2.909141) For the whole surface: X=-710 [v=151256,e=455898,f=303932] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh mar 5 gen 2016, 01.00.47, CET /home/salvatore/freesurfer/subjects/T1-1/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 5 found - 5 modified | TOTAL: 5 pass 2 (xy+): 0 found - 5 modified | TOTAL: 5 pass 1 (xy-): 33 found - 33 modified | TOTAL: 38 pass 2 (xy-): 0 found - 33 modified | TOTAL: 38 pass 1 (yz+): 5 found - 5 modified | TOTAL: 43 pass 2 (yz+): 0 found - 5 modified | TOTAL: 43 pass 1 (yz-): 4 found - 4 modified | TOTAL: 47 pass 2 (yz-): 0 found - 4 modified | TOTAL: 47 pass 1 (xz+): 1 found - 1 modified | TOTAL: 48 pass 2 (xz+): 0 found - 1 modified | TOTAL: 48 pass 1 (xz-): 12 found - 12 modified | TOTAL: 60 pass 2 (xz-): 0 found - 12 modified | TOTAL: 60 Iteration Number : 1 pass 1 (+++): 1 found - 1 modified | TOTAL: 1 pass 2 (+++): 0 found - 1 modified | TOTAL: 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 1 pass 1 (+++): 6 found - 6 modified | TOTAL: 7 pass 2 (+++): 0 found - 6 modified | TOTAL: 7 pass 1 (+++): 0 found - 0 modified | TOTAL: 7 Iteration Number : 1 pass 1 (++): 12 found - 12 modified | TOTAL: 12 pass 2 (++): 0 found - 12 modified | TOTAL: 12 pass 1 (+-): 6 found - 6 modified | TOTAL: 18 pass 2 (+-): 0 found - 6 modified | TOTAL: 18 pass 1 (--): 0 found - 0 modified | TOTAL: 18 pass 1 (-+): 3 found - 3 modified | TOTAL: 21 pass 2 (-+): 0 found - 3 modified | TOTAL: 21 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 89 (out of 255252: 0.034868) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.38 2014/03/22 00:41:04 greve Exp $ $Id: mrisurf.c,v 1.776 2015/12/17 18:09:34 fischl Exp $ slice 40: 316 vertices, 380 faces slice 50: 5313 vertices, 5623 faces slice 60: 14500 vertices, 14867 faces slice 70: 25530 vertices, 25961 faces slice 80: 37470 vertices, 37918 faces slice 90: 49755 vertices, 50286 faces slice 100: 62615 vertices, 63250 faces slice 110: 76332 vertices, 77060 faces slice 120: 89416 vertices, 90192 faces slice 130: 101997 vertices, 102813 faces slice 140: 112353 vertices, 113049 faces slice 150: 120031 vertices, 120687 faces slice 160: 126783 vertices, 127369 faces slice 170: 131355 vertices, 131933 faces slice 180: 135731 vertices, 136274 faces slice 190: 138136 vertices, 138554 faces slice 200: 138136 vertices, 138554 faces slice 210: 138136 vertices, 138554 faces slice 220: 138136 vertices, 138554 faces slice 230: 138136 vertices, 138554 faces slice 240: 138136 vertices, 138554 faces slice 250: 138136 vertices, 138554 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 138136 voxel in cpt #1: X=-418 [v=138136,e=415662,f=277108] located at (25.714361, -22.876644, 7.500890) For the whole surface: X=-418 [v=138136,e=415662,f=277108] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh mar 5 gen 2016, 01.00.52, CET /home/salvatore/freesurfer/subjects/T1-1/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Smooth1 rh mar 5 gen 2016, 01.00.55, CET /home/salvatore/freesurfer/subjects/T1-1/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh mar 5 gen 2016, 01.00.59, CET /home/salvatore/freesurfer/subjects/T1-1/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 47.1 mm, total surface area = 73564 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.4 minutes step 000: RMS=0.206 (target=0.015) step 005: RMS=0.165 (target=0.015) step 010: RMS=0.143 (target=0.015) step 015: RMS=0.133 (target=0.015) step 020: RMS=0.129 (target=0.015) step 025: RMS=0.128 (target=0.015) step 030: RMS=0.127 (target=0.015) step 035: RMS=0.127 (target=0.015) step 040: RMS=0.126 (target=0.015) step 045: RMS=0.124 (target=0.015) step 050: RMS=0.123 (target=0.015) step 055: RMS=0.124 (target=0.015) step 060: RMS=0.125 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# Inflation1 rh mar 5 gen 2016, 01.01.23, CET /home/salvatore/freesurfer/subjects/T1-1/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 45.2 mm, total surface area = 68324 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.4 minutes step 000: RMS=0.188 (target=0.015) step 005: RMS=0.145 (target=0.015) step 010: RMS=0.122 (target=0.015) step 015: RMS=0.115 (target=0.015) step 020: RMS=0.107 (target=0.015) step 025: RMS=0.104 (target=0.015) step 030: RMS=0.102 (target=0.015) step 035: RMS=0.100 (target=0.015) step 040: RMS=0.098 (target=0.015) step 045: RMS=0.097 (target=0.015) step 050: RMS=0.096 (target=0.015) step 055: RMS=0.097 (target=0.015) step 060: RMS=0.097 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh mar 5 gen 2016, 01.01.44, CET /home/salvatore/freesurfer/subjects/T1-1/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 1.60 2015/11/24 20:36:25 greve Exp $ $Id: mrisurf.c,v 1.776 2015/12/17 18:09:34 fischl Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.95 +- 0.76 (0.00-->12.68) (max @ vno 99523 --> 99524) face area 0.03 +- 0.06 (-0.84-->2.02) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.328... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.717, avgs=0 005/300: dt: 0.9000, rms radial error=175.461, avgs=0 010/300: dt: 0.9000, rms radial error=174.914, avgs=0 015/300: dt: 0.9000, rms radial error=174.199, avgs=0 020/300: dt: 0.9000, rms radial error=173.389, avgs=0 025/300: dt: 0.9000, rms radial error=172.522, avgs=0 030/300: dt: 0.9000, rms radial error=171.624, avgs=0 035/300: dt: 0.9000, rms radial error=170.710, avgs=0 040/300: dt: 0.9000, rms radial error=169.789, avgs=0 045/300: dt: 0.9000, rms radial error=168.868, avgs=0 050/300: dt: 0.9000, rms radial error=167.949, avgs=0 055/300: dt: 0.9000, rms radial error=167.035, avgs=0 060/300: dt: 0.9000, rms radial error=166.125, avgs=0 065/300: dt: 0.9000, rms radial error=165.219, avgs=0 070/300: dt: 0.9000, rms radial error=164.318, avgs=0 075/300: dt: 0.9000, rms radial error=163.422, avgs=0 080/300: dt: 0.9000, rms radial error=162.530, avgs=0 085/300: dt: 0.9000, rms radial error=161.642, avgs=0 090/300: dt: 0.9000, rms radial error=160.756, avgs=0 095/300: dt: 0.9000, rms radial error=159.867, avgs=0 100/300: dt: 0.9000, rms radial error=159.002, avgs=0 105/300: dt: 0.9000, rms radial error=158.136, avgs=0 110/300: dt: 0.9000, rms radial error=157.276, avgs=0 115/300: dt: 0.9000, rms radial error=156.422, avgs=0 120/300: dt: 0.9000, rms radial error=155.571, avgs=0 125/300: dt: 0.9000, rms radial error=154.722, avgs=0 130/300: dt: 0.9000, rms radial error=153.882, avgs=0 135/300: dt: 0.9000, rms radial error=153.046, avgs=0 140/300: dt: 0.9000, rms radial error=152.215, avgs=0 145/300: dt: 0.9000, rms radial error=151.391, avgs=0 150/300: dt: 0.9000, rms radial error=150.572, avgs=0 155/300: dt: 0.9000, rms radial error=149.754, avgs=0 160/300: dt: 0.9000, rms radial error=148.942, avgs=0 165/300: dt: 0.9000, rms radial error=148.135, avgs=0 170/300: dt: 0.9000, rms radial error=147.331, avgs=0 175/300: dt: 0.9000, rms radial error=146.532, avgs=0 180/300: dt: 0.9000, rms radial error=145.732, avgs=0 185/300: dt: 0.9000, rms radial error=144.933, avgs=0 190/300: dt: 0.9000, rms radial error=144.139, avgs=0 195/300: dt: 0.9000, rms radial error=143.350, avgs=0 200/300: dt: 0.9000, rms radial error=142.564, avgs=0 205/300: dt: 0.9000, rms radial error=141.783, avgs=0 210/300: dt: 0.9000, rms radial error=141.006, avgs=0 215/300: dt: 0.9000, rms radial error=140.233, avgs=0 220/300: dt: 0.9000, rms radial error=139.464, avgs=0 225/300: dt: 0.9000, rms radial error=138.700, avgs=0 230/300: dt: 0.9000, rms radial error=137.940, avgs=0 235/300: dt: 0.9000, rms radial error=137.184, avgs=0 240/300: dt: 0.9000, rms radial error=136.431, avgs=0 245/300: dt: 0.9000, rms radial error=135.683, avgs=0 250/300: dt: 0.9000, rms radial error=134.939, avgs=0 255/300: dt: 0.9000, rms radial error=134.199, avgs=0 260/300: dt: 0.9000, rms radial error=133.463, avgs=0 265/300: dt: 0.9000, rms radial error=132.731, avgs=0 270/300: dt: 0.9000, rms radial error=132.002, avgs=0 275/300: dt: 0.9000, rms radial error=131.278, avgs=0 280/300: dt: 0.9000, rms radial error=130.558, avgs=0 285/300: dt: 0.9000, rms radial error=129.840, avgs=0 290/300: dt: 0.9000, rms radial error=129.123, avgs=0 295/300: dt: 0.9000, rms radial error=128.410, avgs=0 300/300: dt: 0.9000, rms radial error=127.701, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 18243.94 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00006 epoch 2 (K=40.0), pass 1, starting sse = 3604.38 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/10 = 0.00056 epoch 3 (K=160.0), pass 1, starting sse = 673.82 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.04/10 = 0.00419 epoch 4 (K=640.0), pass 1, starting sse = 173.16 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.14/13 = 0.01080 final distance error %30.95 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.04 hours FSRUNTIME@ mris_sphere 0.0422 hours 1 threads #-------------------------------------------- #@# QSphere rh mar 5 gen 2016, 01.04.16, CET /home/salvatore/freesurfer/subjects/T1-1/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 1.60 2015/11/24 20:36:25 greve Exp $ $Id: mrisurf.c,v 1.776 2015/12/17 18:09:34 fischl Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.03 +- 0.67 (0.00-->12.56) (max @ vno 84909 --> 84921) face area 0.03 +- 0.04 (-0.31-->0.62) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.346... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.034, avgs=0 005/300: dt: 0.9000, rms radial error=175.779, avgs=0 010/300: dt: 0.9000, rms radial error=175.233, avgs=0 015/300: dt: 0.9000, rms radial error=174.515, avgs=0 020/300: dt: 0.9000, rms radial error=173.697, avgs=0 025/300: dt: 0.9000, rms radial error=172.821, avgs=0 030/300: dt: 0.9000, rms radial error=171.912, avgs=0 035/300: dt: 0.9000, rms radial error=170.987, avgs=0 040/300: dt: 0.9000, rms radial error=170.055, avgs=0 045/300: dt: 0.9000, rms radial error=169.121, avgs=0 050/300: dt: 0.9000, rms radial error=168.187, avgs=0 055/300: dt: 0.9000, rms radial error=167.256, avgs=0 060/300: dt: 0.9000, rms radial error=166.327, avgs=0 065/300: dt: 0.9000, rms radial error=165.403, avgs=0 070/300: dt: 0.9000, rms radial error=164.483, avgs=0 075/300: dt: 0.9000, rms radial error=163.567, avgs=0 080/300: dt: 0.9000, rms radial error=162.655, avgs=0 085/300: dt: 0.9000, rms radial error=161.748, avgs=0 090/300: dt: 0.9000, rms radial error=160.847, avgs=0 095/300: dt: 0.9000, rms radial error=159.953, avgs=0 100/300: dt: 0.9000, rms radial error=159.063, avgs=0 105/300: dt: 0.9000, rms radial error=158.178, avgs=0 110/300: dt: 0.9000, rms radial error=157.297, avgs=0 115/300: dt: 0.9000, rms radial error=156.421, avgs=0 120/300: dt: 0.9000, rms radial error=155.550, avgs=0 125/300: dt: 0.9000, rms radial error=154.684, avgs=0 130/300: dt: 0.9000, rms radial error=153.822, avgs=0 135/300: dt: 0.9000, rms radial error=152.965, avgs=0 140/300: dt: 0.9000, rms radial error=152.113, avgs=0 145/300: dt: 0.9000, rms radial error=151.265, avgs=0 150/300: dt: 0.9000, rms radial error=150.422, avgs=0 155/300: dt: 0.9000, rms radial error=149.584, avgs=0 160/300: dt: 0.9000, rms radial error=148.749, avgs=0 165/300: dt: 0.9000, rms radial error=147.919, avgs=0 170/300: dt: 0.9000, rms radial error=147.094, avgs=0 175/300: dt: 0.9000, rms radial error=146.273, avgs=0 180/300: dt: 0.9000, rms radial error=145.456, avgs=0 185/300: dt: 0.9000, rms radial error=144.643, avgs=0 190/300: dt: 0.9000, rms radial error=143.835, avgs=0 195/300: dt: 0.9000, rms radial error=143.032, avgs=0 200/300: dt: 0.9000, rms radial error=142.232, avgs=0 205/300: dt: 0.9000, rms radial error=141.437, avgs=0 210/300: dt: 0.9000, rms radial error=140.647, avgs=0 215/300: dt: 0.9000, rms radial error=139.861, avgs=0 220/300: dt: 0.9000, rms radial error=139.080, avgs=0 225/300: dt: 0.9000, rms radial error=138.302, avgs=0 230/300: dt: 0.9000, rms radial error=137.529, avgs=0 235/300: dt: 0.9000, rms radial error=136.759, avgs=0 240/300: dt: 0.9000, rms radial error=135.994, avgs=0 245/300: dt: 0.9000, rms radial error=135.232, avgs=0 250/300: dt: 0.9000, rms radial error=134.475, avgs=0 255/300: dt: 0.9000, rms radial error=133.722, avgs=0 260/300: dt: 0.9000, rms radial error=132.974, avgs=0 265/300: dt: 0.9000, rms radial error=132.229, avgs=0 270/300: dt: 0.9000, rms radial error=131.488, avgs=0 275/300: dt: 0.9000, rms radial error=130.752, avgs=0 280/300: dt: 0.9000, rms radial error=130.019, avgs=0 285/300: dt: 0.9000, rms radial error=129.290, avgs=0 290/300: dt: 0.9000, rms radial error=128.566, avgs=0 295/300: dt: 0.9000, rms radial error=127.845, avgs=0 300/300: dt: 0.9000, rms radial error=127.129, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 15939.44 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00016 epoch 2 (K=40.0), pass 1, starting sse = 2740.55 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00029 epoch 3 (K=160.0), pass 1, starting sse = 386.54 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.03/10 = 0.00328 epoch 4 (K=640.0), pass 1, starting sse = 83.61 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.11/14 = 0.00757 final distance error %28.03 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.04 hours FSRUNTIME@ mris_sphere 0.0388 hours 1 threads #-------------------------------------------- #@# Fix Topology lh mar 5 gen 2016, 01.06.36, CET /home/salvatore/freesurfer/subjects/T1-1/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology rh mar 5 gen 2016, 01.06.36, CET /home/salvatore/freesurfer/subjects/T1-1/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 T1-1 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 1.49 2015/11/24 20:36:25 greve Exp $ $Id: mrisurf.c,v 1.776 2015/12/17 18:09:34 fischl Exp $ before topology correction, eno=-710 (nv=151256, nf=303932, ne=455898, g=356) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations marking ambiguous vertices... 110974 ambiguous faces found in tessellation segmenting defects... 126 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 25 into 0 -merging segment 91 into 0 -merging segment 102 into 0 -merging segment 4 into 9 -merging segment 24 into 19 -merging segment 28 into 20 -merging segment 29 into 21 -merging segment 39 into 27 -merging segment 67 into 32 -merging segment 85 into 32 -merging segment 77 into 64 -merging segment 82 into 81 -merging segment 111 into 83 -merging segment 122 into 83 -merging segment 123 into 83 -merging segment 96 into 95 -merging segment 98 into 95 -merging segment 106 into 95 108 defects to be corrected 0 vertices coincident reading input surface /home/salvatore/freesurfer/subjects/T1-1/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.3414 (-4.1707) -vertex loglikelihood: -6.2209 (-3.1104) -normal dot loglikelihood: -3.4493 (-3.4493) -quad curv loglikelihood: -6.1047 (-3.0524) Total Loglikelihood : -24.1162 CORRECTING DEFECT 0 (vertices=30357, convex hull=5730) XL defect detected...