Mon Aug 28 16:38:18 CEST 2017 /root/Scrivania/subjects/ENP30S001A /usr/local/freesurfer/bin/recon-all -s ENP30S001A -autorecon1 subjid ENP30S001A setenv SUBJECTS_DIR /root/Scrivania/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux Braindata 3.19.0-15-generic #15-Ubuntu SMP Thu Apr 16 23:32:37 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 128307 maxlocks unlimited maxsignal 128307 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 32869864 4375732 28494132 51744 286104 3294156 -/+ buffers/cache: 795472 32074392 Swap: 33472508 0 33472508 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-14:38:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-14:38:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-14:38:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-14:38:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-14:38:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-14:38:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-14:38:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-14:38:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-14:38:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-14:38:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-14:38:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-14:38:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-14:38:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-14:38:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-14:38:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-14:38:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-14:38:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-14:38:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-14:38:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-14:38:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-14:38:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-14:38:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-14:38:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-14:38:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-14:38:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-14:38:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-14:38:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-14:38:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-14:38:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-14:38:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-14:38:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-14:38:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-14:38:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-14:38:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-14:38:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-14:38:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-14:38:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-14:38:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# MotionCor Mon Aug 28 16:38:20 CEST 2017 Found 1 runs /root/Scrivania/subjects/ENP30S001A/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 /root/Scrivania/subjects/ENP30S001A/mri/orig/001.mgz /root/Scrivania/subjects/ENP30S001A/mri/rawavg.mgz /root/Scrivania/subjects/ENP30S001A mri_convert /root/Scrivania/subjects/ENP30S001A/mri/rawavg.mgz /root/Scrivania/subjects/ENP30S001A/mri/orig.mgz --conform mri_convert /root/Scrivania/subjects/ENP30S001A/mri/rawavg.mgz /root/Scrivania/subjects/ENP30S001A/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /root/Scrivania/subjects/ENP30S001A/mri/rawavg.mgz... TR=8.06, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (1, -0, 0) Original Data has (0.9375, 0.9375, 1) mm size and (256, 256, 160) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /root/Scrivania/subjects/ENP30S001A/mri/orig.mgz... mri_add_xform_to_header -c /root/Scrivania/subjects/ENP30S001A/mri/transforms/talairach.xfm /root/Scrivania/subjects/ENP30S001A/mri/orig.mgz /root/Scrivania/subjects/ENP30S001A/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Mon Aug 28 16:38:28 CEST 2017 /root/Scrivania/subjects/ENP30S001A/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Mon Aug 28 16:40:11 CEST 2017 /root/Scrivania/subjects/ENP30S001A/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6305, pval=0.3663 >= threshold=0.0050) awk -f /usr/local/freesurfer/bin/extract_talairach_avi_QA.awk /root/Scrivania/subjects/ENP30S001A/mri/transforms/talairach_avi.log tal_QC_AZS /root/Scrivania/subjects/ENP30S001A/mri/transforms/talairach_avi.log TalAviQA: 0.97689 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Mon Aug 28 16:40:11 CEST 2017 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /root/Scrivania/subjects/ENP30S001A/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux Braindata 3.19.0-15-generic #15-Ubuntu SMP Thu Apr 16 23:32:37 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux Mon Aug 28 16:40:11 CEST 2017 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 tmpdir is ./tmp.mri_nu_correct.mni.17365 /root/Scrivania/subjects/ENP30S001A/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.17365/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.17365/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig.mgz... TR=8.06, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.17365/nu0.mnc... -------------------------------------------------------- Iteration 1 Mon Aug 28 16:40:13 CEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.17365/nu0.mnc ./tmp.mri_nu_correct.mni.17365/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.17365/0/ defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 165. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 170. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 211. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1051. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1054. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1449. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1455. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1457. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1481. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1631. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1633. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1635. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1637. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1639. (Maybe you should just omit the defined()?) [root@Braindata:/root/Scrivania/subjects/ENP30S001A/mri/] [2017-08-28 16:40:13] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.17365/0/ ./tmp.mri_nu_correct.mni.17365/nu0.mnc ./tmp.mri_nu_correct.mni.17365/nu1.imp Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Number of iterations: 41 CV of field change: 0.00099198 [root@Braindata:/root/Scrivania/subjects/ENP30S001A/mri/] [2017-08-28 16:40:41] running: /usr/local/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.17365/nu0.mnc ./tmp.mri_nu_correct.mni.17365/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Mon Aug 28 16:40:44 CEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.17365/nu1.mnc ./tmp.mri_nu_correct.mni.17365/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.17365/1/ defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 165. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 170. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 211. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1051. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1054. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1449. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1455. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1457. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1481. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1631. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1633. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1635. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1637. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1639. (Maybe you should just omit the defined()?) [root@Braindata:/root/Scrivania/subjects/ENP30S001A/mri/] [2017-08-28 16:40:44] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.17365/1/ ./tmp.mri_nu_correct.mni.17365/nu1.mnc ./tmp.mri_nu_correct.mni.17365/nu2.imp Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Number of iterations: 16 CV of field change: 0.000948112 [root@Braindata:/root/Scrivania/subjects/ENP30S001A/mri/] [2017-08-28 16:40:55] running: /usr/local/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.17365/nu1.mnc ./tmp.mri_nu_correct.mni.17365/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.17365/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.17365/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /root/Scrivania/subjects/ENP30S001A/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.17365/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.17365/ones.mgz sysname Linux hostname Braindata machine x86_64 user root input ./tmp.mri_nu_correct.mni.17365/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.17365/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 Found 16777216 values in range Counting number of voxels Found 16777216 voxels in final mask mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.17365/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.17365/sum.junk --avgwf ./tmp.mri_nu_correct.mni.17365/input.mean.dat $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.17365/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.17365/sum.junk --avgwf ./tmp.mri_nu_correct.mni.17365/input.mean.dat sysname Linux hostname Braindata machine x86_64 user root UseRobust 0 Loading ./tmp.mri_nu_correct.mni.17365/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 16777216.000 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.17365/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.17365/ones.mgz --i ./tmp.mri_nu_correct.mni.17365/nu2.mnc --sum ./tmp.mri_nu_correct.mni.17365/sum.junk --avgwf ./tmp.mri_nu_correct.mni.17365/output.mean.dat $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.17365/ones.mgz --i ./tmp.mri_nu_correct.mni.17365/nu2.mnc --sum ./tmp.mri_nu_correct.mni.17365/sum.junk --avgwf ./tmp.mri_nu_correct.mni.17365/output.mean.dat sysname Linux hostname Braindata machine x86_64 user root UseRobust 0 Loading ./tmp.mri_nu_correct.mni.17365/ones.mgz Loading ./tmp.mri_nu_correct.mni.17365/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 16777216.000 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.17365/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.17365/nu2.mnc ./tmp.mri_nu_correct.mni.17365/nu2.mnc mul .93300822925055696385 Saving result to './tmp.mri_nu_correct.mni.17365/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.17365/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.17365/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.17365/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 4 seconds. mapping (13, 166) to ( 3, 110) Mon Aug 28 16:41:19 CEST 2017 mri_nu_correct.mni done mri_add_xform_to_header -c /root/Scrivania/subjects/ENP30S001A/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Mon Aug 28 16:41:20 CEST 2017 /root/Scrivania/subjects/ENP30S001A/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.027 0.032 0.090 -0.825; -0.111 1.000 0.265 -9.875; -0.103 -0.258 1.044 -0.321; 0.000 0.000 0.000 1.000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 21 Starting OpenSpline(): npoints = 21 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 109 gm peak at 66 (66), valley at 34 (34) csf peak at 33, setting threshold to 55 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 65 (65), valley at 49 (49) csf peak at 32, setting threshold to 54 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 Mon Aug 28 16:42:52 CEST 2017 /root/Scrivania/subjects/ENP30S001A/mri mri_em_register -skull nu.mgz /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta ======= NUMBER OF OPENMP THREADS = 1 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 5 reading 1 input volumes... logging results to talairach_with_skull.log reading '/usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=9.0 skull bounding box = (46, 59, 24) --> (205, 255, 227) using (99, 124, 126) as brain centroid... mean wm in atlas = 126, using box (79,100,101) --> (118, 148,151) to find MRI wm before smoothing, mri peak at 106 after smoothing, mri peak at 106, scaling input intensities by 1.189 scaling channel 0 by 1.18868 initial log_p = -4.7 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.418765 @ (-9.091, -27.273, -9.091) max log p = -4.302748 @ (4.545, 4.545, -4.545) max log p = -4.240008 @ (2.273, 2.273, -2.273) max log p = -4.217508 @ (1.136, -3.409, 1.136) max log p = -4.202054 @ (-0.568, 2.841, 0.568) max log p = -4.202054 @ (0.000, 0.000, 0.000) Found translation: (-1.7, -21.0, -14.2): log p = -4.202 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.2 (thresh=-4.2) 1.046 0.150 -0.099 -17.009; -0.149 1.123 0.185 -41.794; 0.161 -0.119 1.062 -17.830; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 0.981 0.106 0.034 -17.432; -0.126 1.098 0.322 -56.568; 0.041 -0.282 1.033 23.997; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 0.981 0.106 0.034 -17.432; -0.126 1.098 0.322 -56.568; 0.041 -0.282 1.033 23.997; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-4.0 (thresh=-4.0) 1.000 0.047 -0.053 -1.733; -0.066 1.141 0.255 -60.909; 0.092 -0.191 0.993 5.409; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.016 0.086 -0.045 -8.246; -0.101 1.160 0.262 -59.973; 0.092 -0.191 0.993 7.284; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.017 0.077 -0.047 -6.757; -0.091 1.156 0.269 -61.898; 0.093 -0.200 0.991 7.835; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.017 0.077 -0.047 -6.757; -0.091 1.156 0.269 -61.898; 0.093 -0.200 0.991 7.835; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3481 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.01720 0.07659 -0.04740 -6.75725; -0.09125 1.15641 0.26869 -61.89808; 0.09252 -0.20041 0.99118 7.83487; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.01720 0.07659 -0.04740 -6.75725; -0.09125 1.15641 0.26869 -61.89808; 0.09252 -0.20041 0.99118 7.83487; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.017 0.077 -0.047 -6.757; -0.091 1.156 0.269 -61.898; 0.093 -0.200 0.991 7.835; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.9 (old=-4.7) transform before final EM align: 1.017 0.077 -0.047 -6.757; -0.091 1.156 0.269 -61.898; 0.093 -0.200 0.991 7.835; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 382743 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.01720 0.07659 -0.04740 -6.75725; -0.09125 1.15641 0.26869 -61.89808; 0.09252 -0.20041 0.99118 7.83487; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.01720 0.07659 -0.04740 -6.75725; -0.09125 1.15641 0.26869 -61.89808; 0.09252 -0.20041 0.99118 7.83487; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = 4.3 tol 0.000000 final transform: 1.017 0.077 -0.047 -6.757; -0.091 1.156 0.269 -61.898; 0.093 -0.200 0.991 7.835; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 18 minutes and 9 seconds. mri_watershed -T1 -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=126 y=134 z=119 r=82 first estimation of the main basin volume: 2316166 voxels Looking for seedpoints 2 found in the cerebellum 18 found in the rest of the brain global maximum in x=147, y=126, z=80, Imax=255 CSF=12, 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=22657575292 voxels, voxel volume =1.000 = 22657575292 mmm3 = 22657574.912 cm3 done. PostAnalyze...Basin Prior 12 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=125,y=139, z=113, r=9560 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=14 , nb = 43695 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1031396171 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=17 , nb = -1053509517 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=14 , nb = -1117065030 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=13 , nb = 1080428298 OTHER CSF_MIN=0, CSF_intensity=17, CSF_MAX=42 , nb = 1068756966 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 14, 23, 43, 66 after analyzing : 14, 36, 43, 43 RIGHT_CER before analyzing : 4, 7, 48, 73 after analyzing : 4, 34, 48, 43 LEFT_CER before analyzing : 17, 28, 48, 74 after analyzing : 17, 41, 48, 49 RIGHT_BRAIN before analyzing : 14, 23, 42, 66 after analyzing : 14, 35, 42, 42 LEFT_BRAIN before analyzing : 13, 22, 42, 66 after analyzing : 13, 35, 42, 42 OTHER before analyzing : 42, 45, 47, 55 after analyzing : 42, 46, 47, 48 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...64 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.011 curvature mean = 70.619, std = 7.621 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 3.06, sigma = 4.43 after rotation: sse = 3.06, sigma = 4.43 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 3.20, its var is 4.19 before Erosion-Dilatation 0.60% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...43 iterations mri_strip_skull: done peeling brain Brain Size = 1704897 voxels, voxel volume = 1.000 mm3 = 1704897 mmm3 = 1704.897 cm3 ****************************** Saving brainmask.auto.mgz done cp brainmask.auto.mgz brainmask.mgz #------------------------------------------ Started at Mon Aug 28 16:38:18 CEST 2017 Ended at Mon Aug 28 17:01:18 CEST 2017 #@#%# recon-all-run-time-hours 0.383 recon-all -s ENP30S001A finished without error at Mon Aug 28 17:01:18 CEST 2017 New invocation of recon-all Mon Aug 28 17:58:48 CEST 2017 /root/Scrivania/subjects/ENP30S001A /usr/local/freesurfer/bin/recon-all -s ENP30S001A -autorecon2 subjid ENP30S001A setenv SUBJECTS_DIR /root/Scrivania/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux Braindata 3.19.0-15-generic #15-Ubuntu SMP Thu Apr 16 23:32:37 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 128307 maxlocks unlimited maxsignal 128307 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 32869864 4412084 28457780 59908 286140 3327788 -/+ buffers/cache: 798156 32071708 Swap: 33472508 0 33472508 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-15:58:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-15:58:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-15:58:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-15:58:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-15:58:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-15:58:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-15:58:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-15:58:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-15:58:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-15:58:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-15:58:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-15:58:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-15:58:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-15:58:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-15:58:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-15:58:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-15:58:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-15:58:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-15:58:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-15:58:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-15:58:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-15:58:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-15:58:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-15:58:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-15:58:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-15:58:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-15:58:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-15:58:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-15:58:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-15:58:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-15:58:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-15:58:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-15:58:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-15:58:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-15:58:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-15:58:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-15:58:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/28-15:58:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #------------------------------------- #@# EM Registration Mon Aug 28 17:58:52 CEST 2017 /root/Scrivania/subjects/ENP30S001A/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta ======= NUMBER OF OPENMP THREADS = 1 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 14.9 or > 790.2 total sample mean = 84.4 (994 zeros) ************************************************ spacing=8, using 2772 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2772, passno 0, spacing 8 resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=22.9 skull bounding box = (57, 77, 42) --> (195, 207, 201) using (103, 120, 122) as brain centroid... mean wm in atlas = 107, using box (86,104,102) --> (119, 135,141) to find MRI wm before smoothing, mri peak at 105 after smoothing, mri peak at 105, scaling input intensities by 1.019 scaling channel 0 by 1.01905 initial log_p = -4.3 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.028454 @ (-9.091, -27.273, -9.091) max log p = -3.788519 @ (4.545, 4.545, -4.545) max log p = -3.679009 @ (2.273, 6.818, 2.273) max log p = -3.639682 @ (-1.136, -3.409, -1.136) max log p = -3.635263 @ (1.705, 1.705, -0.568) max log p = -3.635263 @ (0.000, 0.000, 0.000) Found translation: (-1.7, -17.6, -13.1): log p = -3.635 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.4, old_max_log_p =-3.6 (thresh=-3.6) 0.991 0.145 0.039 -24.993; -0.131 1.101 0.295 -49.604; 0.000 -0.259 0.966 33.789; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.4, old_max_log_p =-3.4 (thresh=-3.4) 0.991 0.145 0.039 -24.993; -0.131 1.101 0.295 -49.604; 0.000 -0.259 0.966 33.789; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.2, old_max_log_p =-3.4 (thresh=-3.4) 1.012 0.127 -0.036 -14.850; -0.100 1.092 0.255 -49.625; 0.065 -0.223 1.011 13.540; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2) 1.012 0.127 -0.036 -14.850; -0.104 1.120 0.226 -49.632; 0.061 -0.184 1.000 9.900; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2) 1.010 0.123 -0.020 -16.949; -0.103 1.119 0.243 -50.632; 0.046 -0.203 0.993 14.381; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2) 1.008 0.123 -0.020 -16.612; -0.103 1.122 0.243 -51.029; 0.046 -0.204 0.995 14.168; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2) 1.008 0.123 -0.020 -16.612; -0.103 1.119 0.243 -50.631; 0.046 -0.204 0.999 13.847; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2) 1.008 0.123 -0.020 -16.612; -0.103 1.119 0.243 -50.631; 0.046 -0.204 0.999 13.847; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2772 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.00784 0.12282 -0.01976 -16.61161; -0.10285 1.11918 0.24274 -50.63125; 0.04595 -0.20448 0.99897 13.84704; 0.00000 0.00000 0.00000 1.00000; nsamples 2772 Quasinewton: input matrix 1.00784 0.12282 -0.01976 -16.61161; -0.10285 1.11918 0.24274 -50.63125; 0.04595 -0.20448 0.99897 13.84704; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.008 0.123 -0.020 -16.612; -0.103 1.119 0.243 -50.631; 0.046 -0.204 0.999 13.847; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.2 (old=-4.3) transform before final EM align: 1.008 0.123 -0.020 -16.612; -0.103 1.119 0.243 -50.631; 0.046 -0.204 0.999 13.847; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 312841 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.00784 0.12282 -0.01976 -16.61161; -0.10285 1.11918 0.24274 -50.63125; 0.04595 -0.20448 0.99897 13.84704; 0.00000 0.00000 0.00000 1.00000; nsamples 312841 Quasinewton: input matrix 1.00784 0.12282 -0.01976 -16.61161; -0.10285 1.11918 0.24274 -50.63125; 0.04595 -0.20448 0.99897 13.84704; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 012: -log(p) = 3.7 tol 0.000000 final transform: 1.008 0.123 -0.020 -16.612; -0.103 1.119 0.243 -50.631; 0.046 -0.204 0.999 13.847; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 15 minutes and 52 seconds. #-------------------------------------- #@# CA Normalize Mon Aug 28 18:14:44 CEST 2017 /root/Scrivania/subjects/ENP30S001A/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=22.9 skull bounding box = (57, 77, 42) --> (195, 207, 202) using (103, 120, 122) as brain centroid... mean wm in atlas = 107, using box (86,104,102) --> (119, 135,141) to find MRI wm before smoothing, mri peak at 105 after smoothing, mri peak at 105, scaling input intensities by 1.019 scaling channel 0 by 1.01905 using 244171 sample points... INFO: compute sample coordinates transform 1.008 0.123 -0.020 -16.612; -0.103 1.119 0.243 -50.631; 0.046 -0.204 0.999 13.847; 0.000 0.000 0.000 1.000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (120, 81, 39) --> (193, 182, 200) Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 147.0 0 of 490 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (61, 79, 39) --> (131, 175, 201) Right_Cerebral_White_Matter: limiting intensities to 94.0 --> 147.0 0 of 251 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (123, 158, 66) --> (170, 200, 118) Left_Cerebellum_White_Matter: limiting intensities to 103.0 --> 147.0 0 of 10 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (75, 158, 64) --> (124, 193, 120) Right_Cerebellum_White_Matter: limiting intensities to 97.0 --> 147.0 0 of 15 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (106, 148, 100) --> (140, 209, 129) Brain_Stem: limiting intensities to 97.0 --> 147.0 0 of 20 (0.0%) samples deleted using 786 total control points for intensity normalization... bias field = 0.991 +- 0.068 1 of 786 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (120, 81, 39) --> (193, 182, 200) Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 139.0 0 of 534 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (61, 79, 39) --> (131, 175, 201) Right_Cerebral_White_Matter: limiting intensities to 93.0 --> 139.0 0 of 275 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (123, 158, 66) --> (170, 200, 118) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 139.0 0 of 68 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (75, 158, 64) --> (124, 193, 120) Right_Cerebellum_White_Matter: limiting intensities to 87.0 --> 139.0 0 of 68 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (106, 148, 100) --> (140, 209, 129) Brain_Stem: limiting intensities to 83.0 --> 139.0 0 of 85 (0.0%) samples deleted using 1030 total control points for intensity normalization... bias field = 1.004 +- 0.061 0 of 1030 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (120, 81, 39) --> (193, 182, 200) Left_Cerebral_White_Matter: limiting intensities to 93.0 --> 139.0 0 of 601 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (61, 79, 39) --> (131, 175, 201) Right_Cerebral_White_Matter: limiting intensities to 93.0 --> 139.0 1 of 367 (0.3%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (123, 158, 66) --> (170, 200, 118) Left_Cerebellum_White_Matter: limiting intensities to 83.0 --> 139.0 0 of 99 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (75, 158, 64) --> (124, 193, 120) Right_Cerebellum_White_Matter: limiting intensities to 81.0 --> 139.0 0 of 74 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (106, 148, 100) --> (140, 209, 129) Brain_Stem: limiting intensities to 75.0 --> 139.0 0 of 182 (0.0%) samples deleted using 1323 total control points for intensity normalization... bias field = 1.004 +- 0.046 0 of 1322 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 5 seconds. #-------------------------------------- #@# CA Reg Mon Aug 28 18:15:49 CEST 2017 /root/Scrivania/subjects/ENP30S001A/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log ======= NUMBER OF OPENMP THREADS = 1 ======= reading input volume 'norm.mgz'... reading GCA '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.19 (predicted orig area = 6.7) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.768, neg=0, invalid=96777 0001: dt=129.472000, rms=0.705 (8.263%), neg=0, invalid=96777 0002: dt=129.472000, rms=0.692 (1.831%), neg=0, invalid=96777 0003: dt=369.920000, rms=0.681 (1.596%), neg=0, invalid=96777 0004: dt=110.976000, rms=0.676 (0.722%), neg=0, invalid=96777 0005: dt=129.472000, rms=0.674 (0.286%), neg=0, invalid=96777 0006: dt=129.472000, rms=0.672 (0.343%), neg=0, invalid=96777 0007: dt=129.472000, rms=0.670 (0.207%), neg=0, invalid=96777 0008: dt=129.472000, rms=0.669 (0.241%), neg=0, invalid=96777 0009: dt=129.472000, rms=0.666 (0.365%), neg=0, invalid=96777 0010: dt=129.472000, rms=0.664 (0.373%), neg=0, invalid=96777 0011: dt=129.472000, rms=0.661 (0.451%), neg=0, invalid=96777 0012: dt=129.472000, rms=0.658 (0.392%), neg=0, invalid=96777 0013: dt=129.472000, rms=0.656 (0.346%), neg=0, invalid=96777 0014: dt=129.472000, rms=0.654 (0.290%), neg=0, invalid=96777 0015: dt=129.472000, rms=0.653 (0.230%), neg=0, invalid=96777 0016: dt=129.472000, rms=0.651 (0.287%), neg=0, invalid=96777 0017: dt=129.472000, rms=0.649 (0.246%), neg=0, invalid=96777 0018: dt=129.472000, rms=0.647 (0.279%), neg=0, invalid=96777 0019: dt=129.472000, rms=0.646 (0.242%), neg=0, invalid=96777 0020: dt=129.472000, rms=0.644 (0.297%), neg=0, invalid=96777 0021: dt=129.472000, rms=0.642 (0.229%), neg=0, invalid=96777 0022: dt=129.472000, rms=0.641 (0.180%), neg=0, invalid=96777 0023: dt=129.472000, rms=0.640 (0.197%), neg=0, invalid=96777 0024: dt=129.472000, rms=0.639 (0.189%), neg=0, invalid=96777 0025: dt=129.472000, rms=0.638 (0.152%), neg=0, invalid=96777 0026: dt=129.472000, rms=0.637 (0.125%), neg=0, invalid=96777 0027: dt=129.472000, rms=0.636 (0.137%), neg=0, invalid=96777 0028: dt=129.472000, rms=0.635 (0.116%), neg=0, invalid=96777 0029: dt=129.472000, rms=0.635 (0.106%), neg=0, invalid=96777 0030: dt=517.888000, rms=0.635 (0.031%), neg=0, invalid=96777 0031: dt=517.888000, rms=0.634 (0.001%), neg=0, invalid=96777 0032: dt=517.888000, rms=0.635 (-0.597%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.635, neg=0, invalid=96777 0033: dt=129.472000, rms=0.633 (0.186%), neg=0, invalid=96777 0034: dt=517.888000, rms=0.632 (0.137%), neg=0, invalid=96777 0035: dt=517.888000, rms=0.632 (-0.357%), neg=0, invalid=96777 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.637, neg=0, invalid=96777 0036: dt=145.152000, rms=0.630 (1.132%), neg=0, invalid=96777 0037: dt=36.288000, rms=0.627 (0.569%), neg=0, invalid=96777 0038: dt=124.416000, rms=0.621 (0.861%), neg=0, invalid=96777 0039: dt=20.736000, rms=0.618 (0.454%), neg=0, invalid=96777 0040: dt=145.152000, rms=0.616 (0.464%), neg=0, invalid=96777 0041: dt=36.288000, rms=0.612 (0.584%), neg=0, invalid=96777 0042: dt=31.104000, rms=0.611 (0.135%), neg=0, invalid=96777 0043: dt=31.104000, rms=0.610 (0.203%), neg=0, invalid=96777 0044: dt=31.104000, rms=0.608 (0.265%), neg=0, invalid=96777 0045: dt=31.104000, rms=0.606 (0.345%), neg=0, invalid=96777 0046: dt=31.104000, rms=0.604 (0.404%), neg=0, invalid=96777 0047: dt=31.104000, rms=0.601 (0.467%), neg=0, invalid=96777 0048: dt=31.104000, rms=0.598 (0.506%), neg=0, invalid=96777 0049: dt=31.104000, rms=0.595 (0.493%), neg=0, invalid=96777 0050: dt=31.104000, rms=0.592 (0.449%), neg=0, invalid=96777 0051: dt=31.104000, rms=0.590 (0.379%), neg=0, invalid=96777 0052: dt=31.104000, rms=0.588 (0.384%), neg=0, invalid=96777 0053: dt=31.104000, rms=0.586 (0.355%), neg=0, invalid=96777 0054: dt=31.104000, rms=0.584 (0.311%), neg=0, invalid=96777 0055: dt=31.104000, rms=0.582 (0.247%), neg=0, invalid=96777 0056: dt=31.104000, rms=0.581 (0.226%), neg=0, invalid=96777 0057: dt=31.104000, rms=0.580 (0.237%), neg=0, invalid=96777 0058: dt=31.104000, rms=0.578 (0.217%), neg=0, invalid=96777 0059: dt=31.104000, rms=0.577 (0.168%), neg=0, invalid=96777 0060: dt=31.104000, rms=0.577 (0.139%), neg=0, invalid=96777 0061: dt=31.104000, rms=0.576 (0.137%), neg=0, invalid=96777 0062: dt=31.104000, rms=0.575 (0.116%), neg=0, invalid=96777 0063: dt=31.104000, rms=0.575 (0.112%), neg=0, invalid=96777 0064: dt=31.104000, rms=0.574 (0.008%), neg=0, invalid=96777 0065: dt=31.104000, rms=0.574 (0.013%), neg=0, invalid=96777 0066: dt=31.104000, rms=0.574 (0.028%), neg=0, invalid=96777 0067: dt=31.104000, rms=0.574 (0.020%), neg=0, invalid=96777 0068: dt=31.104000, rms=0.574 (0.016%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.574, neg=0, invalid=96777 0069: dt=124.416000, rms=0.573 (0.233%), neg=0, invalid=96777 0070: dt=36.288000, rms=0.572 (0.074%), neg=0, invalid=96777 0071: dt=36.288000, rms=0.572 (0.018%), neg=0, invalid=96777 0072: dt=36.288000, rms=0.572 (0.030%), neg=0, invalid=96777 0073: dt=36.288000, rms=0.572 (0.036%), neg=0, invalid=96777 0074: dt=36.288000, rms=0.572 (0.009%), neg=0, invalid=96777 0075: dt=36.288000, rms=0.572 (-0.016%), neg=0, invalid=96777 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.592, neg=0, invalid=96777 0076: dt=2.000000, rms=0.592 (0.007%), neg=0, invalid=96777 0077: dt=0.700000, rms=0.592 (0.001%), neg=0, invalid=96777 0078: dt=0.700000, rms=0.592 (0.000%), neg=0, invalid=96777 0079: dt=0.700000, rms=0.592 (-0.006%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.592, neg=0, invalid=96777 0080: dt=0.000000, rms=0.592 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.650, neg=0, invalid=96777 0081: dt=5.217893, rms=0.632 (2.803%), neg=0, invalid=96777 0082: dt=2.421053, rms=0.631 (0.100%), neg=0, invalid=96777 0083: dt=2.421053, rms=0.631 (-0.029%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.631, neg=0, invalid=96777 0084: dt=0.000000, rms=0.631 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.686, neg=0, invalid=96777 0085: dt=1.085714, rms=0.682 (0.545%), neg=0, invalid=96777 0086: dt=1.926380, rms=0.678 (0.700%), neg=0, invalid=96777 0087: dt=0.448000, rms=0.677 (0.052%), neg=0, invalid=96777 0088: dt=0.448000, rms=0.677 (0.031%), neg=0, invalid=96777 0089: dt=0.448000, rms=0.677 (0.020%), neg=0, invalid=96777 0090: dt=0.448000, rms=0.677 (-0.018%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.677, neg=0, invalid=96777 0091: dt=1.295455, rms=0.676 (0.173%), neg=0, invalid=96777 0092: dt=0.004000, rms=0.676 (0.001%), neg=0, invalid=96777 0093: dt=0.004000, rms=0.676 (0.000%), neg=0, invalid=96777 0094: dt=0.004000, rms=0.676 (-0.000%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.637, neg=0, invalid=96777 0095: dt=0.448000, rms=0.622 (2.355%), neg=0, invalid=96777 0096: dt=0.000000, rms=0.622 (0.008%), neg=0, invalid=96777 0097: dt=0.050000, rms=0.622 (-0.340%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.622, neg=0, invalid=96777 0098: dt=0.000000, rms=0.622 (0.000%), neg=0, invalid=96777 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.11339 (17) Left_Lateral_Ventricle (4): linear fit = 0.55 x + 0.0 (1546 voxels, overlap=0.005) Left_Lateral_Ventricle (4): linear fit = 0.55 x + 0.0 (1546 voxels, peak = 13), gca=13.1 gca peak = 0.14022 (22) mri peak = 0.11937 (17) Right_Lateral_Ventricle (43): linear fit = 0.68 x + 0.0 (720 voxels, overlap=0.208) Right_Lateral_Ventricle (43): linear fit = 0.68 x + 0.0 (720 voxels, peak = 15), gca=14.9 gca peak = 0.24234 (100) mri peak = 0.09836 (98) Right_Pallidum (52): linear fit = 0.96 x + 0.0 (448 voxels, overlap=0.780) Right_Pallidum (52): linear fit = 0.96 x + 0.0 (448 voxels, peak = 96), gca=96.5 gca peak = 0.19192 (97) mri peak = 0.08027 (86) Left_Pallidum (13): linear fit = 0.88 x + 0.0 (295 voxels, overlap=0.097) Left_Pallidum (13): linear fit = 0.88 x + 0.0 (295 voxels, peak = 85), gca=84.9 gca peak = 0.24007 (63) mri peak = 0.06510 (74) Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (878 voxels, overlap=0.709) Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (878 voxels, peak = 72), gca=71.5 gca peak = 0.29892 (64) mri peak = 0.09758 (68) Left_Hippocampus (17): linear fit = 1.05 x + 0.0 (775 voxels, overlap=0.874) Left_Hippocampus (17): linear fit = 1.05 x + 0.0 (775 voxels, peak = 68), gca=67.5 gca peak = 0.12541 (104) mri peak = 0.08794 (106) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (77538 voxels, overlap=0.812) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (77538 voxels, peak = 106), gca=105.6 gca peak = 0.13686 (104) mri peak = 0.09464 (108) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (78054 voxels, overlap=0.772) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (78054 voxels, peak = 107), gca=106.6 gca peak = 0.11691 (63) mri peak = 0.04233 (63) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (24187 voxels, overlap=0.997) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (24187 voxels, peak = 62), gca=62.1 gca peak = 0.13270 (63) mri peak = 0.04409 (63) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (25940 voxels, overlap=0.997) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (25940 voxels, peak = 63), gca=63.0 gca peak = 0.15182 (70) mri peak = 0.10241 (81) Right_Caudate (50): linear fit = 1.08 x + 0.0 (442 voxels, overlap=0.451) Right_Caudate (50): linear fit = 1.08 x + 0.0 (442 voxels, peak = 75), gca=75.2 gca peak = 0.14251 (76) mri peak = 0.08777 (84) Left_Caudate (11): linear fit = 1.04 x + 0.0 (782 voxels, overlap=0.551) Left_Caudate (11): linear fit = 1.04 x + 0.0 (782 voxels, peak = 79), gca=79.4 gca peak = 0.12116 (60) mri peak = 0.03916 (60) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (27500 voxels, overlap=0.977) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (27500 voxels, peak = 62), gca=61.5 gca peak = 0.12723 (61) mri peak = 0.04462 (61) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (29316 voxels, overlap=0.982) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (29316 voxels, peak = 63), gca=62.5 gca peak = 0.22684 (88) mri peak = 0.08484 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (9023 voxels, overlap=0.689) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (9023 voxels, peak = 94), gca=93.7 gca peak = 0.21067 (87) mri peak = 0.10361 (92) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (8511 voxels, overlap=0.731) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (8511 voxels, peak = 92), gca=91.8 gca peak = 0.25455 (62) mri peak = 0.08931 (71) Left_Amygdala (18): linear fit = 1.12 x + 0.0 (383 voxels, overlap=0.156) Left_Amygdala (18): linear fit = 1.12 x + 0.0 (383 voxels, peak = 69), gca=69.1 gca peak = 0.39668 (62) mri peak = 0.12531 (68) Right_Amygdala (54): linear fit = 1.11 x + 0.0 (399 voxels, overlap=0.387) Right_Amygdala (54): linear fit = 1.11 x + 0.0 (399 voxels, peak = 69), gca=68.5 gca peak = 0.10129 (93) mri peak = 0.06667 (104) Left_Thalamus_Proper (10): linear fit = 1.12 x + 0.0 (5640 voxels, overlap=0.514) Left_Thalamus_Proper (10): linear fit = 1.12 x + 0.0 (5640 voxels, peak = 104), gca=103.7 gca peak = 0.12071 (89) mri peak = 0.06343 (94) Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (4143 voxels, overlap=0.783) Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (4143 voxels, peak = 93), gca=93.0 gca peak = 0.13716 (82) mri peak = 0.05825 (89) Left_Putamen (12): linear fit = 1.07 x + 0.0 (2265 voxels, overlap=0.876) Left_Putamen (12): linear fit = 1.07 x + 0.0 (2265 voxels, peak = 87), gca=87.3 gca peak = 0.15214 (84) mri peak = 0.05826 (89) Right_Putamen (51): linear fit = 1.05 x + 0.0 (2545 voxels, overlap=0.916) Right_Putamen (51): linear fit = 1.05 x + 0.0 (2545 voxels, peak = 89), gca=88.6 gca peak = 0.08983 (85) mri peak = 0.06586 (92) Brain_Stem (16): linear fit = 1.09 x + 0.0 (13471 voxels, overlap=0.666) Brain_Stem (16): linear fit = 1.09 x + 0.0 (13471 voxels, peak = 92), gca=92.2 gca peak = 0.11809 (92) mri peak = 0.07624 (101) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (917 voxels, overlap=0.555) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (917 voxels, peak = 101), gca=100.7 gca peak = 0.12914 (94) mri peak = 0.08480 (101) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (1213 voxels, overlap=0.423) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (1213 voxels, peak = 102), gca=102.0 gca peak = 0.21100 (36) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13542 (27) mri peak = 0.18261 (20) Fourth_Ventricle (15): linear fit = 0.71 x + 0.0 (269 voxels, overlap=0.149) Fourth_Ventricle (15): linear fit = 0.71 x + 0.0 (269 voxels, peak = 19), gca=19.3 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21802 (40) gca peak Third_Ventricle = 0.21100 (36) gca peak CSF = 0.17123 (45) gca peak Left_Accumbens_area = 0.25875 (69) gca peak Left_undetermined = 0.96240 (36) gca peak Left_vessel = 0.33262 (65) gca peak Left_choroid_plexus = 0.09846 (46) gca peak Right_Inf_Lat_Vent = 0.28113 (34) gca peak Right_Accumbens_area = 0.27120 (72) gca peak Right_vessel = 0.61915 (60) gca peak Right_choroid_plexus = 0.12775 (51) gca peak Fifth_Ventricle = 0.45329 (44) gca peak WM_hypointensities = 0.11729 (81) gca peak non_WM_hypointensities = 0.10912 (56) gca peak Optic_Chiasm = 0.33287 (75) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 1.07 x + 0.0 estimating mean wm scale to be 1.02 x + 0.0 estimating mean csf scale to be 0.64 x + 0.0 saving intensity scales to talairach.label_intensities.txt **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.633, neg=0, invalid=96777 0099: dt=129.472000, rms=0.628 (0.774%), neg=0, invalid=96777 0100: dt=129.472000, rms=0.626 (0.238%), neg=0, invalid=96777 0101: dt=129.472000, rms=0.625 (0.202%), neg=0, invalid=96777 0102: dt=110.976000, rms=0.624 (0.125%), neg=0, invalid=96777 0103: dt=129.472000, rms=0.623 (0.140%), neg=0, invalid=96777 0104: dt=110.976000, rms=0.623 (0.088%), neg=0, invalid=96777 0105: dt=129.472000, rms=0.622 (0.104%), neg=0, invalid=96777 0106: dt=92.480000, rms=0.622 (0.065%), neg=0, invalid=96777 0107: dt=129.472000, rms=0.621 (0.088%), neg=0, invalid=96777 0108: dt=73.984000, rms=0.621 (0.051%), neg=0, invalid=96777 0109: dt=129.472000, rms=0.621 (0.071%), neg=0, invalid=96777 0110: dt=110.976000, rms=0.620 (0.041%), neg=0, invalid=96777 0111: dt=110.976000, rms=0.620 (0.060%), neg=0, invalid=96777 0112: dt=110.976000, rms=0.619 (0.085%), neg=0, invalid=96777 0113: dt=110.976000, rms=0.619 (0.098%), neg=0, invalid=96777 0114: dt=110.976000, rms=0.618 (0.120%), neg=0, invalid=96777 0115: dt=110.976000, rms=0.617 (0.125%), neg=0, invalid=96777 0116: dt=110.976000, rms=0.617 (0.099%), neg=0, invalid=96777 0117: dt=110.976000, rms=0.616 (0.101%), neg=0, invalid=96777 0118: dt=110.976000, rms=0.616 (0.088%), neg=0, invalid=96777 0119: dt=110.976000, rms=0.615 (0.107%), neg=0, invalid=96777 0120: dt=110.976000, rms=0.614 (0.091%), neg=0, invalid=96777 0121: dt=110.976000, rms=0.614 (0.081%), neg=0, invalid=96777 0122: dt=110.976000, rms=0.613 (0.086%), neg=0, invalid=96777 0123: dt=110.976000, rms=0.613 (0.080%), neg=0, invalid=96777 0124: dt=110.976000, rms=0.612 (0.094%), neg=0, invalid=96777 0125: dt=110.976000, rms=0.612 (0.092%), neg=0, invalid=96777 0126: dt=110.976000, rms=0.611 (0.092%), neg=0, invalid=96777 0127: dt=110.976000, rms=0.611 (0.068%), neg=0, invalid=96777 0128: dt=110.976000, rms=0.610 (0.068%), neg=0, invalid=96777 0129: dt=110.976000, rms=0.610 (0.058%), neg=0, invalid=96777 0130: dt=110.976000, rms=0.610 (0.064%), neg=0, invalid=96777 0131: dt=110.976000, rms=0.609 (0.070%), neg=0, invalid=96777 0132: dt=110.976000, rms=0.609 (0.047%), neg=0, invalid=96777 0133: dt=110.976000, rms=0.608 (0.064%), neg=0, invalid=96777 0134: dt=110.976000, rms=0.608 (0.040%), neg=0, invalid=96777 0135: dt=110.976000, rms=0.608 (0.057%), neg=0, invalid=96777 0136: dt=110.976000, rms=0.607 (0.054%), neg=0, invalid=96777 0137: dt=110.976000, rms=0.607 (0.051%), neg=0, invalid=96777 0138: dt=110.976000, rms=0.607 (0.042%), neg=0, invalid=96777 0139: dt=110.976000, rms=0.607 (0.060%), neg=0, invalid=96777 0140: dt=110.976000, rms=0.606 (0.055%), neg=0, invalid=96777 0141: dt=110.976000, rms=0.606 (0.035%), neg=0, invalid=96777 0142: dt=110.976000, rms=0.606 (0.044%), neg=0, invalid=96777 0143: dt=110.976000, rms=0.605 (0.044%), neg=0, invalid=96777 0144: dt=110.976000, rms=0.605 (0.051%), neg=0, invalid=96777 0145: dt=110.976000, rms=0.605 (0.036%), neg=0, invalid=96777 0146: dt=110.976000, rms=0.605 (0.057%), neg=0, invalid=96777 0147: dt=110.976000, rms=0.604 (0.046%), neg=0, invalid=96777 0148: dt=110.976000, rms=0.604 (0.041%), neg=0, invalid=96777 0149: dt=110.976000, rms=0.604 (0.032%), neg=0, invalid=96777 0150: dt=110.976000, rms=0.604 (0.033%), neg=0, invalid=96777 0151: dt=110.976000, rms=0.603 (0.037%), neg=0, invalid=96777 0152: dt=110.976000, rms=0.603 (0.039%), neg=0, invalid=96777 0153: dt=110.976000, rms=0.603 (0.033%), neg=0, invalid=96777 0154: dt=110.976000, rms=0.603 (0.040%), neg=0, invalid=96777 0155: dt=110.976000, rms=0.603 (0.034%), neg=0, invalid=96777 0156: dt=110.976000, rms=0.602 (0.029%), neg=0, invalid=96777 0157: dt=110.976000, rms=0.602 (0.023%), neg=0, invalid=96777 0158: dt=110.976000, rms=0.602 (0.028%), neg=0, invalid=96777 0159: dt=110.976000, rms=0.602 (0.034%), neg=0, invalid=96777 0160: dt=110.976000, rms=0.602 (0.038%), neg=0, invalid=96777 0161: dt=110.976000, rms=0.601 (0.032%), neg=0, invalid=96777 0162: dt=110.976000, rms=0.601 (0.027%), neg=0, invalid=96777 0163: dt=110.976000, rms=0.601 (0.022%), neg=0, invalid=96777 0164: dt=110.976000, rms=0.601 (0.018%), neg=0, invalid=96777 0165: dt=129.472000, rms=0.601 (0.009%), neg=0, invalid=96777 0166: dt=129.472000, rms=0.601 (0.000%), neg=0, invalid=96777 0167: dt=129.472000, rms=0.601 (0.006%), neg=0, invalid=96777 0168: dt=129.472000, rms=0.601 (0.009%), neg=0, invalid=96777 0169: dt=129.472000, rms=0.601 (0.006%), neg=0, invalid=96777 0170: dt=129.472000, rms=0.601 (0.006%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.601, neg=0, invalid=96777 0171: dt=295.936000, rms=0.600 (0.167%), neg=0, invalid=96777 0172: dt=110.976000, rms=0.600 (0.058%), neg=0, invalid=96777 0173: dt=129.472000, rms=0.599 (0.036%), neg=0, invalid=96777 0174: dt=129.472000, rms=0.599 (0.021%), neg=0, invalid=96777 0175: dt=129.472000, rms=0.599 (0.046%), neg=0, invalid=96777 0176: dt=129.472000, rms=0.599 (0.041%), neg=0, invalid=96777 0177: dt=129.472000, rms=0.598 (0.064%), neg=0, invalid=96777 0178: dt=129.472000, rms=0.598 (0.035%), neg=0, invalid=96777 0179: dt=129.472000, rms=0.598 (0.059%), neg=0, invalid=96777 0180: dt=129.472000, rms=0.598 (0.016%), neg=0, invalid=96777 0181: dt=129.472000, rms=0.597 (0.059%), neg=0, invalid=96777 0182: dt=129.472000, rms=0.597 (0.024%), neg=0, invalid=96777 0183: dt=129.472000, rms=0.597 (0.030%), neg=0, invalid=96777 0184: dt=129.472000, rms=0.597 (0.028%), neg=0, invalid=96777 0185: dt=129.472000, rms=0.597 (0.021%), neg=0, invalid=96777 0186: dt=129.472000, rms=0.597 (0.011%), neg=0, invalid=96777 0187: dt=129.472000, rms=0.596 (0.021%), neg=0, invalid=96777 0188: dt=129.472000, rms=0.596 (0.013%), neg=0, invalid=96777 0189: dt=129.472000, rms=0.596 (0.008%), neg=0, invalid=96777 0190: dt=129.472000, rms=0.596 (0.018%), neg=0, invalid=96777 0191: dt=129.472000, rms=0.596 (0.012%), neg=0, invalid=96777 0192: dt=129.472000, rms=0.596 (0.011%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.597, neg=0, invalid=96777 0193: dt=124.416000, rms=0.594 (0.501%), neg=0, invalid=96777 0194: dt=103.680000, rms=0.591 (0.472%), neg=0, invalid=96777 0195: dt=25.920000, rms=0.589 (0.423%), neg=0, invalid=96777 0196: dt=145.152000, rms=0.586 (0.430%), neg=0, invalid=96777 0197: dt=31.104000, rms=0.584 (0.386%), neg=0, invalid=96777 0198: dt=36.288000, rms=0.583 (0.175%), neg=0, invalid=96777 0199: dt=82.944000, rms=0.581 (0.260%), neg=0, invalid=96777 0200: dt=25.920000, rms=0.580 (0.196%), neg=0, invalid=96777 0201: dt=145.152000, rms=0.578 (0.349%), neg=0, invalid=96777 0202: dt=20.736000, rms=0.577 (0.233%), neg=0, invalid=96777 0203: dt=580.608000, rms=0.570 (1.103%), neg=0, invalid=96777 0204: dt=20.736000, rms=0.568 (0.485%), neg=0, invalid=96777 0205: dt=82.944000, rms=0.567 (0.204%), neg=0, invalid=96777 0206: dt=36.288000, rms=0.566 (0.075%), neg=0, invalid=96777 0207: dt=82.944000, rms=0.565 (0.142%), neg=0, invalid=96777 0208: dt=25.920000, rms=0.565 (0.079%), neg=0, invalid=96777 0209: dt=248.832000, rms=0.563 (0.280%), neg=0, invalid=96777 0210: dt=20.736000, rms=0.563 (0.118%), neg=0, invalid=96777 0211: dt=82.944000, rms=0.562 (0.102%), neg=0, invalid=96777 0212: dt=36.288000, rms=0.561 (0.106%), neg=0, invalid=96777 0213: dt=31.104000, rms=0.561 (0.021%), neg=0, invalid=96777 0214: dt=31.104000, rms=0.561 (0.059%), neg=0, invalid=96777 0215: dt=31.104000, rms=0.561 (0.081%), neg=0, invalid=96777 0216: dt=31.104000, rms=0.560 (0.102%), neg=0, invalid=96777 0217: dt=31.104000, rms=0.559 (0.113%), neg=0, invalid=96777 0218: dt=31.104000, rms=0.558 (0.151%), neg=0, invalid=96777 0219: dt=31.104000, rms=0.557 (0.183%), neg=0, invalid=96777 0220: dt=31.104000, rms=0.556 (0.181%), neg=0, invalid=96777 0221: dt=31.104000, rms=0.555 (0.179%), neg=0, invalid=96777 0222: dt=31.104000, rms=0.555 (0.167%), neg=0, invalid=96777 0223: dt=31.104000, rms=0.554 (0.182%), neg=0, invalid=96777 0224: dt=31.104000, rms=0.552 (0.184%), neg=0, invalid=96777 0225: dt=31.104000, rms=0.551 (0.181%), neg=0, invalid=96777 0226: dt=31.104000, rms=0.551 (0.175%), neg=0, invalid=96777 0227: dt=31.104000, rms=0.550 (0.155%), neg=0, invalid=96777 0228: dt=31.104000, rms=0.549 (0.141%), neg=0, invalid=96777 0229: dt=31.104000, rms=0.548 (0.147%), neg=0, invalid=96777 0230: dt=31.104000, rms=0.547 (0.127%), neg=0, invalid=96777 0231: dt=31.104000, rms=0.547 (0.107%), neg=0, invalid=96777 0232: dt=31.104000, rms=0.546 (0.097%), neg=0, invalid=96777 0233: dt=31.104000, rms=0.546 (0.116%), neg=0, invalid=96777 0234: dt=31.104000, rms=0.545 (0.119%), neg=0, invalid=96777 0235: dt=31.104000, rms=0.544 (0.110%), neg=0, invalid=96777 0236: dt=31.104000, rms=0.544 (0.088%), neg=0, invalid=96777 0237: dt=31.104000, rms=0.543 (0.092%), neg=0, invalid=96777 0238: dt=31.104000, rms=0.543 (0.089%), neg=0, invalid=96777 0239: dt=31.104000, rms=0.542 (0.097%), neg=0, invalid=96777 0240: dt=31.104000, rms=0.542 (0.097%), neg=0, invalid=96777 0241: dt=31.104000, rms=0.542 (0.069%), neg=0, invalid=96777 0242: dt=31.104000, rms=0.541 (0.084%), neg=0, invalid=96777 0243: dt=31.104000, rms=0.541 (0.081%), neg=0, invalid=96777 0244: dt=31.104000, rms=0.540 (0.082%), neg=0, invalid=96777 0245: dt=31.104000, rms=0.540 (0.089%), neg=0, invalid=96777 0246: dt=31.104000, rms=0.539 (0.065%), neg=0, invalid=96777 0247: dt=31.104000, rms=0.539 (0.079%), neg=0, invalid=96777 0248: dt=31.104000, rms=0.539 (0.077%), neg=0, invalid=96777 0249: dt=31.104000, rms=0.538 (0.070%), neg=0, invalid=96777 0250: dt=31.104000, rms=0.538 (0.054%), neg=0, invalid=96777 0251: dt=31.104000, rms=0.537 (0.070%), neg=0, invalid=96777 0252: dt=31.104000, rms=0.537 (0.066%), neg=0, invalid=96777 0253: dt=31.104000, rms=0.537 (0.063%), neg=0, invalid=96777 0254: dt=31.104000, rms=0.537 (0.050%), neg=0, invalid=96777 0255: dt=31.104000, rms=0.536 (0.046%), neg=0, invalid=96777 0256: dt=31.104000, rms=0.536 (0.045%), neg=0, invalid=96777 0257: dt=31.104000, rms=0.536 (0.043%), neg=0, invalid=96777 0258: dt=31.104000, rms=0.535 (0.054%), neg=0, invalid=96777 0259: dt=31.104000, rms=0.535 (0.059%), neg=0, invalid=96777 0260: dt=31.104000, rms=0.535 (0.048%), neg=0, invalid=96777 0261: dt=31.104000, rms=0.535 (0.032%), neg=0, invalid=96777 0262: dt=31.104000, rms=0.535 (0.031%), neg=0, invalid=96777 0263: dt=31.104000, rms=0.534 (0.053%), neg=0, invalid=96777 0264: dt=31.104000, rms=0.534 (0.049%), neg=0, invalid=96777 0265: dt=31.104000, rms=0.534 (0.033%), neg=0, invalid=96777 0266: dt=31.104000, rms=0.534 (0.023%), neg=0, invalid=96777 0267: dt=31.104000, rms=0.534 (0.038%), neg=0, invalid=96777 0268: dt=31.104000, rms=0.533 (0.044%), neg=0, invalid=96777 0269: dt=31.104000, rms=0.533 (0.041%), neg=0, invalid=96777 0270: dt=31.104000, rms=0.533 (0.037%), neg=0, invalid=96777 0271: dt=31.104000, rms=0.533 (0.024%), neg=0, invalid=96777 0272: dt=31.104000, rms=0.533 (0.035%), neg=0, invalid=96777 0273: dt=31.104000, rms=0.532 (0.028%), neg=0, invalid=96777 0274: dt=31.104000, rms=0.532 (0.030%), neg=0, invalid=96777 0275: dt=31.104000, rms=0.532 (0.039%), neg=0, invalid=96777 0276: dt=31.104000, rms=0.532 (0.039%), neg=0, invalid=96777 0277: dt=31.104000, rms=0.532 (0.035%), neg=0, invalid=96777 0278: dt=31.104000, rms=0.532 (0.025%), neg=0, invalid=96777 0279: dt=31.104000, rms=0.531 (0.018%), neg=0, invalid=96777 0280: dt=31.104000, rms=0.531 (0.010%), neg=0, invalid=96777 0281: dt=36.288000, rms=0.531 (0.025%), neg=0, invalid=96777 0282: dt=20.736000, rms=0.531 (0.002%), neg=0, invalid=96777 0283: dt=20.736000, rms=0.531 (0.012%), neg=0, invalid=96777 0284: dt=20.736000, rms=0.531 (0.006%), neg=0, invalid=96777 0285: dt=20.736000, rms=0.531 (0.005%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.531, neg=0, invalid=96777 0286: dt=145.152000, rms=0.529 (0.394%), neg=0, invalid=96777 0287: dt=36.288000, rms=0.529 (0.097%), neg=0, invalid=96777 0288: dt=36.288000, rms=0.528 (0.042%), neg=0, invalid=96777 0289: dt=36.288000, rms=0.528 (0.023%), neg=0, invalid=96777 0290: dt=36.288000, rms=0.528 (0.054%), neg=0, invalid=96777 0291: dt=36.288000, rms=0.527 (0.079%), neg=0, invalid=96777 0292: dt=36.288000, rms=0.527 (0.081%), neg=0, invalid=96777 0293: dt=36.288000, rms=0.527 (0.095%), neg=0, invalid=96777 0294: dt=36.288000, rms=0.526 (0.081%), neg=0, invalid=96777 0295: dt=36.288000, rms=0.526 (0.080%), neg=0, invalid=96777 0296: dt=36.288000, rms=0.525 (0.073%), neg=0, invalid=96777 0297: dt=36.288000, rms=0.525 (0.065%), neg=0, invalid=96777 0298: dt=36.288000, rms=0.525 (0.056%), neg=0, invalid=96777 0299: dt=36.288000, rms=0.524 (0.052%), neg=0, invalid=96777 0300: dt=36.288000, rms=0.524 (0.048%), neg=0, invalid=96777 0301: dt=36.288000, rms=0.524 (0.044%), neg=0, invalid=96777 0302: dt=36.288000, rms=0.524 (0.035%), neg=0, invalid=96777 0303: dt=36.288000, rms=0.523 (0.057%), neg=0, invalid=96777 0304: dt=36.288000, rms=0.523 (0.041%), neg=0, invalid=96777 0305: dt=36.288000, rms=0.523 (0.028%), neg=0, invalid=96777 0306: dt=36.288000, rms=0.523 (0.044%), neg=0, invalid=96777 0307: dt=36.288000, rms=0.523 (0.050%), neg=0, invalid=96777 0308: dt=36.288000, rms=0.522 (0.029%), neg=0, invalid=96777 0309: dt=36.288000, rms=0.522 (0.038%), neg=0, invalid=96777 0310: dt=36.288000, rms=0.522 (0.029%), neg=0, invalid=96777 0311: dt=36.288000, rms=0.522 (0.032%), neg=0, invalid=96777 0312: dt=36.288000, rms=0.522 (0.033%), neg=0, invalid=96777 0313: dt=36.288000, rms=0.521 (0.052%), neg=0, invalid=96777 0314: dt=36.288000, rms=0.521 (0.036%), neg=0, invalid=96777 0315: dt=36.288000, rms=0.521 (0.039%), neg=0, invalid=96777 0316: dt=36.288000, rms=0.521 (0.035%), neg=0, invalid=96777 0317: dt=36.288000, rms=0.521 (0.021%), neg=0, invalid=96777 0318: dt=36.288000, rms=0.521 (0.021%), neg=0, invalid=96777 0319: dt=36.288000, rms=0.521 (0.027%), neg=0, invalid=96777 0320: dt=36.288000, rms=0.520 (0.040%), neg=0, invalid=96777 0321: dt=36.288000, rms=0.520 (0.020%), neg=0, invalid=96777 0322: dt=36.288000, rms=0.520 (0.022%), neg=0, invalid=96777 0323: dt=36.288000, rms=0.520 (0.033%), neg=0, invalid=96777 0324: dt=36.288000, rms=0.520 (0.019%), neg=0, invalid=96777 0325: dt=36.288000, rms=0.520 (0.025%), neg=0, invalid=96777 0326: dt=36.288000, rms=0.520 (0.033%), neg=0, invalid=96777 0327: dt=36.288000, rms=0.519 (0.031%), neg=0, invalid=96777 0328: dt=36.288000, rms=0.519 (0.023%), neg=0, invalid=96777 0329: dt=36.288000, rms=0.519 (0.018%), neg=0, invalid=96777 0330: dt=15.552000, rms=0.519 (0.003%), neg=0, invalid=96777 0331: dt=15.552000, rms=0.519 (0.008%), neg=0, invalid=96777 0332: dt=15.552000, rms=0.519 (0.003%), neg=0, invalid=96777 0333: dt=15.552000, rms=0.519 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.527, neg=0, invalid=96777 0334: dt=25.600000, rms=0.526 (0.199%), neg=0, invalid=96777 0335: dt=44.800000, rms=0.524 (0.306%), neg=0, invalid=96777 0336: dt=32.000000, rms=0.522 (0.303%), neg=0, invalid=96777 0337: dt=9.600000, rms=0.522 (0.161%), neg=0, invalid=96777 0338: dt=25.600000, rms=0.520 (0.219%), neg=0, invalid=96777 0339: dt=7.607843, rms=0.520 (0.125%), neg=0, invalid=96777 0340: dt=44.800000, rms=0.518 (0.281%), neg=0, invalid=96777 0341: dt=8.936937, rms=0.517 (0.188%), neg=0, invalid=96777 0342: dt=38.400000, rms=0.516 (0.227%), neg=0, invalid=96777 0343: dt=7.796610, rms=0.515 (0.155%), neg=0, invalid=96777 0344: dt=38.400000, rms=0.514 (0.210%), neg=0, invalid=96777 0345: dt=8.323232, rms=0.514 (0.138%), neg=0, invalid=96777 0346: dt=25.600000, rms=0.513 (0.122%), neg=0, invalid=96777 0347: dt=9.600000, rms=0.512 (0.103%), neg=0, invalid=96777 0348: dt=11.200000, rms=0.512 (0.082%), neg=0, invalid=96777 0349: dt=38.400000, rms=0.511 (0.149%), neg=0, invalid=96777 0350: dt=7.472527, rms=0.511 (0.090%), neg=0, invalid=96777 0351: dt=179.200000, rms=0.508 (0.493%), neg=0, invalid=96777 0352: dt=11.970803, rms=0.506 (0.402%), neg=0, invalid=96777 0353: dt=9.600000, rms=0.506 (0.089%), neg=0, invalid=96777 0354: dt=38.400000, rms=0.505 (0.089%), neg=0, invalid=96777 0355: dt=11.200000, rms=0.505 (0.072%), neg=0, invalid=96777 0356: dt=11.200000, rms=0.505 (0.062%), neg=0, invalid=96777 0357: dt=11.200000, rms=0.504 (0.037%), neg=0, invalid=96777 0358: dt=11.200000, rms=0.504 (0.047%), neg=0, invalid=96777 0359: dt=11.200000, rms=0.504 (0.073%), neg=0, invalid=96777 0360: dt=11.200000, rms=0.503 (0.085%), neg=0, invalid=96777 0361: dt=11.200000, rms=0.503 (0.107%), neg=0, invalid=96777 0362: dt=11.200000, rms=0.502 (0.142%), neg=0, invalid=96777 0363: dt=11.200000, rms=0.501 (0.156%), neg=0, invalid=96777 0364: dt=11.200000, rms=0.501 (0.164%), neg=0, invalid=96777 0365: dt=11.200000, rms=0.500 (0.170%), neg=0, invalid=96777 0366: dt=11.200000, rms=0.499 (0.163%), neg=0, invalid=96777 0367: dt=11.200000, rms=0.498 (0.160%), neg=0, invalid=96777 0368: dt=11.200000, rms=0.497 (0.156%), neg=0, invalid=96777 0369: dt=11.200000, rms=0.497 (0.167%), neg=0, invalid=96777 0370: dt=11.200000, rms=0.496 (0.151%), neg=0, invalid=96777 0371: dt=11.200000, rms=0.495 (0.149%), neg=0, invalid=96777 0372: dt=11.200000, rms=0.494 (0.134%), neg=0, invalid=96777 0373: dt=11.200000, rms=0.494 (0.130%), neg=0, invalid=96777 0374: dt=11.200000, rms=0.493 (0.127%), neg=0, invalid=96777 0375: dt=11.200000, rms=0.493 (0.114%), neg=0, invalid=96777 0376: dt=11.200000, rms=0.492 (0.110%), neg=0, invalid=96777 0377: dt=11.200000, rms=0.491 (0.110%), neg=0, invalid=96777 0378: dt=11.200000, rms=0.491 (0.103%), neg=0, invalid=96777 0379: dt=11.200000, rms=0.491 (0.085%), neg=0, invalid=96777 0380: dt=11.200000, rms=0.490 (0.081%), neg=0, invalid=96777 0381: dt=11.200000, rms=0.490 (0.086%), neg=0, invalid=96777 0382: dt=11.200000, rms=0.489 (0.074%), neg=0, invalid=96777 0383: dt=11.200000, rms=0.489 (0.061%), neg=0, invalid=96777 0384: dt=11.200000, rms=0.489 (0.051%), neg=0, invalid=96777 0385: dt=11.200000, rms=0.489 (0.058%), neg=0, invalid=96777 0386: dt=11.200000, rms=0.488 (0.072%), neg=0, invalid=96777 0387: dt=11.200000, rms=0.488 (0.061%), neg=0, invalid=96777 0388: dt=11.200000, rms=0.488 (0.045%), neg=0, invalid=96777 0389: dt=11.200000, rms=0.487 (0.052%), neg=0, invalid=96777 0390: dt=11.200000, rms=0.487 (0.034%), neg=0, invalid=96777 0391: dt=11.200000, rms=0.487 (0.028%), neg=0, invalid=96777 0392: dt=11.200000, rms=0.487 (0.015%), neg=0, invalid=96777 0393: dt=11.200000, rms=0.487 (0.039%), neg=0, invalid=96777 0394: dt=11.200000, rms=0.487 (0.063%), neg=0, invalid=96777 0395: dt=11.200000, rms=0.486 (0.045%), neg=0, invalid=96777 0396: dt=11.200000, rms=0.486 (0.032%), neg=0, invalid=96777 0397: dt=11.200000, rms=0.486 (0.028%), neg=0, invalid=96777 0398: dt=11.200000, rms=0.486 (0.016%), neg=0, invalid=96777 0399: dt=11.200000, rms=0.486 (0.011%), neg=0, invalid=96777 0400: dt=25.600000, rms=0.486 (0.046%), neg=0, invalid=96777 0401: dt=6.400000, rms=0.486 (0.008%), neg=0, invalid=96777 0402: dt=6.400000, rms=0.486 (0.001%), neg=0, invalid=96777 0403: dt=6.400000, rms=0.486 (0.003%), neg=0, invalid=96777 0404: dt=6.400000, rms=0.486 (0.001%), neg=0, invalid=96777 0405: dt=6.400000, rms=0.486 (0.002%), neg=0, invalid=96777 0406: dt=6.400000, rms=0.486 (0.006%), neg=0, invalid=96777 0407: dt=6.400000, rms=0.486 (0.010%), neg=0, invalid=96777 0408: dt=6.400000, rms=0.486 (0.002%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.486, neg=0, invalid=96777 0409: dt=38.400000, rms=0.484 (0.279%), neg=0, invalid=96777 0410: dt=11.200000, rms=0.484 (0.124%), neg=0, invalid=96777 0411: dt=44.800000, rms=0.483 (0.114%), neg=0, invalid=96777 0412: dt=11.200000, rms=0.483 (0.039%), neg=0, invalid=96777 0413: dt=11.200000, rms=0.483 (0.022%), neg=0, invalid=96777 0414: dt=11.200000, rms=0.483 (0.031%), neg=0, invalid=96777 0415: dt=11.200000, rms=0.482 (0.021%), neg=0, invalid=96777 0416: dt=11.200000, rms=0.482 (0.033%), neg=0, invalid=96777 0417: dt=11.200000, rms=0.482 (0.028%), neg=0, invalid=96777 0418: dt=11.200000, rms=0.482 (0.018%), neg=0, invalid=96777 0419: dt=11.200000, rms=0.482 (-0.001%), neg=0, invalid=96777 0420: dt=19.200000, rms=0.482 (0.008%), neg=0, invalid=96777 0421: dt=11.200000, rms=0.482 (0.019%), neg=0, invalid=96777 0422: dt=19.200000, rms=0.482 (0.005%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.502, neg=0, invalid=96777 0423: dt=0.000000, rms=0.502 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.502, neg=0, invalid=96777 0424: dt=0.000000, rms=0.502 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.541, neg=0, invalid=96777 0425: dt=1.336735, rms=0.537 (0.766%), neg=0, invalid=96777 0426: dt=0.384000, rms=0.537 (0.027%), neg=0, invalid=96777 0427: dt=0.384000, rms=0.537 (-0.013%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.537, neg=0, invalid=96777 0428: dt=0.832000, rms=0.536 (0.116%), neg=0, invalid=96777 0429: dt=0.227273, rms=0.536 (0.007%), neg=0, invalid=96777 0430: dt=0.227273, rms=0.536 (-0.004%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.497, neg=0, invalid=96777 0431: dt=0.448000, rms=0.483 (2.929%), neg=0, invalid=96777 0432: dt=0.448000, rms=0.480 (0.553%), neg=0, invalid=96777 0433: dt=0.448000, rms=0.479 (0.361%), neg=0, invalid=96777 0434: dt=0.448000, rms=0.477 (0.232%), neg=0, invalid=96777 0435: dt=0.448000, rms=0.477 (0.170%), neg=0, invalid=96777 0436: dt=0.448000, rms=0.476 (0.122%), neg=0, invalid=96777 0437: dt=0.800000, rms=0.475 (0.166%), neg=0, invalid=96777 0438: dt=0.112000, rms=0.475 (0.024%), neg=0, invalid=96777 0439: dt=0.112000, rms=0.475 (0.020%), neg=0, invalid=96777 0440: dt=0.112000, rms=0.475 (0.031%), neg=0, invalid=96777 0441: dt=0.112000, rms=0.475 (0.040%), neg=0, invalid=96777 0442: dt=0.112000, rms=0.474 (0.048%), neg=0, invalid=96777 0443: dt=0.112000, rms=0.474 (0.050%), neg=0, invalid=96777 0444: dt=0.112000, rms=0.474 (0.056%), neg=0, invalid=96777 0445: dt=0.112000, rms=0.474 (0.059%), neg=0, invalid=96777 0446: dt=0.112000, rms=0.473 (0.053%), neg=0, invalid=96777 0447: dt=0.112000, rms=0.473 (0.046%), neg=0, invalid=96777 0448: dt=0.112000, rms=0.473 (0.046%), neg=0, invalid=96777 0449: dt=0.112000, rms=0.473 (0.038%), neg=0, invalid=96777 0450: dt=0.112000, rms=0.473 (0.035%), neg=0, invalid=96777 0451: dt=0.112000, rms=0.472 (0.029%), neg=0, invalid=96777 0452: dt=0.112000, rms=0.472 (0.020%), neg=0, invalid=96777 0453: dt=0.112000, rms=0.472 (0.018%), neg=0, invalid=96777 0454: dt=0.112000, rms=0.472 (0.001%), neg=0, invalid=96777 0455: dt=0.112000, rms=0.472 (-0.002%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.472, neg=0, invalid=96777 0456: dt=0.448000, rms=0.468 (0.989%), neg=0, invalid=96777 0457: dt=0.384000, rms=0.468 (0.002%), neg=0, invalid=96777 0458: dt=0.384000, rms=0.468 (0.002%), neg=0, invalid=96777 0459: dt=0.384000, rms=0.468 (-0.016%), neg=0, invalid=96777 label assignment complete, 0 changed (0.00%) ********************************************************************************************* ********************************************************************************************* ********************************************************************************************* ********************* ALLOWING NEGATIVE NODES IN DEFORMATION ******************************** ********************************************************************************************* ********************************************************************************************* ********************************************************************************************* **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.465, neg=0, invalid=96777 0460: dt=0.000000, rms=0.465 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.465, neg=0, invalid=96777 0461: dt=129.472000, rms=0.465 (0.062%), neg=0, invalid=96777 0462: dt=110.976000, rms=0.465 (0.033%), neg=0, invalid=96777 0463: dt=110.976000, rms=0.465 (0.012%), neg=0, invalid=96777 0464: dt=110.976000, rms=0.465 (0.036%), neg=0, invalid=96777 0465: dt=110.976000, rms=0.465 (0.031%), neg=0, invalid=96777 0466: dt=110.976000, rms=0.464 (0.025%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.465, neg=0, invalid=96777 0467: dt=25.920000, rms=0.464 (0.028%), neg=0, invalid=96777 0468: dt=25.920000, rms=0.464 (0.008%), neg=0, invalid=96777 0469: dt=25.920000, rms=0.464 (0.011%), neg=0, invalid=96777 0470: dt=25.920000, rms=0.464 (-0.007%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.464, neg=0, invalid=96777 0471: dt=145.152000, rms=0.462 (0.430%), neg=0, invalid=96777 0472: dt=36.288000, rms=0.462 (0.135%), neg=0, invalid=96777 0473: dt=36.288000, rms=0.461 (0.050%), neg=0, invalid=96777 0474: dt=36.288000, rms=0.461 (0.069%), neg=0, invalid=96777 0475: dt=36.288000, rms=0.461 (0.089%), neg=0, invalid=96777 0476: dt=36.288000, rms=0.460 (0.116%), neg=0, invalid=96777 0477: dt=36.288000, rms=0.460 (0.141%), neg=0, invalid=96777 0478: dt=36.288000, rms=0.459 (0.138%), neg=0, invalid=96777 0479: dt=36.288000, rms=0.458 (0.116%), neg=0, invalid=96777 0480: dt=36.288000, rms=0.458 (0.093%), neg=0, invalid=96777 0481: dt=25.920000, rms=0.458 (0.011%), neg=0, invalid=96777 0482: dt=25.920000, rms=0.458 (0.004%), neg=0, invalid=96777 0483: dt=25.920000, rms=0.458 (0.021%), neg=0, invalid=96777 0484: dt=25.920000, rms=0.458 (0.020%), neg=0, invalid=96777 0485: dt=25.920000, rms=0.458 (0.024%), neg=0, invalid=96777 0486: dt=25.920000, rms=0.457 (0.032%), neg=0, invalid=96777 0487: dt=25.920000, rms=0.457 (0.028%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.458, neg=0, invalid=96777 iter 0, gcam->neg = 4 after 6 iterations, nbhd size=1, neg = 0 0488: dt=32.000000, rms=0.456 (0.361%), neg=0, invalid=96777 0489: dt=11.200000, rms=0.455 (0.157%), neg=0, invalid=96777 0490: dt=11.200000, rms=0.455 (0.163%), neg=0, invalid=96777 0491: dt=11.200000, rms=0.454 (0.203%), neg=0, invalid=96777 0492: dt=11.200000, rms=0.453 (0.228%), neg=0, invalid=96777 0493: dt=11.200000, rms=0.452 (0.209%), neg=0, invalid=96777 0494: dt=11.200000, rms=0.451 (0.220%), neg=0, invalid=96777 0495: dt=11.200000, rms=0.450 (0.187%), neg=0, invalid=96777 0496: dt=11.200000, rms=0.449 (0.175%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0497: dt=11.200000, rms=0.448 (0.186%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0498: dt=11.200000, rms=0.447 (0.210%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0499: dt=11.200000, rms=0.446 (0.192%), neg=0, invalid=96777 0500: dt=11.200000, rms=0.446 (0.180%), neg=0, invalid=96777 0501: dt=11.200000, rms=0.445 (0.156%), neg=0, invalid=96777 0502: dt=11.200000, rms=0.444 (0.182%), neg=0, invalid=96777 0503: dt=11.200000, rms=0.443 (0.139%), neg=0, invalid=96777 0504: dt=11.200000, rms=0.443 (0.129%), neg=0, invalid=96777 0505: dt=11.200000, rms=0.442 (0.116%), neg=0, invalid=96777 0506: dt=11.200000, rms=0.442 (0.116%), neg=0, invalid=96777 0507: dt=11.200000, rms=0.441 (0.090%), neg=0, invalid=96777 0508: dt=8.000000, rms=0.441 (0.025%), neg=0, invalid=96777 0509: dt=8.000000, rms=0.441 (0.017%), neg=0, invalid=96777 0510: dt=8.000000, rms=0.441 (0.029%), neg=0, invalid=96777 0511: dt=8.000000, rms=0.441 (0.027%), neg=0, invalid=96777 0512: dt=8.000000, rms=0.441 (0.028%), neg=0, invalid=96777 0513: dt=8.000000, rms=0.441 (0.033%), neg=0, invalid=96777 0514: dt=8.000000, rms=0.441 (0.023%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.441, neg=0, invalid=96777 0515: dt=44.800000, rms=0.438 (0.660%), neg=0, invalid=96777 0516: dt=11.200000, rms=0.437 (0.125%), neg=0, invalid=96777 0517: dt=11.200000, rms=0.437 (0.075%), neg=0, invalid=96777 0518: dt=11.200000, rms=0.436 (0.097%), neg=0, invalid=96777 0519: dt=11.200000, rms=0.436 (0.129%), neg=0, invalid=96777 0520: dt=11.200000, rms=0.435 (0.123%), neg=0, invalid=96777 0521: dt=11.200000, rms=0.435 (0.102%), neg=0, invalid=96777 0522: dt=11.200000, rms=0.435 (0.029%), neg=0, invalid=96777 0523: dt=11.200000, rms=0.435 (0.020%), neg=0, invalid=96777 0524: dt=11.200000, rms=0.435 (0.028%), neg=0, invalid=96777 0525: dt=11.200000, rms=0.434 (0.041%), neg=0, invalid=96777 0526: dt=11.200000, rms=0.434 (0.036%), neg=0, invalid=96777 0527: dt=11.200000, rms=0.434 (0.046%), neg=0, invalid=96777 0528: dt=11.200000, rms=0.434 (0.055%), neg=0, invalid=96777 0529: dt=11.200000, rms=0.434 (0.050%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.439, neg=0, invalid=96777 0530: dt=0.252000, rms=0.439 (-0.003%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.439, neg=0, invalid=96777 0531: dt=2.880000, rms=0.438 (0.028%), neg=0, invalid=96777 0532: dt=2.304000, rms=0.438 (0.012%), neg=0, invalid=96777 0533: dt=2.304000, rms=0.438 (-0.000%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.447, neg=0, invalid=96777 0534: dt=0.448000, rms=0.447 (0.053%), neg=0, invalid=96777 0535: dt=0.384000, rms=0.447 (0.008%), neg=0, invalid=96777 0536: dt=0.384000, rms=0.447 (-0.008%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.447, neg=0, invalid=96777 0537: dt=1.280000, rms=0.446 (0.135%), neg=0, invalid=96777 0538: dt=0.448000, rms=0.446 (0.015%), neg=0, invalid=96777 0539: dt=0.448000, rms=0.446 (-0.005%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.437, neg=0, invalid=96777 iter 0, gcam->neg = 565 after 11 iterations, nbhd size=1, neg = 0 0540: dt=1.899000, rms=0.404 (7.507%), neg=0, invalid=96777 0541: dt=0.000250, rms=0.404 (0.004%), neg=0, invalid=96777 0542: dt=0.000250, rms=0.404 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.404, neg=0, invalid=96777 0543: dt=0.000750, rms=0.404 (0.001%), neg=0, invalid=96777 0544: dt=0.000000, rms=0.404 (0.001%), neg=0, invalid=96777 0545: dt=0.000000, rms=0.404 (0.000%), neg=0, invalid=96777 label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.390, neg=0, invalid=96777 0546: dt=0.000000, rms=0.391 (-0.189%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.391, neg=0, invalid=96777 0547: dt=32.368000, rms=0.391 (0.003%), neg=0, invalid=96777 0548: dt=32.368000, rms=0.391 (0.001%), neg=0, invalid=96777 0549: dt=32.368000, rms=0.391 (0.001%), neg=0, invalid=96777 0550: dt=32.368000, rms=0.391 (0.000%), neg=0, invalid=96777 0551: dt=32.368000, rms=0.391 (-0.001%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.391, neg=0, invalid=96777 0552: dt=0.000000, rms=0.391 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.391, neg=0, invalid=96777 0553: dt=82.944000, rms=0.391 (0.038%), neg=0, invalid=96777 0554: dt=145.152000, rms=0.390 (0.046%), neg=0, invalid=96777 0555: dt=36.288000, rms=0.390 (0.010%), neg=0, invalid=96777 0556: dt=36.288000, rms=0.390 (0.008%), neg=0, invalid=96777 0557: dt=36.288000, rms=0.390 (0.013%), neg=0, invalid=96777 0558: dt=36.288000, rms=0.390 (0.016%), neg=0, invalid=96777 0559: dt=36.288000, rms=0.390 (0.018%), neg=0, invalid=96777 0560: dt=36.288000, rms=0.390 (0.017%), neg=0, invalid=96777 0561: dt=36.288000, rms=0.390 (0.014%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.391, neg=0, invalid=96777 0562: dt=8.000000, rms=0.391 (0.029%), neg=0, invalid=96777 0563: dt=2.800000, rms=0.391 (0.004%), neg=0, invalid=96777 0564: dt=2.800000, rms=0.391 (0.004%), neg=0, invalid=96777 0565: dt=2.800000, rms=0.391 (0.001%), neg=0, invalid=96777 0566: dt=2.800000, rms=0.391 (-0.013%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.391, neg=0, invalid=96777 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0567: dt=44.800000, rms=0.389 (0.340%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 5 iterations, nbhd size=1, neg = 0 0568: dt=25.600000, rms=0.388 (0.207%), neg=0, invalid=96777 0569: dt=25.600000, rms=0.388 (0.063%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0570: dt=25.600000, rms=0.388 (0.145%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0571: dt=25.600000, rms=0.387 (0.137%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0572: dt=25.600000, rms=0.387 (0.156%), neg=0, invalid=96777 iter 0, gcam->neg = 6 after 6 iterations, nbhd size=1, neg = 0 0573: dt=25.600000, rms=0.386 (0.232%), neg=0, invalid=96777 iter 0, gcam->neg = 7 after 8 iterations, nbhd size=1, neg = 0 0574: dt=25.600000, rms=0.385 (0.148%), neg=0, invalid=96777 iter 0, gcam->neg = 7 after 6 iterations, nbhd size=1, neg = 0 0575: dt=25.600000, rms=0.384 (0.196%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0576: dt=25.600000, rms=0.384 (0.059%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 6 iterations, nbhd size=1, neg = 0 0577: dt=25.600000, rms=0.384 (0.087%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0578: dt=25.600000, rms=0.383 (0.146%), neg=0, invalid=96777 iter 0, gcam->neg = 5 after 7 iterations, nbhd size=1, neg = 0 0579: dt=25.600000, rms=0.383 (0.075%), neg=0, invalid=96777 iter 0, gcam->neg = 6 after 7 iterations, nbhd size=1, neg = 0 0580: dt=25.600000, rms=0.383 (0.047%), neg=0, invalid=96777 0581: dt=32.000000, rms=0.382 (0.136%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 6 iterations, nbhd size=1, neg = 0 0582: dt=38.400000, rms=0.382 (0.082%), neg=0, invalid=96777 0583: dt=38.400000, rms=0.382 (0.046%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 14 iterations, nbhd size=2, neg = 0 0584: dt=38.400000, rms=0.382 (0.022%), neg=0, invalid=96777 iter 0, gcam->neg = 32 after 37 iterations, nbhd size=3, neg = 0 0585: dt=38.400000, rms=0.382 (-0.046%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.385, neg=0, invalid=96777 0586: dt=0.864000, rms=0.385 (0.003%), neg=0, invalid=96777 0587: dt=1.008000, rms=0.385 (0.004%), neg=0, invalid=96777 0588: dt=0.252000, rms=0.385 (0.000%), neg=0, invalid=96777 0589: dt=0.252000, rms=0.385 (0.000%), neg=0, invalid=96777 0590: dt=0.252000, rms=0.385 (-0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.385, neg=0, invalid=96777 iter 0, gcam->neg = 5 after 6 iterations, nbhd size=1, neg = 0 0591: dt=4.032000, rms=0.385 (0.056%), neg=0, invalid=96777 0592: dt=0.576000, rms=0.385 (0.001%), neg=0, invalid=96777 0593: dt=0.576000, rms=0.385 (0.006%), neg=0, invalid=96777 0594: dt=0.576000, rms=0.385 (0.010%), neg=0, invalid=96777 0595: dt=0.576000, rms=0.385 (0.011%), neg=0, invalid=96777 0596: dt=0.576000, rms=0.385 (0.006%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0597: dt=0.576000, rms=0.385 (0.002%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.392, neg=0, invalid=96777 0598: dt=0.000000, rms=0.392 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.392, neg=0, invalid=96777 0599: dt=0.000000, rms=0.392 (0.000%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.381, neg=0, invalid=96777 iter 0, gcam->neg = 616 after 35 iterations, nbhd size=3, neg = 0 0600: dt=1.004587, rms=0.368 (3.234%), neg=0, invalid=96777 0601: dt=0.000078, rms=0.368 (0.001%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0602: dt=0.000078, rms=0.368 (0.000%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0603: dt=0.000078, rms=0.368 (0.000%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0604: dt=0.000078, rms=0.368 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.368, neg=0, invalid=96777 0605: dt=0.000438, rms=0.368 (0.000%), neg=0, invalid=96777 0606: dt=0.000000, rms=0.368 (0.000%), neg=0, invalid=96777 writing output transformation to transforms/talairach.m3z... GCAMwrite registration took 1 hours, 49 minutes and 12 seconds. #-------------------------------------- #@# CA Reg Inv Mon Aug 28 20:05:01 CEST 2017 /root/Scrivania/subjects/ENP30S001A/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z Inverting GCAM Saving inverse #-------------------------------------- #@# Remove Neck Mon Aug 28 20:05:38 CEST 2017 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2008-03-26.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... removing structures at least 25 mm from brain... 11060657 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 0 minutes and 40 seconds. #-------------------------------------- #@# SkullLTA Mon Aug 28 20:06:18 CEST 2017 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull_2.lta ======= NUMBER OF OPENMP THREADS = 1 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 5 using previously computed transform transforms/talairach.lta reading 1 input volumes... logging results to talairach_with_skull_2.log reading '/usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu_noneck.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=10.0 skull bounding box = (46, 59, 24) --> (206, 240, 224) using (99, 119, 124) as brain centroid... mean wm in atlas = 126, using box (79,97,99) --> (118, 141,148) to find MRI wm before smoothing, mri peak at 105 after smoothing, mri peak at 105, scaling input intensities by 1.200 scaling channel 0 by 1.2 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-3.9 (thresh=-3.9) 1.008 0.123 -0.020 -16.612; -0.103 1.119 0.243 -50.631; 0.046 -0.204 0.999 13.847; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 1 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-4.0 (thresh=-4.0) 0.990 0.115 0.013 -17.013; -0.106 1.145 0.215 -52.552; 0.010 -0.174 1.026 12.904; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 0.990 0.115 0.013 -17.013; -0.106 1.145 0.215 -52.552; 0.010 -0.174 1.026 12.904; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 3 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 0.990 0.115 0.013 -17.013; -0.106 1.143 0.214 -52.145; 0.010 -0.174 1.027 12.794; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 0.990 0.115 0.013 -17.013; -0.106 1.143 0.214 -52.145; 0.010 -0.174 1.029 12.576; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3481 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.98977 0.11511 0.01295 -17.01270; -0.10588 1.14264 0.21442 -52.14524; 0.00965 -0.17411 1.02927 12.57591; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 0.98977 0.11511 0.01295 -17.01270; -0.10588 1.14264 0.21442 -52.14524; 0.00965 -0.17411 1.02927 12.57591; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 006: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.990 0.115 0.013 -17.013; -0.106 1.143 0.214 -52.145; 0.010 -0.174 1.029 12.576; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.9 (old=-3.9) transform before final EM align: 0.990 0.115 0.013 -17.013; -0.106 1.143 0.214 -52.145; 0.010 -0.174 1.029 12.576; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 382743 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.98977 0.11511 0.01295 -17.01270; -0.10588 1.14264 0.21442 -52.14524; 0.00965 -0.17411 1.02927 12.57591; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 0.98977 0.11511 0.01295 -17.01270; -0.10588 1.14264 0.21442 -52.14524; 0.00965 -0.17411 1.02927 12.57591; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = 4.4 tol 0.000000 final transform: 0.990 0.115 0.013 -17.013; -0.106 1.143 0.214 -52.145; 0.010 -0.174 1.029 12.576; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull_2.lta... registration took 13 minutes and 9 seconds. #-------------------------------------- #@# SubCort Seg Mon Aug 28 20:19:27 CEST 2017 mri_ca_label -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz sysname Linux hostname Braindata machine x86_64 setenv SUBJECTS_DIR /root/Scrivania/subjects cd /root/Scrivania/subjects/ENP30S001A/mri mri_ca_label -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes... reading classifier array from /usr/local/freesurfer/average/RB_all_2008-03-26.gca... reading input volume from norm.mgz... average std[0] = 6.9 reading transform from transforms/talairach.m3z... Atlas used for the 3D morph was /usr/local/freesurfer/average/RB_all_2008-03-26.gca average std = 6.9 using min determinant for regularization = 4.7 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15151 (27) mri peak = 0.10621 (17) Left_Lateral_Ventricle (4): linear fit = 0.67 x + 0.0 (539 voxels, overlap=0.068) Left_Lateral_Ventricle (4): linear fit = 0.67 x + 0.0 (539 voxels, peak = 18), gca=18.0 gca peak = 0.14982 (20) mri peak = 0.14418 (17) Right_Lateral_Ventricle (43): linear fit = 0.71 x + 0.0 (480 voxels, overlap=0.398) Right_Lateral_Ventricle (43): linear fit = 0.71 x + 0.0 (480 voxels, peak = 14), gca=14.3 gca peak = 0.28003 (97) mri peak = 0.14546 (98) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (325 voxels, overlap=1.019) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (325 voxels, peak = 96), gca=95.5 gca peak = 0.18160 (96) mri peak = 0.08548 (88) Left_Pallidum (13): linear fit = 0.94 x + 0.0 (154 voxels, overlap=0.912) Left_Pallidum (13): linear fit = 0.94 x + 0.0 (154 voxels, peak = 91), gca=90.7 gca peak = 0.27536 (62) mri peak = 0.09314 (67) Right_Hippocampus (53): linear fit = 1.07 x + 0.0 (788 voxels, overlap=0.726) Right_Hippocampus (53): linear fit = 1.07 x + 0.0 (788 voxels, peak = 66), gca=66.0 gca peak = 0.32745 (63) mri peak = 0.11444 (68) Left_Hippocampus (17): linear fit = 1.07 x + 0.0 (900 voxels, overlap=1.007) Left_Hippocampus (17): linear fit = 1.07 x + 0.0 (900 voxels, peak = 67), gca=67.1 gca peak = 0.08597 (105) mri peak = 0.08675 (106) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (57425 voxels, overlap=0.743) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (57425 voxels, peak = 107), gca=106.6 gca peak = 0.09209 (106) mri peak = 0.09645 (108) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (58838 voxels, overlap=0.703) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (58838 voxels, peak = 108), gca=107.6 gca peak = 0.07826 (63) mri peak = 0.04755 (63) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (20006 voxels, overlap=0.921) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (20006 voxels, peak = 62), gca=62.1 gca peak = 0.08598 (64) mri peak = 0.04507 (60) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (18139 voxels, overlap=0.940) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (18139 voxels, peak = 63), gca=63.0 gca peak = 0.24164 (71) mri peak = 0.11489 (81) Right_Caudate (50): linear fit = 1.08 x + 0.0 (724 voxels, overlap=0.447) Right_Caudate (50): linear fit = 1.08 x + 0.0 (724 voxels, peak = 76), gca=76.3 gca peak = 0.18227 (75) mri peak = 0.11054 (81) Left_Caudate (11): linear fit = 1.05 x + 0.0 (963 voxels, overlap=0.693) Left_Caudate (11): linear fit = 1.05 x + 0.0 (963 voxels, peak = 79), gca=79.1 gca peak = 0.10629 (62) mri peak = 0.04631 (62) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (22881 voxels, overlap=0.977) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (22881 voxels, peak = 64), gca=63.5 gca peak = 0.11668 (59) mri peak = 0.05203 (64) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (22676 voxels, overlap=0.972) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (22676 voxels, peak = 60), gca=60.5 gca peak = 0.17849 (88) mri peak = 0.11564 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (6188 voxels, overlap=0.722) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (6188 voxels, peak = 93), gca=92.8 gca peak = 0.16819 (86) mri peak = 0.12368 (92) Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (5867 voxels, overlap=0.827) Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (5867 voxels, peak = 90), gca=89.9 gca peak = 0.41688 (64) mri peak = 0.09705 (74) Left_Amygdala (18): linear fit = 1.16 x + 0.0 (287 voxels, overlap=0.056) Left_Amygdala (18): linear fit = 1.16 x + 0.0 (287 voxels, peak = 75), gca=74.6 gca peak = 0.42394 (62) mri peak = 0.11856 (72) Right_Amygdala (54): linear fit = 1.13 x + 0.0 (319 voxels, overlap=0.061) Right_Amygdala (54): linear fit = 1.13 x + 0.0 (319 voxels, peak = 70), gca=70.4 gca peak = 0.10041 (96) mri peak = 0.07555 (97) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (3963 voxels, overlap=0.664) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (3963 voxels, peak = 102), gca=102.2 gca peak = 0.13978 (88) mri peak = 0.08098 (94) Right_Thalamus_Proper (49): linear fit = 1.05 x + 0.0 (3614 voxels, overlap=0.872) Right_Thalamus_Proper (49): linear fit = 1.05 x + 0.0 (3614 voxels, peak = 93), gca=92.8 gca peak = 0.08514 (81) mri peak = 0.07270 (88) Left_Putamen (12): linear fit = 1.03 x + 0.0 (1245 voxels, overlap=0.831) Left_Putamen (12): linear fit = 1.03 x + 0.0 (1245 voxels, peak = 84), gca=83.8 gca peak = 0.09624 (82) mri peak = 0.07603 (85) Right_Putamen (51): linear fit = 1.05 x + 0.0 (1682 voxels, overlap=0.747) Right_Putamen (51): linear fit = 1.05 x + 0.0 (1682 voxels, peak = 87), gca=86.5 gca peak = 0.07543 (88) mri peak = 0.06935 (92) Brain_Stem (16): linear fit = 1.07 x + 0.0 (12279 voxels, overlap=0.687) Brain_Stem (16): linear fit = 1.07 x + 0.0 (12279 voxels, peak = 94), gca=93.7 gca peak = 0.12757 (95) mri peak = 0.07476 (104) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1278 voxels, overlap=0.616) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1278 voxels, peak = 103), gca=103.1 gca peak = 0.17004 (92) mri peak = 0.08651 (101) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (1301 voxels, overlap=0.537) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (1301 voxels, peak = 100), gca=99.8 gca peak = 0.21361 (36) mri peak = 0.11422 (22) gca peak = 0.26069 (23) mri peak = 0.17362 (19) Fourth_Ventricle (15): linear fit = 0.77 x + 0.0 (90 voxels, overlap=0.603) Fourth_Ventricle (15): linear fit = 0.77 x + 0.0 (90 voxels, peak = 18), gca=17.8 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.31795 (35) gca peak Third_Ventricle = 0.21361 (36) gca peak CSF = 0.14367 (38) gca peak Left_Accumbens_area = 0.57033 (70) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65201 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.31129 (32) gca peak Right_Accumbens_area = 0.30219 (72) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.72939 (42) gca peak WM_hypointensities = 0.14821 (82) gca peak non_WM_hypointensities = 0.10354 (53) gca peak Optic_Chiasm = 0.34849 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.07 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 0.72 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.19757 (18) mri peak = 0.10621 (17) Left_Lateral_Ventricle (4): linear fit = 0.95 x + 0.0 (539 voxels, overlap=0.941) Left_Lateral_Ventricle (4): linear fit = 0.95 x + 0.0 (539 voxels, peak = 17), gca=17.2 gca peak = 0.19392 (15) mri peak = 0.14418 (17) Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (480 voxels, overlap=0.887) Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (480 voxels, peak = 15), gca=15.4 gca peak = 0.32703 (96) mri peak = 0.14546 (98) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (325 voxels, overlap=1.010) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (325 voxels, peak = 97), gca=97.4 gca peak = 0.19619 (91) mri peak = 0.08548 (88) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (154 voxels, overlap=1.004) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (154 voxels, peak = 91), gca=91.5 gca peak = 0.24887 (66) mri peak = 0.09314 (67) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (788 voxels, overlap=1.005) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (788 voxels, peak = 66), gca=66.0 gca peak = 0.28946 (67) mri peak = 0.11444 (68) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (900 voxels, overlap=1.003) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (900 voxels, peak = 67), gca=67.0 gca peak = 0.08542 (107) mri peak = 0.08675 (106) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (57425 voxels, overlap=0.780) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (57425 voxels, peak = 106), gca=106.5 gca peak = 0.08742 (107) mri peak = 0.09645 (108) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (58838 voxels, overlap=0.730) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (58838 voxels, peak = 107), gca=107.0 gca peak = 0.07876 (62) mri peak = 0.04755 (63) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (20006 voxels, overlap=0.949) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (20006 voxels, peak = 64), gca=63.5 gca peak = 0.08738 (63) mri peak = 0.04507 (60) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (18139 voxels, overlap=0.960) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (18139 voxels, peak = 62), gca=62.1 gca peak = 0.27738 (79) mri peak = 0.11489 (81) Right_Caudate (50): linear fit = 1.01 x + 0.0 (724 voxels, overlap=1.002) Right_Caudate (50): linear fit = 1.01 x + 0.0 (724 voxels, peak = 80), gca=80.2 gca peak = 0.18126 (79) mri peak = 0.11054 (81) Left_Caudate (11): linear fit = 1.00 x + 0.0 (963 voxels, overlap=0.953) Left_Caudate (11): linear fit = 1.00 x + 0.0 (963 voxels, peak = 79), gca=79.0 gca peak = 0.10281 (63) mri peak = 0.04631 (62) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (22881 voxels, overlap=0.992) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (22881 voxels, peak = 65), gca=64.6 gca peak = 0.12584 (61) mri peak = 0.05203 (64) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (22676 voxels, overlap=0.991) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (22676 voxels, peak = 63), gca=62.5 gca peak = 0.17071 (92) mri peak = 0.11564 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6188 voxels, overlap=0.971) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6188 voxels, peak = 92), gca=91.5 gca peak = 0.15955 (90) mri peak = 0.12368 (92) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5867 voxels, overlap=0.981) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5867 voxels, peak = 90), gca=89.6 gca peak = 0.29786 (74) mri peak = 0.09705 (74) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (287 voxels, overlap=1.004) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (287 voxels, peak = 75), gca=75.1 gca peak = 0.30975 (71) mri peak = 0.11856 (72) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (319 voxels, overlap=1.007) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (319 voxels, peak = 71), gca=71.0 gca peak = 0.11099 (102) mri peak = 0.07555 (97) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3963 voxels, overlap=0.930) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3963 voxels, peak = 103), gca=102.5 gca peak = 0.10579 (93) mri peak = 0.08098 (94) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3614 voxels, overlap=0.912) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3614 voxels, peak = 93), gca=93.5 gca peak = 0.08482 (85) mri peak = 0.07270 (88) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1245 voxels, overlap=0.950) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1245 voxels, peak = 85), gca=84.6 gca peak = 0.10379 (80) mri peak = 0.07603 (85) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1682 voxels, overlap=0.922) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1682 voxels, peak = 79), gca=78.8 gca peak = 0.06628 (88) mri peak = 0.06935 (92) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12279 voxels, overlap=0.844) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12279 voxels, peak = 88), gca=88.0 gca peak = 0.10874 (99) mri peak = 0.07476 (104) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1278 voxels, overlap=0.815) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1278 voxels, peak = 99), gca=99.0 gca peak = 0.17076 (100) mri peak = 0.08651 (101) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1301 voxels, overlap=0.872) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1301 voxels, peak = 100), gca=100.5 gca peak = 0.25515 (27) mri peak = 0.11422 (22) gca peak = 0.27522 (18) mri peak = 0.17362 (19) Fourth_Ventricle (15): linear fit = 0.99 x + 0.0 (90 voxels, overlap=0.767) Fourth_Ventricle (15): linear fit = 0.99 x + 0.0 (90 voxels, peak = 18), gca=17.7 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21381 (38) gca peak Third_Ventricle = 0.25515 (27) gca peak CSF = 0.24868 (28) gca peak Left_Accumbens_area = 0.49915 (74) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65267 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.31109 (34) gca peak Right_Accumbens_area = 0.43827 (77) gca peak Right_vessel = 0.83457 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.45329 (31) gca peak WM_hypointensities = 0.17562 (83) gca peak non_WM_hypointensities = 0.10249 (54) gca peak Optic_Chiasm = 0.34853 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.99 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 19722 gm and wm labels changed (%20 to gray, %80 to white out of all changed labels) 328 hippocampal voxels changed. 2 amygdala voxels changed. pass 1: 76490 changed. image ll: -2.169, PF=1.000 pass 2: 11252 changed. image ll: -2.166, PF=1.000 pass 3: 3466 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 9 minutes and 44 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /root/Scrivania/subjects/ENP30S001A/mri/transforms/cc_up.lta ENP30S001A will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /root/Scrivania/subjects/ENP30S001A/mri/transforms/cc_up.lta reading aseg from /root/Scrivania/subjects/ENP30S001A/mri/aseg.auto_noCCseg.mgz reading norm from /root/Scrivania/subjects/ENP30S001A/mri/norm.mgz 35834 voxels in left wm, 62890 in right wm, xrange [121, 132] searching rotation angles z=[-13 1], y=[-9 5] searching scale 1 Z rot -13.3 searching scale 1 Z rot -13.0 searching scale 1 Z rot -12.8 searching scale 1 Z rot -12.5 searching scale 1 Z rot -12.3 searching scale 1 Z rot -12.0 searching scale 1 Z rot -11.8 searching scale 1 Z rot -11.5 searching scale 1 Z rot -11.3 searching scale 1 Z rot -11.0 searching scale 1 Z rot -10.8 searching scale 1 Z rot -10.5 searching scale 1 Z rot -10.3 searching scale 1 Z rot -10.0 searching scale 1 Z rot -9.8 searching scale 1 Z rot -9.5 searching scale 1 Z rot -9.3 searching scale 1 Z rot -9.0 searching scale 1 Z rot -8.8 searching scale 1 Z rot -8.5 searching scale 1 Z rot -8.3 searching scale 1 Z rot -8.0 searching scale 1 Z rot -7.8 searching scale 1 Z rot -7.5 searching scale 1 Z rot -7.3 searching scale 1 Z rot -7.0 searching scale 1 Z rot -6.8 searching scale 1 Z rot -6.5 searching scale 1 Z rot -6.3 searching scale 1 Z rot -6.0 searching scale 1 Z rot -5.8 searching scale 1 Z rot -5.5 searching scale 1 Z rot -5.3 searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.8 searching scale 1 Z rot -4.5 searching scale 1 Z rot -4.3 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.8 searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.3 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.8 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.3 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.8 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.3 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.8 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.3 searching scale 1 Z rot -0.0 global minimum found at slice 127.0, rotations (-1.78, -6.77) final transformation (x=127.0, yr=-1.775, zr=-6.766): 0.993 0.118 -0.031 -9.362; -0.118 0.993 0.004 17.414; 0.031 -0.000 1.000 9.120; 0.000 0.000 0.000 1.000; updating x range to be [126, 130] in xformed coordinates best xformed slice 128 cc center is found at 128 147 110 eigenvectors: -0.001 -0.006 1.000; -0.132 -0.991 -0.006; 0.991 -0.132 0.000; error in mid anterior detected - correcting... writing aseg with callosum to /root/Scrivania/subjects/ENP30S001A/mri/aseg.auto.mgz... corpus callosum matter segmentation took 0.6 minutes #-------------------------------------- #@# Merge ASeg Mon Aug 28 20:29:50 CEST 2017 cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# Intensity Normalization2 Mon Aug 28 20:29:50 CEST 2017 /root/Scrivania/subjects/ENP30S001A/mri mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 1887 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 70 (70), valley at 31 (31) csf peak at 35, setting threshold to 58 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 70 (70), valley at 32 (32) csf peak at 35, setting threshold to 58 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 2 minutes and 16 seconds. #-------------------------------------------- #@# Mask BFS Mon Aug 28 20:32:07 CEST 2017 /root/Scrivania/subjects/ENP30S001A/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1639089 voxels in mask (pct= 9.77) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Mon Aug 28 20:32:08 CEST 2017 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 (105.0): 104.7 +- 6.3 [80.0 --> 125.0] GM (73.0) : 71.9 +- 9.1 [30.0 --> 96.0] setting bottom of white matter range to 81.1 setting top of gray matter range to 90.2 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... 3925 sparsely connected voxels removed... thickening thin strands.... 20 segments, 4846 filled 76 bright non-wm voxels segmented. 2292 diagonally connected voxels added... white matter segmentation took 1.1 minutes writing output to wm.seg.mgz... mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.34 minutes reading wm segmentation from wm.seg.mgz... 14 voxels added to wm to prevent paths from MTL structures to cortex 1866 additional wm voxels added 0 additional wm voxels added SEG EDIT: 30991 voxels turned on, 47286 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 105 new 105 115,126,128 old 105 new 105 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 14 found - 14 modified | TOTAL: 14 pass 2 (xy+): 0 found - 14 modified | TOTAL: 14 pass 1 (xy-): 21 found - 21 modified | TOTAL: 35 pass 2 (xy-): 0 found - 21 modified | TOTAL: 35 pass 1 (yz+): 32 found - 32 modified | TOTAL: 67 pass 2 (yz+): 0 found - 32 modified | TOTAL: 67 pass 1 (yz-): 16 found - 16 modified | TOTAL: 83 pass 2 (yz-): 0 found - 16 modified | TOTAL: 83 pass 1 (xz+): 12 found - 12 modified | TOTAL: 95 pass 2 (xz+): 0 found - 12 modified | TOTAL: 95 pass 1 (xz-): 12 found - 12 modified | TOTAL: 107 pass 2 (xz-): 0 found - 12 modified | TOTAL: 107 Iteration Number : 1 pass 1 (+++): 20 found - 20 modified | TOTAL: 20 pass 2 (+++): 0 found - 20 modified | TOTAL: 20 pass 1 (+++): 11 found - 11 modified | TOTAL: 31 pass 2 (+++): 0 found - 11 modified | TOTAL: 31 pass 1 (+++): 16 found - 16 modified | TOTAL: 47 pass 2 (+++): 0 found - 16 modified | TOTAL: 47 pass 1 (+++): 8 found - 8 modified | TOTAL: 55 pass 2 (+++): 0 found - 8 modified | TOTAL: 55 Iteration Number : 1 pass 1 (++): 57 found - 57 modified | TOTAL: 57 pass 2 (++): 0 found - 57 modified | TOTAL: 57 pass 1 (+-): 66 found - 66 modified | TOTAL: 123 pass 2 (+-): 0 found - 66 modified | TOTAL: 123 pass 1 (--): 71 found - 71 modified | TOTAL: 194 pass 2 (--): 0 found - 71 modified | TOTAL: 194 pass 1 (-+): 61 found - 61 modified | TOTAL: 255 pass 2 (-+): 0 found - 61 modified | TOTAL: 255 Iteration Number : 2 pass 1 (xy+): 4 found - 4 modified | TOTAL: 4 pass 2 (xy+): 0 found - 4 modified | TOTAL: 4 pass 1 (xy-): 0 found - 0 modified | TOTAL: 4 pass 1 (yz+): 4 found - 4 modified | TOTAL: 8 pass 2 (yz+): 0 found - 4 modified | TOTAL: 8 pass 1 (yz-): 2 found - 2 modified | TOTAL: 10 pass 2 (yz-): 0 found - 2 modified | TOTAL: 10 pass 1 (xz+): 4 found - 4 modified | TOTAL: 14 pass 2 (xz+): 0 found - 4 modified | TOTAL: 14 pass 1 (xz-): 5 found - 5 modified | TOTAL: 19 pass 2 (xz-): 0 found - 5 modified | TOTAL: 19 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 2 pass 1 (++): 2 found - 2 modified | TOTAL: 2 pass 2 (++): 0 found - 2 modified | TOTAL: 2 pass 1 (+-): 5 found - 5 modified | TOTAL: 7 pass 2 (+-): 0 found - 5 modified | TOTAL: 7 pass 1 (--): 3 found - 3 modified | TOTAL: 10 pass 2 (--): 0 found - 3 modified | TOTAL: 10 pass 1 (-+): 1 found - 1 modified | TOTAL: 11 pass 2 (-+): 0 found - 1 modified | TOTAL: 11 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 1 found - 1 modified | TOTAL: 2 pass 2 (yz-): 0 found - 1 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 1 found - 1 modified | TOTAL: 1 pass 2 (--): 0 found - 1 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 452 (out of 641267: 0.070485) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Mon Aug 28 20:33:39 CEST 2017 /root/Scrivania/subjects/ENP30S001A/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 1.008 0.123 -0.020 -16.612; -0.103 1.119 0.243 -50.631; 0.046 -0.204 0.999 13.847; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.008 0.123 -0.020 -16.612; -0.103 1.119 0.243 -50.631; 0.046 -0.204 0.999 13.847; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1435 (min = 350, max = 1400), aspect = 0.43 (min = 0.10, max = 0.75) need search nearby using seed (125, 109, 93), TAL = (3.0, -35.0, 19.0) talairach voxel to voxel transform 0.980 -0.100 0.044 10.635; 0.096 0.846 -0.204 47.233; -0.026 0.178 0.957 -4.682; 0.000 0.000 0.000 1.000; segmentation indicates cc at (125, 109, 93) --> (3.0, -35.0, 19.0) done. writing output to filled.mgz... filling took 0.5 minutes talairach cc position changed to (3.00, -35.00, 19.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(21.00, -35.00, 19.00) SRC: (108.70, 130.72, 100.99) search lh wm seed point around talairach space (-15.00, -35.00, 19.00), SRC: (143.98, 134.16, 100.07) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Mon Aug 28 20:34:07 CEST 2017 /root/Scrivania/subjects/ENP30S001A/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 3 found - 3 modified | TOTAL: 3 pass 2 (yz+): 0 found - 3 modified | TOTAL: 3 pass 1 (yz-): 1 found - 1 modified | TOTAL: 4 pass 2 (yz-): 0 found - 1 modified | TOTAL: 4 pass 1 (xz+): 0 found - 0 modified | TOTAL: 4 pass 1 (xz-): 1 found - 1 modified | TOTAL: 5 pass 2 (xz-): 0 found - 1 modified | TOTAL: 5 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 5 (out of 311038: 0.001608) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 40: 240 vertices, 301 faces slice 50: 5017 vertices, 5273 faces slice 60: 14697 vertices, 15073 faces slice 70: 26857 vertices, 27315 faces slice 80: 39435 vertices, 39879 faces slice 90: 51347 vertices, 51735 faces slice 100: 63743 vertices, 64174 faces slice 110: 75955 vertices, 76387 faces slice 120: 87780 vertices, 88161 faces slice 130: 98924 vertices, 99342 faces slice 140: 110269 vertices, 110710 faces slice 150: 120356 vertices, 120693 faces slice 160: 129325 vertices, 129654 faces slice 170: 136817 vertices, 137075 faces slice 180: 143299 vertices, 143547 faces slice 190: 148357 vertices, 148522 faces slice 200: 150098 vertices, 150132 faces slice 210: 150098 vertices, 150132 faces slice 220: 150098 vertices, 150132 faces slice 230: 150098 vertices, 150132 faces slice 240: 150098 vertices, 150132 faces slice 250: 150098 vertices, 150132 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 150098 voxel in cpt #1: X=-34 [v=150098,e=450396,f=300264] located at (-26.846394, -17.426208, -7.505356) For the whole surface: X=-34 [v=150098,e=450396,f=300264] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Mon Aug 28 20:34:11 CEST 2017 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /root/Scrivania/subjects/ENP30S001A/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Mon Aug 28 20:34:14 CEST 2017 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /root/Scrivania/subjects/ENP30S001A/scripts avg radius = 48.0 mm, total surface area = 78883 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.4 minutes Not saving sulc step 000: RMS=0.100 (target=0.015) step 005: RMS=0.072 (target=0.015) step 010: RMS=0.054 (target=0.015) step 015: RMS=0.046 (target=0.015) step 020: RMS=0.040 (target=0.015) step 025: RMS=0.036 (target=0.015) step 030: RMS=0.033 (target=0.015) step 035: RMS=0.031 (target=0.015) step 040: RMS=0.030 (target=0.015) step 045: RMS=0.028 (target=0.015) step 050: RMS=0.028 (target=0.015) step 055: RMS=0.027 (target=0.015) step 060: RMS=0.027 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Mon Aug 28 20:34:35 CEST 2017 /root/Scrivania/subjects/ENP30S001A/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.96 +- 0.55 (0.00-->6.23) (max @ vno 112361 --> 113534) face area 0.03 +- 0.03 (-0.19-->0.67) scaling brain by 0.316... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.685, avgs=0 005/300: dt: 0.9000, rms radial error=175.428, avgs=0 010/300: dt: 0.9000, rms radial error=174.877, avgs=0 015/300: dt: 0.9000, rms radial error=174.153, avgs=0 020/300: dt: 0.9000, rms radial error=173.328, avgs=0 025/300: dt: 0.9000, rms radial error=172.447, avgs=0 030/300: dt: 0.9000, rms radial error=171.533, avgs=0 035/300: dt: 0.9000, rms radial error=170.603, avgs=0 040/300: dt: 0.9000, rms radial error=169.665, avgs=0 045/300: dt: 0.9000, rms radial error=168.724, avgs=0 050/300: dt: 0.9000, rms radial error=167.784, avgs=0 055/300: dt: 0.9000, rms radial error=166.846, avgs=0 060/300: dt: 0.9000, rms radial error=165.912, avgs=0 065/300: dt: 0.9000, rms radial error=164.982, avgs=0 070/300: dt: 0.9000, rms radial error=164.056, avgs=0 075/300: dt: 0.9000, rms radial error=163.135, avgs=0 080/300: dt: 0.9000, rms radial error=162.219, avgs=0 085/300: dt: 0.9000, rms radial error=161.307, avgs=0 090/300: dt: 0.9000, rms radial error=160.400, avgs=0 095/300: dt: 0.9000, rms radial error=159.499, avgs=0 100/300: dt: 0.9000, rms radial error=158.602, avgs=0 105/300: dt: 0.9000, rms radial error=157.711, avgs=0 110/300: dt: 0.9000, rms radial error=156.824, avgs=0 115/300: dt: 0.9000, rms radial error=155.942, avgs=0 120/300: dt: 0.9000, rms radial error=155.065, avgs=0 125/300: dt: 0.9000, rms radial error=154.193, avgs=0 130/300: dt: 0.9000, rms radial error=153.325, avgs=0 135/300: dt: 0.9000, rms radial error=152.463, avgs=0 140/300: dt: 0.9000, rms radial error=151.605, avgs=0 145/300: dt: 0.9000, rms radial error=150.751, avgs=0 150/300: dt: 0.9000, rms radial error=149.903, avgs=0 155/300: dt: 0.9000, rms radial error=149.059, avgs=0 160/300: dt: 0.9000, rms radial error=148.219, avgs=0 165/300: dt: 0.9000, rms radial error=147.385, avgs=0 170/300: dt: 0.9000, rms radial error=146.555, avgs=0 175/300: dt: 0.9000, rms radial error=145.729, avgs=0 180/300: dt: 0.9000, rms radial error=144.908, avgs=0 185/300: dt: 0.9000, rms radial error=144.092, avgs=0 190/300: dt: 0.9000, rms radial error=143.280, avgs=0 195/300: dt: 0.9000, rms radial error=142.473, avgs=0 200/300: dt: 0.9000, rms radial error=141.670, avgs=0 205/300: dt: 0.9000, rms radial error=140.872, avgs=0 210/300: dt: 0.9000, rms radial error=140.078, avgs=0 215/300: dt: 0.9000, rms radial error=139.289, avgs=0 220/300: dt: 0.9000, rms radial error=138.504, avgs=0 225/300: dt: 0.9000, rms radial error=137.723, avgs=0 230/300: dt: 0.9000, rms radial error=136.947, avgs=0 235/300: dt: 0.9000, rms radial error=136.174, avgs=0 240/300: dt: 0.9000, rms radial error=135.407, avgs=0 245/300: dt: 0.9000, rms radial error=134.643, avgs=0 250/300: dt: 0.9000, rms radial error=133.885, avgs=0 255/300: dt: 0.9000, rms radial error=133.130, avgs=0 260/300: dt: 0.9000, rms radial error=132.379, avgs=0 265/300: dt: 0.9000, rms radial error=131.632, avgs=0 270/300: dt: 0.9000, rms radial error=130.890, avgs=0 275/300: dt: 0.9000, rms radial error=130.151, avgs=0 280/300: dt: 0.9000, rms radial error=129.418, avgs=0 285/300: dt: 0.9000, rms radial error=128.688, avgs=0 290/300: dt: 0.9000, rms radial error=127.963, avgs=0 295/300: dt: 0.9000, rms radial error=127.242, avgs=0 300/300: dt: 0.9000, rms radial error=126.524, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 17474.52 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00014 epoch 2 (K=40.0), pass 1, starting sse = 2884.86 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00003 epoch 3 (K=160.0), pass 1, starting sse = 282.40 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/12 = 0.00590 epoch 4 (K=640.0), pass 1, starting sse = 17.74 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.11/14 = 0.00754 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.05 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Mon Aug 28 20:37:37 CEST 2017 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /root/Scrivania/subjects/ENP30S001A/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 ENP30S001A lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ before topology correction, eno=-34 (nv=150098, nf=300264, ne=450396, g=18) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 8 iterations marking ambiguous vertices... 5420 ambiguous faces found in tessellation segmenting defects... 19 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 8 into 6 18 defects to be corrected 0 vertices coincident reading input surface /root/Scrivania/subjects/ENP30S001A/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.1187 (-4.5593) -vertex loglikelihood: -6.1454 (-3.0727) -normal dot loglikelihood: -3.6411 (-3.6411) -quad curv loglikelihood: -6.5283 (-3.2641) Total Loglikelihood : -25.4335 CORRECTING DEFECT 0 (vertices=16, convex hull=54) After retessellation of defect 0, euler #=-16 (147015,440266,293235) : difference with theory (-15) = 1 CORRECTING DEFECT 1 (vertices=311, convex hull=227) After retessellation of defect 1, euler #=-15 (147025,440411,293371) : difference with theory (-14) = 1 CORRECTING DEFECT 2 (vertices=13, convex hull=28) After retessellation of defect 2, euler #=-14 (147028,440428,293386) : difference with theory (-13) = 1 CORRECTING DEFECT 3 (vertices=254, convex hull=151) After retessellation of defect 3, euler #=-13 (147114,440766,293639) : difference with theory (-12) = 1 CORRECTING DEFECT 4 (vertices=338, convex hull=99) After retessellation of defect 4, euler #=-12 (147139,440878,293727) : difference with theory (-11) = 1 CORRECTING DEFECT 5 (vertices=5, convex hull=27) After retessellation of defect 5, euler #=-11 (147141,440892,293740) : difference with theory (-10) = 1 CORRECTING DEFECT 6 (vertices=725, convex hull=456) After retessellation of defect 6, euler #=-9 (147313,441641,294319) : difference with theory (-9) = 0 CORRECTING DEFECT 7 (vertices=64, convex hull=113) After retessellation of defect 7, euler #=-8 (147330,441741,294403) : difference with theory (-8) = 0 CORRECTING DEFECT 8 (vertices=40, convex hull=63) After retessellation of defect 8, euler #=-7 (147347,441815,294461) : difference with theory (-7) = 0 CORRECTING DEFECT 9 (vertices=30, convex hull=57) After retessellation of defect 9, euler #=-6 (147365,441893,294522) : difference with theory (-6) = 0 CORRECTING DEFECT 10 (vertices=161, convex hull=74) After retessellation of defect 10, euler #=-5 (147385,441979,294589) : difference with theory (-5) = 0 CORRECTING DEFECT 11 (vertices=88, convex hull=33) After retessellation of defect 11, euler #=-4 (147395,442019,294620) : difference with theory (-4) = 0 CORRECTING DEFECT 12 (vertices=19, convex hull=44) After retessellation of defect 12, euler #=-3 (147404,442063,294656) : difference with theory (-3) = 0 CORRECTING DEFECT 13 (vertices=855, convex hull=139) After retessellation of defect 13, euler #=-2 (147444,442250,294804) : difference with theory (-2) = 0 CORRECTING DEFECT 14 (vertices=13, convex hull=33) After retessellation of defect 14, euler #=-1 (147447,442267,294819) : difference with theory (-1) = 0 CORRECTING DEFECT 15 (vertices=66, convex hull=32) After retessellation of defect 15, euler #=0 (147452,442294,294842) : difference with theory (0) = 0 CORRECTING DEFECT 16 (vertices=75, convex hull=128) After retessellation of defect 16, euler #=1 (147499,442486,294988) : difference with theory (1) = 0 CORRECTING DEFECT 17 (vertices=17, convex hull=20) After retessellation of defect 17, euler #=2 (147504,442506,295004) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.22 (0.11-->9.97) (max @ vno 54443 --> 60501) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.22 (0.11-->9.97) (max @ vno 54443 --> 60501) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 65 mutations (34.4%), 124 crossovers (65.6%), 320 vertices were eliminated building final representation... 2594 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=147504, nf=295004, ne=442506, g=0) writing corrected surface to /root/Scrivania/subjects/ENP30S001A/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 16.4 minutes 0 defective edges removing intersecting faces 000: 266 intersecting 001: 13 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 147504 - 442506 + 295004 = 2 --> 0 holes F =2V-4: 295004 = 295008-4 (0) 2E=3F: 885012 = 885012 (0) total defect index = 0 /root/Scrivania/subjects/ENP30S001A/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 51 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Mon Aug 28 20:54:03 CEST 2017 /root/Scrivania/subjects/ENP30S001A/scripts mris_make_surfaces -noaparc -mgz -T1 brain.finalsurfs ENP30S001A lh not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /root/Scrivania/subjects/ENP30S001A/mri/filled.mgz... reading volume /root/Scrivania/subjects/ENP30S001A/mri/brain.finalsurfs.mgz... reading volume /root/Scrivania/subjects/ENP30S001A/mri/wm.mgz... 15082 bright wm thresholded. 257 bright non-wm voxels segmented. reading original surface position from /root/Scrivania/subjects/ENP30S001A/surf/lh.orig... computing class statistics... border white: 279213 voxels (1.66%) border gray 305834 voxels (1.82%) WM (95.0): 96.2 +- 8.0 [70.0 --> 110.0] GM (82.0) : 80.5 +- 11.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 58.3 (was 70) setting MAX_BORDER_WHITE to 113.0 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 46.5 (was 40) setting MAX_GRAY to 97.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.1 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 34.8 (was 40) repositioning cortical surface to gray/white boundary reading volume /root/Scrivania/subjects/ENP30S001A/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.03-->5.11) (max @ vno 147215 --> 147225) face area 0.28 +- 0.12 (0.00-->4.41) mean absolute distance = 0.72 +- 0.92 3158 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=70 mean inside = 95.4, mean outside = 76.9 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group mean border=81.6, 63 (63) missing vertices, mean dist 0.2 [0.6 (%38.5)->0.8 (%61.5))] %67 local maxima, %28 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=Brain, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.25 (0.11-->5.56) (max @ vno 61866 --> 70213) face area 0.28 +- 0.13 (0.00-->6.01) mean absolute distance = 0.36 +- 0.60 2966 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5657202.0, rms=10.37 001: dt: 0.5000, sse=6295746.5, rms=7.264 (0.000%) 002: dt: 0.5000, sse=6680853.5, rms=5.396 (0.000%) 003: dt: 0.5000, sse=7001209.0, rms=4.303 (0.000%) 004: dt: 0.5000, sse=7266023.0, rms=3.652 (0.000%) 005: dt: 0.5000, sse=7439146.5, rms=3.382 (0.000%) 006: dt: 0.5000, sse=7540030.0, rms=3.209 (0.000%) rms = 3.18, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=7586327.5, rms=3.183 (0.000%) 008: dt: 0.2500, sse=4553411.0, rms=2.071 (0.000%) 009: dt: 0.2500, sse=4131929.8, rms=1.782 (0.000%) 010: dt: 0.2500, sse=3965712.2, rms=1.710 (0.000%) rms = 1.68, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=3908679.0, rms=1.676 (0.000%) rms = 1.64, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=3844914.5, rms=1.641 (0.000%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=84.6, 66 (36) missing vertices, mean dist -0.2 [0.4 (%71.6)->0.2 (%28.4))] %77 local maxima, %18 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=Brain, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.24 (0.06-->5.69) (max @ vno 61866 --> 70213) face area 0.35 +- 0.16 (0.00-->8.23) mean absolute distance = 0.25 +- 0.36 3616 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4533491.0, rms=4.76 013: dt: 0.5000, sse=4869790.0, rms=3.016 (0.000%) 014: dt: 0.5000, sse=5351834.0, rms=2.934 (0.000%) 015: dt: 0.5000, sse=5945726.0, rms=2.811 (0.000%) rms = 3.09, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=4769637.5, rms=1.935 (0.000%) 017: dt: 0.2500, sse=4371681.0, rms=1.530 (0.000%) 018: dt: 0.2500, sse=4226138.5, rms=1.406 (0.000%) rms = 1.39, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=4156737.2, rms=1.388 (0.000%) rms = 1.35, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=4108307.5, rms=1.354 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group mean border=87.2, 49 (16) missing vertices, mean dist -0.1 [0.3 (%73.9)->0.2 (%26.1))] %87 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=Brain, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.24 (0.08-->5.74) (max @ vno 61866 --> 70213) face area 0.33 +- 0.16 (0.00-->8.32) mean absolute distance = 0.20 +- 0.29 3258 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4361166.0, rms=3.43 021: dt: 0.5000, sse=4636350.0, rms=2.533 (0.000%) rms = 2.78, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=4330722.5, rms=1.774 (0.000%) 023: dt: 0.2500, sse=4220126.5, rms=1.366 (0.000%) 024: dt: 0.2500, sse=4199025.0, rms=1.247 (0.000%) rms = 1.24, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=4164955.8, rms=1.245 (0.000%) rms = 1.22, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=4127032.5, rms=1.218 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group mean border=88.1, 36 (6) missing vertices, mean dist -0.0 [0.2 (%58.9)->0.2 (%41.1))] %89 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=Brain, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /root/Scrivania/subjects/ENP30S001A/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=4143982.5, rms=1.63 rms = 1.68, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=4199977.5, rms=1.167 (0.000%) 028: dt: 0.2500, sse=4331419.5, rms=0.922 (0.000%) rms = 0.95, time step reduction 2 of 3 to 0.125... rms = 0.92, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=4329852.5, rms=0.922 (0.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 10 non-cortical segments detected only using segment with 1859 vertices erasing segment 1 (vno[0] = 92979) erasing segment 2 (vno[0] = 105518) erasing segment 3 (vno[0] = 108730) erasing segment 4 (vno[0] = 108850) erasing segment 5 (vno[0] = 111033) erasing segment 6 (vno[0] = 112129) erasing segment 7 (vno[0] = 116319) erasing segment 8 (vno[0] = 117171) erasing segment 9 (vno[0] = 147408) writing cortex label to /root/Scrivania/subjects/ENP30S001A/label/lh.cortex.label... writing curvature file /root/Scrivania/subjects/ENP30S001A/surf/lh.curv writing smoothed area to lh.area writing curvature file /root/Scrivania/subjects/ENP30S001A/surf/lh.area vertex spacing 0.88 +- 0.24 (0.08-->5.76) (max @ vno 61866 --> 70213) face area 0.33 +- 0.16 (0.00-->8.18) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... smoothing surface for 5 iterations... mean border=59.8, 57 (57) missing vertices, mean dist 1.7 [0.2 (%0.0)->2.4 (%100.0))] %20 local maxima, %45 large gradients and %30 min vals, 1962 gradients ignored tol=1.0e-04, sigma=2.0, host=Brain, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=25543636.0, rms=28.38 001: dt: 0.5000, sse=19441656.0, rms=24.277 (0.000%) 002: dt: 0.5000, sse=14907747.0, rms=20.745 (0.000%) 003: dt: 0.5000, sse=11703384.0, rms=17.777 (0.000%) 004: dt: 0.5000, sse=9613071.0, rms=15.318 (0.000%) 005: dt: 0.5000, sse=8222695.5, rms=13.315 (0.000%) 006: dt: 0.5000, sse=7359229.5, rms=11.672 (0.000%) 007: dt: 0.5000, sse=6819032.5, rms=10.212 (0.000%) 008: dt: 0.5000, sse=6524053.0, rms=8.846 (0.000%) 009: dt: 0.5000, sse=6316680.5, rms=7.540 (0.000%) 010: dt: 0.5000, sse=6258585.5, rms=6.337 (0.000%) 011: dt: 0.5000, sse=6311766.0, rms=5.357 (0.000%) 012: dt: 0.5000, sse=6463550.0, rms=4.687 (0.000%) 013: dt: 0.5000, sse=6660345.5, rms=4.288 (0.000%) 014: dt: 0.5000, sse=6717485.5, rms=4.037 (0.000%) 015: dt: 0.5000, sse=6826577.5, rms=3.904 (0.000%) 016: dt: 0.5000, sse=6821763.0, rms=3.798 (0.000%) rms = 3.76, time step reduction 1 of 3 to 0.250... 017: dt: 0.5000, sse=6889647.0, rms=3.757 (0.000%) 018: dt: 0.2500, sse=4698488.0, rms=2.954 (0.000%) 019: dt: 0.2500, sse=4505496.0, rms=2.726 (0.000%) rms = 2.69, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=4381880.5, rms=2.686 (0.000%) 021: dt: 0.1250, sse=4165291.0, rms=2.545 (0.000%) rms = 2.52, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=4134977.8, rms=2.525 (0.000%) positioning took 1.5 minutes mean border=57.4, 1035 (15) missing vertices, mean dist 0.1 [0.2 (%45.1)->0.5 (%54.9))] %38 local maxima, %34 large gradients and %24 min vals, 679 gradients ignored tol=1.0e-04, sigma=1.0, host=Brain, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4821551.0, rms=4.87 023: dt: 0.5000, sse=4970073.5, rms=3.754 (0.000%) 024: dt: 0.5000, sse=6358176.0, rms=3.693 (0.000%) rms = 3.75, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=5224813.0, rms=2.911 (0.000%) 026: dt: 0.2500, sse=4772492.5, rms=2.586 (0.000%) 027: dt: 0.2500, sse=4732135.0, rms=2.515 (0.000%) rms = 2.49, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=4692478.5, rms=2.490 (0.000%) 029: dt: 0.1250, sse=4516331.0, rms=2.335 (0.000%) rms = 2.31, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=4499261.5, rms=2.313 (0.000%) positioning took 0.6 minutes mean border=55.7, 1397 (13) missing vertices, mean dist 0.1 [0.2 (%39.9)->0.3 (%60.1))] %51 local maxima, %21 large gradients and %23 min vals, 736 gradients ignored tol=1.0e-04, sigma=0.5, host=Brain, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4683497.0, rms=3.35 rms = 3.49, time step reduction 1 of 3 to 0.250... 031: dt: 0.2500, sse=4496808.5, rms=2.792 (0.000%) 032: dt: 0.2500, sse=4486482.0, rms=2.455 (0.000%) 033: dt: 0.2500, sse=4679203.5, rms=2.367 (0.000%) rms = 2.35, time step reduction 2 of 3 to 0.125... 034: dt: 0.2500, sse=4710668.0, rms=2.354 (0.000%) 035: dt: 0.1250, sse=4578261.0, rms=2.235 (0.000%) rms = 2.22, time step reduction 3 of 3 to 0.062... 036: dt: 0.1250, sse=4588261.5, rms=2.216 (0.000%) positioning took 0.5 minutes mean border=54.8, 2958 (13) missing vertices, mean dist 0.0 [0.2 (%45.4)->0.3 (%54.6))] %55 local maxima, %16 large gradients and %22 min vals, 625 gradients ignored tol=1.0e-04, sigma=0.2, host=Brain, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /root/Scrivania/subjects/ENP30S001A/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=4627021.0, rms=2.52 rms = 3.06, time step reduction 1 of 3 to 0.250... 037: dt: 0.2500, sse=4527738.0, rms=2.305 (0.000%) 038: dt: 0.2500, sse=4683505.5, rms=2.241 (0.000%) rms = 2.23, time step reduction 2 of 3 to 0.125... 039: dt: 0.2500, sse=4742968.0, rms=2.227 (0.000%) 040: dt: 0.1250, sse=4663334.5, rms=2.142 (0.000%) rms = 2.13, time step reduction 3 of 3 to 0.062... 041: dt: 0.1250, sse=4669977.0, rms=2.128 (0.000%) positioning took 0.4 minutes writing curvature file /root/Scrivania/subjects/ENP30S001A/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /root/Scrivania/subjects/ENP30S001A/surf/lh.area.pial vertex spacing 0.97 +- 0.39 (0.08-->8.02) (max @ vno 54443 --> 54444) face area 0.38 +- 0.27 (0.00-->9.50) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 147504 vertices processed 25000 of 147504 vertices processed 50000 of 147504 vertices processed 75000 of 147504 vertices processed 100000 of 147504 vertices processed 125000 of 147504 vertices processed 0 of 147504 vertices processed 25000 of 147504 vertices processed 50000 of 147504 vertices processed 75000 of 147504 vertices processed 100000 of 147504 vertices processed 125000 of 147504 vertices processed thickness calculation complete, 540:705 truncations. 34277 vertices at 0 distance 105816 vertices at 1 distance 90224 vertices at 2 distance 35317 vertices at 3 distance 11366 vertices at 4 distance 3668 vertices at 5 distance 1200 vertices at 6 distance 403 vertices at 7 distance 104 vertices at 8 distance 47 vertices at 9 distance 51 vertices at 10 distance 25 vertices at 11 distance 15 vertices at 12 distance 19 vertices at 13 distance 13 vertices at 14 distance 3 vertices at 15 distance 12 vertices at 16 distance 4 vertices at 17 distance 4 vertices at 18 distance 6 vertices at 19 distance 6 vertices at 20 distance writing curvature file /root/Scrivania/subjects/ENP30S001A/surf/lh.thickness positioning took 7.6 minutes #-------------------------------------------- #@# Smooth2 lh Mon Aug 28 21:01:37 CEST 2017 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /root/Scrivania/subjects/ENP30S001A/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 lh Mon Aug 28 21:01:39 CEST 2017 /root/Scrivania/subjects/ENP30S001A/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 48.3 mm, total surface area = 88495 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.114 (target=0.015) step 005: RMS=0.078 (target=0.015) step 010: RMS=0.056 (target=0.015) step 015: RMS=0.046 (target=0.015) step 020: RMS=0.038 (target=0.015) step 025: RMS=0.031 (target=0.015) step 030: RMS=0.027 (target=0.015) step 035: RMS=0.023 (target=0.015) step 040: RMS=0.020 (target=0.015) step 045: RMS=0.018 (target=0.015) step 050: RMS=0.016 (target=0.015) inflation complete. inflation took 0.3 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 194 vertices thresholded to be in k1 ~ [-0.19 1.79], k2 ~ [-0.09 0.07] total integrated curvature = 0.591*4pi (7.423) --> 0 handles ICI = 1.8, FI = 11.5, variation=195.178 104 vertices thresholded to be in [-0.02 0.01] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 110 vertices thresholded to be in [-0.11 0.42] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.015, std = 0.025 done. #----------------------------------------- #@# Curvature Stats lh Mon Aug 28 21:02:55 CEST 2017 /root/Scrivania/subjects/ENP30S001A/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm ENP30S001A lh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/lh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ ENP30S001A/lh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 274 ] Gb_filter = 0 WARN: S lookup min: -0.235098 WARN: S explicit min: 0.000000 vertex = 910 #-------------------------------------------- #@# Tessellate rh Mon Aug 28 21:02:58 CEST 2017 /root/Scrivania/subjects/ENP30S001A/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 2 found - 2 modified | TOTAL: 3 pass 2 (xy-): 0 found - 2 modified | TOTAL: 3 pass 1 (yz+): 1 found - 1 modified | TOTAL: 4 pass 2 (yz+): 0 found - 1 modified | TOTAL: 4 pass 1 (yz-): 1 found - 1 modified | TOTAL: 5 pass 2 (yz-): 0 found - 1 modified | TOTAL: 5 pass 1 (xz+): 1 found - 1 modified | TOTAL: 6 pass 2 (xz+): 0 found - 1 modified | TOTAL: 6 pass 1 (xz-): 4 found - 4 modified | TOTAL: 10 pass 2 (xz-): 0 found - 4 modified | TOTAL: 10 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 2 found - 2 modified | TOTAL: 3 pass 2 (--): 0 found - 2 modified | TOTAL: 3 pass 1 (-+): 3 found - 3 modified | TOTAL: 6 pass 2 (-+): 0 found - 3 modified | TOTAL: 6 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 16 (out of 306836: 0.005215) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 50: 1741 vertices, 1865 faces slice 60: 8006 vertices, 8296 faces slice 70: 17928 vertices, 18288 faces slice 80: 29254 vertices, 29637 faces slice 90: 40592 vertices, 40993 faces slice 100: 52403 vertices, 52788 faces slice 110: 64349 vertices, 64762 faces slice 120: 76555 vertices, 76977 faces slice 130: 88923 vertices, 89377 faces slice 140: 100892 vertices, 101335 faces slice 150: 111863 vertices, 112236 faces slice 160: 121972 vertices, 122349 faces slice 170: 130708 vertices, 131005 faces slice 180: 138064 vertices, 138334 faces slice 190: 144573 vertices, 144824 faces slice 200: 148115 vertices, 148184 faces slice 210: 148266 vertices, 148304 faces slice 220: 148266 vertices, 148304 faces slice 230: 148266 vertices, 148304 faces slice 240: 148266 vertices, 148304 faces slice 250: 148266 vertices, 148304 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 148266 voxel in cpt #1: X=-38 [v=148266,e=444912,f=296608] located at (29.803556, -10.062510, 0.052271) For the whole surface: X=-38 [v=148266,e=444912,f=296608] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Mon Aug 28 21:03:03 CEST 2017 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /root/Scrivania/subjects/ENP30S001A/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 rh Mon Aug 28 21:03:05 CEST 2017 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /root/Scrivania/subjects/ENP30S001A/scripts avg radius = 47.3 mm, total surface area = 77888 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.3 minutes Not saving sulc step 000: RMS=0.099 (target=0.015) step 005: RMS=0.072 (target=0.015) step 010: RMS=0.052 (target=0.015) step 015: RMS=0.044 (target=0.015) step 020: RMS=0.037 (target=0.015) step 025: RMS=0.033 (target=0.015) step 030: RMS=0.030 (target=0.015) step 035: RMS=0.027 (target=0.015) step 040: RMS=0.026 (target=0.015) step 045: RMS=0.025 (target=0.015) step 050: RMS=0.024 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.022 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere rh Mon Aug 28 21:03:26 CEST 2017 /root/Scrivania/subjects/ENP30S001A/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.97 +- 0.53 (0.00-->6.32) (max @ vno 58132 --> 59359) face area 0.03 +- 0.03 (-0.19-->0.51) scaling brain by 0.318... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.914, avgs=0 005/300: dt: 0.9000, rms radial error=175.655, avgs=0 010/300: dt: 0.9000, rms radial error=175.098, avgs=0 015/300: dt: 0.9000, rms radial error=174.368, avgs=0 020/300: dt: 0.9000, rms radial error=173.537, avgs=0 025/300: dt: 0.9000, rms radial error=172.647, avgs=0 030/300: dt: 0.9000, rms radial error=171.725, avgs=0 035/300: dt: 0.9000, rms radial error=170.791, avgs=0 040/300: dt: 0.9000, rms radial error=169.850, avgs=0 045/300: dt: 0.9000, rms radial error=168.906, avgs=0 050/300: dt: 0.9000, rms radial error=167.962, avgs=0 055/300: dt: 0.9000, rms radial error=167.021, avgs=0 060/300: dt: 0.9000, rms radial error=166.084, avgs=0 065/300: dt: 0.9000, rms radial error=165.151, avgs=0 070/300: dt: 0.9000, rms radial error=164.223, avgs=0 075/300: dt: 0.9000, rms radial error=163.299, avgs=0 080/300: dt: 0.9000, rms radial error=162.380, avgs=0 085/300: dt: 0.9000, rms radial error=161.467, avgs=0 090/300: dt: 0.9000, rms radial error=160.558, avgs=0 095/300: dt: 0.9000, rms radial error=159.654, avgs=0 100/300: dt: 0.9000, rms radial error=158.755, avgs=0 105/300: dt: 0.9000, rms radial error=157.861, avgs=0 110/300: dt: 0.9000, rms radial error=156.972, avgs=0 115/300: dt: 0.9000, rms radial error=156.088, avgs=0 120/300: dt: 0.9000, rms radial error=155.208, avgs=0 125/300: dt: 0.9000, rms radial error=154.334, avgs=0 130/300: dt: 0.9000, rms radial error=153.465, avgs=0 135/300: dt: 0.9000, rms radial error=152.600, avgs=0 140/300: dt: 0.9000, rms radial error=151.740, avgs=0 145/300: dt: 0.9000, rms radial error=150.885, avgs=0 150/300: dt: 0.9000, rms radial error=150.035, avgs=0 155/300: dt: 0.9000, rms radial error=149.189, avgs=0 160/300: dt: 0.9000, rms radial error=148.348, avgs=0 165/300: dt: 0.9000, rms radial error=147.513, avgs=0 170/300: dt: 0.9000, rms radial error=146.681, avgs=0 175/300: dt: 0.9000, rms radial error=145.855, avgs=0 180/300: dt: 0.9000, rms radial error=145.033, avgs=0 185/300: dt: 0.9000, rms radial error=144.215, avgs=0 190/300: dt: 0.9000, rms radial error=143.402, avgs=0 195/300: dt: 0.9000, rms radial error=142.594, avgs=0 200/300: dt: 0.9000, rms radial error=141.790, avgs=0 205/300: dt: 0.9000, rms radial error=140.991, avgs=0 210/300: dt: 0.9000, rms radial error=140.196, avgs=0 215/300: dt: 0.9000, rms radial error=139.406, avgs=0 220/300: dt: 0.9000, rms radial error=138.620, avgs=0 225/300: dt: 0.9000, rms radial error=137.839, avgs=0 230/300: dt: 0.9000, rms radial error=137.062, avgs=0 235/300: dt: 0.9000, rms radial error=136.289, avgs=0 240/300: dt: 0.9000, rms radial error=135.521, avgs=0 245/300: dt: 0.9000, rms radial error=134.757, avgs=0 250/300: dt: 0.9000, rms radial error=133.998, avgs=0 255/300: dt: 0.9000, rms radial error=133.242, avgs=0 260/300: dt: 0.9000, rms radial error=132.491, avgs=0 265/300: dt: 0.9000, rms radial error=131.745, avgs=0 270/300: dt: 0.9000, rms radial error=131.002, avgs=0 275/300: dt: 0.9000, rms radial error=130.263, avgs=0 280/300: dt: 0.9000, rms radial error=129.529, avgs=0 285/300: dt: 0.9000, rms radial error=128.799, avgs=0 290/300: dt: 0.9000, rms radial error=128.073, avgs=0 295/300: dt: 0.9000, rms radial error=127.351, avgs=0 300/300: dt: 0.9000, rms radial error=126.633, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 17188.96 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00014 epoch 2 (K=40.0), pass 1, starting sse = 2770.32 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00003 epoch 3 (K=160.0), pass 1, starting sse = 255.64 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.08/11 = 0.00712 epoch 4 (K=640.0), pass 1, starting sse = 14.72 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.13/16 = 0.00796 final writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.05 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology rh Mon Aug 28 21:06:28 CEST 2017 cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated /root/Scrivania/subjects/ENP30S001A/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 ENP30S001A rh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ before topology correction, eno=-38 (nv=148266, nf=296608, ne=444912, g=20) 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 6 iterations marking ambiguous vertices... 4017 ambiguous faces found in tessellation segmenting defects... 17 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 10 into 9 16 defects to be corrected 0 vertices coincident reading input surface /root/Scrivania/subjects/ENP30S001A/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.1666 (-4.5833) -vertex loglikelihood: -6.1626 (-3.0813) -normal dot loglikelihood: -3.6725 (-3.6725) -quad curv loglikelihood: -6.5927 (-3.2963) Total Loglikelihood : -25.5943 CORRECTING DEFECT 0 (vertices=65, convex hull=108) After retessellation of defect 0, euler #=-14 (145942,437112,291156) : difference with theory (-13) = 1 CORRECTING DEFECT 1 (vertices=38, convex hull=84) After retessellation of defect 1, euler #=-13 (145959,437196,291224) : difference with theory (-12) = 1 CORRECTING DEFECT 2 (vertices=23, convex hull=55) After retessellation of defect 2, euler #=-12 (145970,437250,291268) : difference with theory (-11) = 1 CORRECTING DEFECT 3 (vertices=20, convex hull=33) After retessellation of defect 3, euler #=-11 (145974,437275,291290) : difference with theory (-10) = 1 CORRECTING DEFECT 4 (vertices=127, convex hull=116) After retessellation of defect 4, euler #=-10 (145992,437377,291375) : difference with theory (-9) = 1 CORRECTING DEFECT 5 (vertices=33, convex hull=49) After retessellation of defect 5, euler #=-9 (146002,437423,291412) : difference with theory (-8) = 1 CORRECTING DEFECT 6 (vertices=22, convex hull=20) After retessellation of defect 6, euler #=-8 (146006,437442,291428) : difference with theory (-7) = 1 CORRECTING DEFECT 7 (vertices=7, convex hull=27) After retessellation of defect 7, euler #=-7 (146009,437459,291443) : difference with theory (-6) = 1 CORRECTING DEFECT 8 (vertices=5, convex hull=27) After retessellation of defect 8, euler #=-6 (146011,437472,291455) : difference with theory (-5) = 1 CORRECTING DEFECT 9 (vertices=949, convex hull=468) After retessellation of defect 9, euler #=-4 (146276,438502,292222) : difference with theory (-4) = 0 CORRECTING DEFECT 10 (vertices=30, convex hull=62) After retessellation of defect 10, euler #=-3 (146293,438581,292285) : difference with theory (-3) = 0 CORRECTING DEFECT 11 (vertices=73, convex hull=29) After retessellation of defect 11, euler #=-2 (146300,438613,292311) : difference with theory (-2) = 0 CORRECTING DEFECT 12 (vertices=195, convex hull=83) After retessellation of defect 12, euler #=-1 (146318,438706,292387) : difference with theory (-1) = 0 CORRECTING DEFECT 13 (vertices=676, convex hull=329) After retessellation of defect 13, euler #=0 (146436,439229,292793) : difference with theory (0) = 0 CORRECTING DEFECT 14 (vertices=73, convex hull=128) normal vector of length zero at vertex 148223 with 3 faces After retessellation of defect 14, euler #=1 (146488,439443,292956) : difference with theory (1) = 0 CORRECTING DEFECT 15 (vertices=19, convex hull=44) After retessellation of defect 15, euler #=2 (146494,439476,292984) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.22 (0.08-->10.07) (max @ vno 57834 --> 57844) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.22 (0.08-->10.07) (max @ vno 57834 --> 57844) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 69 mutations (37.9%), 113 crossovers (62.1%), 162 vertices were eliminated building final representation... 1772 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=146494, nf=292984, ne=439476, g=0) writing corrected surface to /root/Scrivania/subjects/ENP30S001A/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 9.6 minutes 0 defective edges removing intersecting faces 000: 190 intersecting 001: 6 intersecting 002: 2 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 146494 - 439476 + 292984 = 2 --> 0 holes F =2V-4: 292984 = 292988-4 (0) 2E=3F: 878952 = 878952 (0) total defect index = 0 /root/Scrivania/subjects/ENP30S001A/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 60 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Mon Aug 28 21:16:05 CEST 2017 /root/Scrivania/subjects/ENP30S001A/scripts mris_make_surfaces -noaparc -mgz -T1 brain.finalsurfs ENP30S001A rh not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /root/Scrivania/subjects/ENP30S001A/mri/filled.mgz... reading volume /root/Scrivania/subjects/ENP30S001A/mri/brain.finalsurfs.mgz... reading volume /root/Scrivania/subjects/ENP30S001A/mri/wm.mgz... 15270 bright wm thresholded. 253 bright non-wm voxels segmented. reading original surface position from /root/Scrivania/subjects/ENP30S001A/surf/rh.orig... computing class statistics... border white: 279213 voxels (1.66%) border gray 305834 voxels (1.82%) WM (95.0): 96.2 +- 8.0 [70.0 --> 110.0] GM (82.0) : 80.5 +- 11.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 59.2 (was 70) setting MAX_BORDER_WHITE to 113.0 (was 105) setting MIN_BORDER_WHITE to 71.0 (was 85) setting MAX_CSF to 47.5 (was 40) setting MAX_GRAY to 97.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 65.1 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 35.7 (was 40) repositioning cortical surface to gray/white boundary reading volume /root/Scrivania/subjects/ENP30S001A/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.04-->4.93) (max @ vno 115644 --> 146363) face area 0.28 +- 0.12 (0.00-->3.16) mean absolute distance = 0.72 +- 0.94 3175 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=71 mean inside = 95.4, mean outside = 76.9 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group mean border=81.7, 44 (44) missing vertices, mean dist 0.2 [0.7 (%38.7)->0.8 (%61.3))] %63 local maxima, %32 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=Brain, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.25 (0.09-->7.17) (max @ vno 146363 --> 105868) face area 0.28 +- 0.13 (0.00-->3.99) mean absolute distance = 0.35 +- 0.62 2794 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5702343.0, rms=10.46 001: dt: 0.5000, sse=6405871.0, rms=7.318 (0.000%) 002: dt: 0.5000, sse=6826688.5, rms=5.434 (0.000%) 003: dt: 0.5000, sse=7166785.5, rms=4.323 (0.000%) 004: dt: 0.5000, sse=7463928.5, rms=3.664 (0.000%) 005: dt: 0.5000, sse=7598569.5, rms=3.406 (0.000%) 006: dt: 0.5000, sse=7705287.5, rms=3.236 (0.000%) rms = 3.22, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=7724298.0, rms=3.216 (0.000%) 008: dt: 0.2500, sse=4660595.5, rms=2.092 (0.000%) 009: dt: 0.2500, sse=4222490.5, rms=1.798 (0.000%) 010: dt: 0.2500, sse=4037516.8, rms=1.727 (0.000%) rms = 1.69, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=3981314.8, rms=1.690 (0.000%) rms = 1.65, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=3912573.2, rms=1.653 (0.000%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=84.7, 50 (27) missing vertices, mean dist -0.2 [0.4 (%71.8)->0.2 (%28.2))] %74 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=Brain, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.24 (0.10-->7.62) (max @ vno 146363 --> 105868) face area 0.35 +- 0.16 (0.00-->5.36) mean absolute distance = 0.25 +- 0.39 3400 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4544403.0, rms=4.50 013: dt: 0.5000, sse=4911992.5, rms=2.799 (0.000%) rms = 2.85, time step reduction 1 of 3 to 0.250... 014: dt: 0.2500, sse=4552014.5, rms=2.210 (0.000%) 015: dt: 0.2500, sse=4360258.0, rms=1.699 (0.000%) 016: dt: 0.2500, sse=4265820.5, rms=1.489 (0.000%) 017: dt: 0.2500, sse=4205783.0, rms=1.427 (0.000%) rms = 1.40, time step reduction 2 of 3 to 0.125... 018: dt: 0.2500, sse=4178903.5, rms=1.398 (0.000%) rms = 1.37, time step reduction 3 of 3 to 0.062... 019: dt: 0.1250, sse=4130657.8, rms=1.370 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=87.3, 34 (24) missing vertices, mean dist -0.2 [0.3 (%74.1)->0.2 (%25.9))] %85 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=Brain, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.24 (0.06-->7.81) (max @ vno 146363 --> 105868) face area 0.34 +- 0.16 (0.00-->5.50) mean absolute distance = 0.20 +- 0.29 2761 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4372754.0, rms=3.38 020: dt: 0.5000, sse=4658310.0, rms=2.480 (0.000%) rms = 2.77, time step reduction 1 of 3 to 0.250... 021: dt: 0.2500, sse=4366053.0, rms=1.737 (0.000%) 022: dt: 0.2500, sse=4271424.0, rms=1.355 (0.000%) 023: dt: 0.2500, sse=4252276.0, rms=1.251 (0.000%) rms = 1.25, time step reduction 2 of 3 to 0.125... rms = 1.24, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=4226660.0, rms=1.236 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=88.2, 30 (17) missing vertices, mean dist -0.0 [0.2 (%58.0)->0.2 (%42.0))] %88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=Brain, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /root/Scrivania/subjects/ENP30S001A/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=4242564.0, rms=1.61 rms = 1.75, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=4273110.5, rms=1.149 (0.000%) 026: dt: 0.2500, sse=4404211.5, rms=0.936 (0.000%) rms = 0.96, time step reduction 2 of 3 to 0.125... rms = 0.93, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=4402747.0, rms=0.935 (0.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 19 non-cortical segments detected only using segment with 2202 vertices erasing segment 1 (vno[0] = 62620) erasing segment 2 (vno[0] = 92515) erasing segment 3 (vno[0] = 94741) erasing segment 4 (vno[0] = 95898) erasing segment 5 (vno[0] = 95914) erasing segment 6 (vno[0] = 102530) erasing segment 7 (vno[0] = 103624) erasing segment 8 (vno[0] = 103688) erasing segment 9 (vno[0] = 103728) erasing segment 10 (vno[0] = 104751) erasing segment 11 (vno[0] = 104822) erasing segment 12 (vno[0] = 106808) erasing segment 13 (vno[0] = 107794) erasing segment 14 (vno[0] = 109732) erasing segment 15 (vno[0] = 111591) erasing segment 16 (vno[0] = 111600) erasing segment 17 (vno[0] = 111619) erasing segment 18 (vno[0] = 111654) writing cortex label to /root/Scrivania/subjects/ENP30S001A/label/rh.cortex.label... writing curvature file /root/Scrivania/subjects/ENP30S001A/surf/rh.curv writing smoothed area to rh.area writing curvature file /root/Scrivania/subjects/ENP30S001A/surf/rh.area vertex spacing 0.89 +- 0.25 (0.06-->7.87) (max @ vno 105868 --> 146363) face area 0.33 +- 0.16 (0.00-->5.42) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... smoothing surface for 5 iterations... mean border=60.5, 38 (38) missing vertices, mean dist 1.7 [0.1 (%0.0)->2.3 (%100.0))] %22 local maxima, %47 large gradients and %26 min vals, 2197 gradients ignored tol=1.0e-04, sigma=2.0, host=Brain, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=24539720.0, rms=27.79 001: dt: 0.5000, sse=18647480.0, rms=23.718 (0.000%) 002: dt: 0.5000, sse=14287355.0, rms=20.215 (0.000%) 003: dt: 0.5000, sse=11284376.0, rms=17.302 (0.000%) 004: dt: 0.5000, sse=9317794.0, rms=14.879 (0.000%) 005: dt: 0.5000, sse=8024025.5, rms=12.890 (0.000%) 006: dt: 0.5000, sse=7175750.5, rms=11.253 (0.000%) 007: dt: 0.5000, sse=6657254.5, rms=9.798 (0.000%) 008: dt: 0.5000, sse=6366998.0, rms=8.468 (0.000%) 009: dt: 0.5000, sse=6185964.0, rms=7.222 (0.000%) 010: dt: 0.5000, sse=6137974.0, rms=6.101 (0.000%) 011: dt: 0.5000, sse=6207756.0, rms=5.199 (0.000%) 012: dt: 0.5000, sse=6282500.0, rms=4.569 (0.000%) 013: dt: 0.5000, sse=6451894.0, rms=4.184 (0.000%) 014: dt: 0.5000, sse=6508639.5, rms=3.928 (0.000%) 015: dt: 0.5000, sse=6616787.5, rms=3.790 (0.000%) 016: dt: 0.5000, sse=6596986.0, rms=3.695 (0.000%) rms = 3.66, time step reduction 1 of 3 to 0.250... 017: dt: 0.5000, sse=6679531.0, rms=3.661 (0.000%) 018: dt: 0.2500, sse=4492114.0, rms=2.857 (0.000%) 019: dt: 0.2500, sse=4287860.5, rms=2.629 (0.000%) rms = 2.59, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=4171476.8, rms=2.591 (0.000%) 021: dt: 0.1250, sse=3977533.8, rms=2.449 (0.000%) rms = 2.43, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=3951687.8, rms=2.431 (0.000%) positioning took 1.5 minutes mean border=57.6, 740 (11) missing vertices, mean dist 0.2 [0.2 (%43.6)->0.5 (%56.4))] %41 local maxima, %35 large gradients and %20 min vals, 606 gradients ignored tol=1.0e-04, sigma=1.0, host=Brain, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4768926.0, rms=5.29 023: dt: 0.5000, sse=4797700.5, rms=3.869 (0.000%) 024: dt: 0.5000, sse=6160785.5, rms=3.720 (0.000%) rms = 3.78, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=5046288.0, rms=2.916 (0.000%) 026: dt: 0.2500, sse=4597392.5, rms=2.574 (0.000%) 027: dt: 0.2500, sse=4552962.5, rms=2.495 (0.000%) rms = 2.48, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=4524732.5, rms=2.475 (0.000%) 029: dt: 0.1250, sse=4341472.5, rms=2.296 (0.000%) rms = 2.27, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=4323674.0, rms=2.270 (0.000%) positioning took 0.6 minutes mean border=55.7, 950 (3) missing vertices, mean dist 0.1 [0.2 (%37.9)->0.3 (%62.1))] %54 local maxima, %22 large gradients and %19 min vals, 660 gradients ignored tol=1.0e-04, sigma=0.5, host=Brain, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4546630.5, rms=3.52 rms = 3.53, time step reduction 1 of 3 to 0.250... 031: dt: 0.2500, sse=4351162.0, rms=2.900 (0.000%) 032: dt: 0.2500, sse=4324523.0, rms=2.468 (0.000%) 033: dt: 0.2500, sse=4493762.0, rms=2.366 (0.000%) rms = 2.35, time step reduction 2 of 3 to 0.125... 034: dt: 0.2500, sse=4545132.5, rms=2.354 (0.000%) 035: dt: 0.1250, sse=4408806.0, rms=2.218 (0.000%) rms = 2.19, time step reduction 3 of 3 to 0.062... 036: dt: 0.1250, sse=4412772.5, rms=2.195 (0.000%) positioning took 0.5 minutes mean border=54.8, 2296 (2) missing vertices, mean dist 0.0 [0.2 (%44.0)->0.3 (%56.0))] %59 local maxima, %17 large gradients and %19 min vals, 534 gradients ignored tol=1.0e-04, sigma=0.2, host=Brain, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /root/Scrivania/subjects/ENP30S001A/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=4454894.0, rms=2.53 rms = 3.08, time step reduction 1 of 3 to 0.250... 037: dt: 0.2500, sse=4351642.0, rms=2.274 (0.000%) 038: dt: 0.2500, sse=4487932.5, rms=2.176 (0.000%) rms = 2.16, time step reduction 2 of 3 to 0.125... 039: dt: 0.2500, sse=4553325.5, rms=2.159 (0.000%) 040: dt: 0.1250, sse=4474079.5, rms=2.062 (0.000%) rms = 2.04, time step reduction 3 of 3 to 0.062... 041: dt: 0.1250, sse=4481417.0, rms=2.045 (0.000%) positioning took 0.4 minutes writing curvature file /root/Scrivania/subjects/ENP30S001A/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /root/Scrivania/subjects/ENP30S001A/surf/rh.area.pial vertex spacing 0.98 +- 0.40 (0.10-->8.78) (max @ vno 95909 --> 95896) face area 0.38 +- 0.27 (0.00-->7.96) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 146494 vertices processed 25000 of 146494 vertices processed 50000 of 146494 vertices processed 75000 of 146494 vertices processed 100000 of 146494 vertices processed 125000 of 146494 vertices processed 0 of 146494 vertices processed 25000 of 146494 vertices processed 50000 of 146494 vertices processed 75000 of 146494 vertices processed 100000 of 146494 vertices processed 125000 of 146494 vertices processed thickness calculation complete, 468:642 truncations. 35696 vertices at 0 distance 105049 vertices at 1 distance 88664 vertices at 2 distance 35183 vertices at 3 distance 11107 vertices at 4 distance 3442 vertices at 5 distance 1051 vertices at 6 distance 356 vertices at 7 distance 139 vertices at 8 distance 51 vertices at 9 distance 30 vertices at 10 distance 20 vertices at 11 distance 14 vertices at 12 distance 20 vertices at 13 distance 11 vertices at 14 distance 17 vertices at 15 distance 17 vertices at 16 distance 10 vertices at 17 distance 6 vertices at 18 distance 3 vertices at 19 distance 6 vertices at 20 distance writing curvature file /root/Scrivania/subjects/ENP30S001A/surf/rh.thickness positioning took 7.4 minutes #-------------------------------------------- #@# Smooth2 rh Mon Aug 28 21:23:27 CEST 2017 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /root/Scrivania/subjects/ENP30S001A/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 rh Mon Aug 28 21:23:29 CEST 2017 /root/Scrivania/subjects/ENP30S001A/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 47.4 mm, total surface area = 87954 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.114 (target=0.015) step 005: RMS=0.077 (target=0.015) step 010: RMS=0.055 (target=0.015) step 015: RMS=0.045 (target=0.015) step 020: RMS=0.037 (target=0.015) step 025: RMS=0.031 (target=0.015) step 030: RMS=0.025 (target=0.015) step 035: RMS=0.021 (target=0.015) step 040: RMS=0.018 (target=0.015) step 045: RMS=0.016 (target=0.015) inflation complete. inflation took 0.3 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 275 vertices thresholded to be in k1 ~ [-0.23 0.35], k2 ~ [-0.09 0.06] total integrated curvature = 0.547*4pi (6.868) --> 0 handles ICI = 1.9, FI = 14.3, variation=235.454 139 vertices thresholded to be in [-0.01 0.01] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 148 vertices thresholded to be in [-0.12 0.18] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.015, std = 0.028 done. #----------------------------------------- #@# Curvature Stats rh Mon Aug 28 21:24:44 CEST 2017 /root/Scrivania/subjects/ENP30S001A/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm ENP30S001A rh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/rh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ ENP30S001A/rh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 252 ] Gb_filter = 0 WARN: S lookup min: -0.036446 WARN: S explicit min: 0.000000 vertex = 321 #-------------------------------------------- #@# ASeg Stats Mon Aug 28 21:24:47 CEST 2017 INFO: mri_segstats will not calculate Supratentorial due to missing ribbon.mgz file /root/Scrivania/subjects/ENP30S001A mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/freesurfer/ASegStatsLUT.txt --subject ENP30S001A $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/freesurfer/ASegStatsLUT.txt --subject ENP30S001A sysname Linux hostname Braindata machine x86_64 user root UseRobust 0 atlas_icv (eTIV) = 1682783 mm^3 (det: 1.157669 ) mghRead(/root/Scrivania/subjects/ENP30S001A/mri/ribbon.mgz, -1): could not open file Computing euler number orig.nofix lheno = -34, rheno = -38 orig.nofix lhholes = 18, rhholes = 20 Loading mri/aseg.mgz Getting Brain Volume Statistics Linux Braindata 3.19.0-15-generic #15-Ubuntu SMP Thu Apr 16 23:32:37 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux recon-all -s ENP30S001A exited with ERRORS at Mon Aug 28 21:24:53 CEST 2017 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all Tue Aug 29 16:07:46 CEST 2017 /root/Scrivania/subjects/ENP30S001A /usr/local/freesurfer/bin/recon-all -s ENP30S001A -autorecon2 subjid ENP30S001A setenv SUBJECTS_DIR /root/Scrivania/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux Braindata 3.19.0-15-generic #15-Ubuntu SMP Thu Apr 16 23:32:37 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 128307 maxlocks unlimited maxsignal 128307 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 32869864 5068300 27801564 60964 286184 3701964 -/+ buffers/cache: 1080152 31789712 Swap: 33472508 0 33472508 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/29-14:07:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/29-14:07:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/29-14:07:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/29-14:07:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/29-14:07:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/29-14:07:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/29-14:07:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/29-14:07:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/29-14:07:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/29-14:07:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/29-14:07:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/29-14:07:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/29-14:07:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/29-14:07:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/29-14:07:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/29-14:07:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/29-14:07:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/29-14:07:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/29-14:07:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/29-14:07:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/29-14:07:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/29-14:07:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/29-14:07:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/29-14:07:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/29-14:07:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/29-14:07:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/29-14:07:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/29-14:07:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/29-14:07:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/29-14:07:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/29-14:07:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/29-14:07:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/29-14:07:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/29-14:07:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/29-14:07:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/29-14:07:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/29-14:07:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/08/29-14:07:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #------------------------------------- #@# EM Registration Tue Aug 29 16:07:50 CEST 2017 /root/Scrivania/subjects/ENP30S001A/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta ======= NUMBER OF OPENMP THREADS = 1 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 14.9 or > 790.2 total sample mean = 84.4 (994 zeros) ************************************************ spacing=8, using 2772 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2772, passno 0, spacing 8 resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=22.9 skull bounding box = (57, 77, 42) --> (195, 207, 201) using (103, 120, 122) as brain centroid... mean wm in atlas = 107, using box (86,104,102) --> (119, 135,141) to find MRI wm before smoothing, mri peak at 105 after smoothing, mri peak at 105, scaling input intensities by 1.019 scaling channel 0 by 1.01905 initial log_p = -4.3 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.028454 @ (-9.091, -27.273, -9.091) max log p = -3.788519 @ (4.545, 4.545, -4.545) max log p = -3.679009 @ (2.273, 6.818, 2.273) max log p = -3.639682 @ (-1.136, -3.409, -1.136) max log p = -3.635263 @ (1.705, 1.705, -0.568) max log p = -3.635263 @ (0.000, 0.000, 0.000) Found translation: (-1.7, -17.6, -13.1): log p = -3.635 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.4, old_max_log_p =-3.6 (thresh=-3.6) 0.991 0.145 0.039 -24.993; -0.131 1.101 0.295 -49.604; 0.000 -0.259 0.966 33.789; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.4, old_max_log_p =-3.4 (thresh=-3.4) 0.991 0.145 0.039 -24.993; -0.131 1.101 0.295 -49.604; 0.000 -0.259 0.966 33.789; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.2, old_max_log_p =-3.4 (thresh=-3.4) 1.012 0.127 -0.036 -14.850; -0.100 1.092 0.255 -49.625; 0.065 -0.223 1.011 13.540; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2) 1.012 0.127 -0.036 -14.850; -0.104 1.120 0.226 -49.632; 0.061 -0.184 1.000 9.900; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2) 1.010 0.123 -0.020 -16.949; -0.103 1.119 0.243 -50.632; 0.046 -0.203 0.993 14.381; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2) 1.008 0.123 -0.020 -16.612; -0.103 1.122 0.243 -51.029; 0.046 -0.204 0.995 14.168; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2) 1.008 0.123 -0.020 -16.612; -0.103 1.119 0.243 -50.631; 0.046 -0.204 0.999 13.847; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2) 1.008 0.123 -0.020 -16.612; -0.103 1.119 0.243 -50.631; 0.046 -0.204 0.999 13.847; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2772 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.00784 0.12282 -0.01976 -16.61161; -0.10285 1.11918 0.24274 -50.63125; 0.04595 -0.20448 0.99897 13.84704; 0.00000 0.00000 0.00000 1.00000; nsamples 2772 Quasinewton: input matrix 1.00784 0.12282 -0.01976 -16.61161; -0.10285 1.11918 0.24274 -50.63125; 0.04595 -0.20448 0.99897 13.84704; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.008 0.123 -0.020 -16.612; -0.103 1.119 0.243 -50.631; 0.046 -0.204 0.999 13.847; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.2 (old=-4.3) transform before final EM align: 1.008 0.123 -0.020 -16.612; -0.103 1.119 0.243 -50.631; 0.046 -0.204 0.999 13.847; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 312841 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.00784 0.12282 -0.01976 -16.61161; -0.10285 1.11918 0.24274 -50.63125; 0.04595 -0.20448 0.99897 13.84704; 0.00000 0.00000 0.00000 1.00000; nsamples 312841 Quasinewton: input matrix 1.00784 0.12282 -0.01976 -16.61161; -0.10285 1.11918 0.24274 -50.63125; 0.04595 -0.20448 0.99897 13.84704; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 012: -log(p) = 3.7 tol 0.000000 final transform: 1.008 0.123 -0.020 -16.612; -0.103 1.119 0.243 -50.631; 0.046 -0.204 0.999 13.847; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 15 minutes and 43 seconds. #-------------------------------------- #@# CA Normalize Tue Aug 29 16:23:34 CEST 2017 /root/Scrivania/subjects/ENP30S001A/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=22.9 skull bounding box = (57, 77, 42) --> (195, 207, 202) using (103, 120, 122) as brain centroid... mean wm in atlas = 107, using box (86,104,102) --> (119, 135,141) to find MRI wm before smoothing, mri peak at 105 after smoothing, mri peak at 105, scaling input intensities by 1.019 scaling channel 0 by 1.01905 using 244171 sample points... INFO: compute sample coordinates transform 1.008 0.123 -0.020 -16.612; -0.103 1.119 0.243 -50.631; 0.046 -0.204 0.999 13.847; 0.000 0.000 0.000 1.000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (120, 81, 39) --> (193, 182, 200) Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 147.0 0 of 490 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (61, 79, 39) --> (131, 175, 201) Right_Cerebral_White_Matter: limiting intensities to 94.0 --> 147.0 0 of 251 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (123, 158, 66) --> (170, 200, 118) Left_Cerebellum_White_Matter: limiting intensities to 103.0 --> 147.0 0 of 10 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (75, 158, 64) --> (124, 193, 120) Right_Cerebellum_White_Matter: limiting intensities to 97.0 --> 147.0 0 of 15 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (106, 148, 100) --> (140, 209, 129) Brain_Stem: limiting intensities to 97.0 --> 147.0 0 of 20 (0.0%) samples deleted using 786 total control points for intensity normalization... bias field = 0.991 +- 0.068 1 of 786 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (120, 81, 39) --> (193, 182, 200) Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 139.0 0 of 534 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (61, 79, 39) --> (131, 175, 201) Right_Cerebral_White_Matter: limiting intensities to 93.0 --> 139.0 0 of 275 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (123, 158, 66) --> (170, 200, 118) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 139.0 0 of 68 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (75, 158, 64) --> (124, 193, 120) Right_Cerebellum_White_Matter: limiting intensities to 87.0 --> 139.0 0 of 68 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (106, 148, 100) --> (140, 209, 129) Brain_Stem: limiting intensities to 83.0 --> 139.0 0 of 85 (0.0%) samples deleted using 1030 total control points for intensity normalization... bias field = 1.004 +- 0.061 0 of 1030 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (120, 81, 39) --> (193, 182, 200) Left_Cerebral_White_Matter: limiting intensities to 93.0 --> 139.0 0 of 601 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (61, 79, 39) --> (131, 175, 201) Right_Cerebral_White_Matter: limiting intensities to 93.0 --> 139.0 1 of 367 (0.3%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (123, 158, 66) --> (170, 200, 118) Left_Cerebellum_White_Matter: limiting intensities to 83.0 --> 139.0 0 of 99 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (75, 158, 64) --> (124, 193, 120) Right_Cerebellum_White_Matter: limiting intensities to 81.0 --> 139.0 0 of 74 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (106, 148, 100) --> (140, 209, 129) Brain_Stem: limiting intensities to 75.0 --> 139.0 0 of 182 (0.0%) samples deleted using 1323 total control points for intensity normalization... bias field = 1.004 +- 0.046 0 of 1322 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 5 seconds. #-------------------------------------- #@# CA Reg Tue Aug 29 16:24:38 CEST 2017 /root/Scrivania/subjects/ENP30S001A/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log ======= NUMBER OF OPENMP THREADS = 1 ======= reading input volume 'norm.mgz'... reading GCA '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.19 (predicted orig area = 6.7) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.768, neg=0, invalid=96777 0001: dt=129.472000, rms=0.705 (8.263%), neg=0, invalid=96777 0002: dt=129.472000, rms=0.692 (1.831%), neg=0, invalid=96777 0003: dt=369.920000, rms=0.681 (1.596%), neg=0, invalid=96777 0004: dt=110.976000, rms=0.676 (0.722%), neg=0, invalid=96777 0005: dt=129.472000, rms=0.674 (0.286%), neg=0, invalid=96777 0006: dt=129.472000, rms=0.672 (0.343%), neg=0, invalid=96777 0007: dt=129.472000, rms=0.670 (0.207%), neg=0, invalid=96777 0008: dt=129.472000, rms=0.669 (0.241%), neg=0, invalid=96777 0009: dt=129.472000, rms=0.666 (0.365%), neg=0, invalid=96777 0010: dt=129.472000, rms=0.664 (0.373%), neg=0, invalid=96777 0011: dt=129.472000, rms=0.661 (0.451%), neg=0, invalid=96777 0012: dt=129.472000, rms=0.658 (0.392%), neg=0, invalid=96777 0013: dt=129.472000, rms=0.656 (0.346%), neg=0, invalid=96777 0014: dt=129.472000, rms=0.654 (0.290%), neg=0, invalid=96777 0015: dt=129.472000, rms=0.653 (0.230%), neg=0, invalid=96777 0016: dt=129.472000, rms=0.651 (0.287%), neg=0, invalid=96777 0017: dt=129.472000, rms=0.649 (0.246%), neg=0, invalid=96777 0018: dt=129.472000, rms=0.647 (0.279%), neg=0, invalid=96777 0019: dt=129.472000, rms=0.646 (0.242%), neg=0, invalid=96777 0020: dt=129.472000, rms=0.644 (0.297%), neg=0, invalid=96777 0021: dt=129.472000, rms=0.642 (0.229%), neg=0, invalid=96777 0022: dt=129.472000, rms=0.641 (0.180%), neg=0, invalid=96777 0023: dt=129.472000, rms=0.640 (0.197%), neg=0, invalid=96777 0024: dt=129.472000, rms=0.639 (0.189%), neg=0, invalid=96777 0025: dt=129.472000, rms=0.638 (0.152%), neg=0, invalid=96777 0026: dt=129.472000, rms=0.637 (0.125%), neg=0, invalid=96777 0027: dt=129.472000, rms=0.636 (0.137%), neg=0, invalid=96777 0028: dt=129.472000, rms=0.635 (0.116%), neg=0, invalid=96777 0029: dt=129.472000, rms=0.635 (0.106%), neg=0, invalid=96777 0030: dt=517.888000, rms=0.635 (0.031%), neg=0, invalid=96777 0031: dt=517.888000, rms=0.634 (0.001%), neg=0, invalid=96777 0032: dt=517.888000, rms=0.635 (-0.597%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.635, neg=0, invalid=96777 0033: dt=129.472000, rms=0.633 (0.186%), neg=0, invalid=96777 0034: dt=517.888000, rms=0.632 (0.137%), neg=0, invalid=96777 0035: dt=517.888000, rms=0.632 (-0.357%), neg=0, invalid=96777 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.637, neg=0, invalid=96777 0036: dt=145.152000, rms=0.630 (1.132%), neg=0, invalid=96777 0037: dt=36.288000, rms=0.627 (0.569%), neg=0, invalid=96777 0038: dt=124.416000, rms=0.621 (0.861%), neg=0, invalid=96777 0039: dt=20.736000, rms=0.618 (0.454%), neg=0, invalid=96777 0040: dt=145.152000, rms=0.616 (0.464%), neg=0, invalid=96777 0041: dt=36.288000, rms=0.612 (0.584%), neg=0, invalid=96777 0042: dt=31.104000, rms=0.611 (0.135%), neg=0, invalid=96777 0043: dt=31.104000, rms=0.610 (0.203%), neg=0, invalid=96777 0044: dt=31.104000, rms=0.608 (0.265%), neg=0, invalid=96777 0045: dt=31.104000, rms=0.606 (0.345%), neg=0, invalid=96777 0046: dt=31.104000, rms=0.604 (0.404%), neg=0, invalid=96777 0047: dt=31.104000, rms=0.601 (0.467%), neg=0, invalid=96777 0048: dt=31.104000, rms=0.598 (0.506%), neg=0, invalid=96777 0049: dt=31.104000, rms=0.595 (0.493%), neg=0, invalid=96777 0050: dt=31.104000, rms=0.592 (0.449%), neg=0, invalid=96777 0051: dt=31.104000, rms=0.590 (0.379%), neg=0, invalid=96777 0052: dt=31.104000, rms=0.588 (0.384%), neg=0, invalid=96777 0053: dt=31.104000, rms=0.586 (0.355%), neg=0, invalid=96777 0054: dt=31.104000, rms=0.584 (0.311%), neg=0, invalid=96777 0055: dt=31.104000, rms=0.582 (0.247%), neg=0, invalid=96777 0056: dt=31.104000, rms=0.581 (0.226%), neg=0, invalid=96777 0057: dt=31.104000, rms=0.580 (0.237%), neg=0, invalid=96777 0058: dt=31.104000, rms=0.578 (0.217%), neg=0, invalid=96777 0059: dt=31.104000, rms=0.577 (0.168%), neg=0, invalid=96777 0060: dt=31.104000, rms=0.577 (0.139%), neg=0, invalid=96777 0061: dt=31.104000, rms=0.576 (0.137%), neg=0, invalid=96777 0062: dt=31.104000, rms=0.575 (0.116%), neg=0, invalid=96777 0063: dt=31.104000, rms=0.575 (0.112%), neg=0, invalid=96777 0064: dt=31.104000, rms=0.574 (0.008%), neg=0, invalid=96777 0065: dt=31.104000, rms=0.574 (0.013%), neg=0, invalid=96777 0066: dt=31.104000, rms=0.574 (0.028%), neg=0, invalid=96777 0067: dt=31.104000, rms=0.574 (0.020%), neg=0, invalid=96777 0068: dt=31.104000, rms=0.574 (0.016%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.574, neg=0, invalid=96777 0069: dt=124.416000, rms=0.573 (0.233%), neg=0, invalid=96777 0070: dt=36.288000, rms=0.572 (0.074%), neg=0, invalid=96777 0071: dt=36.288000, rms=0.572 (0.018%), neg=0, invalid=96777 0072: dt=36.288000, rms=0.572 (0.030%), neg=0, invalid=96777 0073: dt=36.288000, rms=0.572 (0.036%), neg=0, invalid=96777 0074: dt=36.288000, rms=0.572 (0.009%), neg=0, invalid=96777 0075: dt=36.288000, rms=0.572 (-0.016%), neg=0, invalid=96777 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.592, neg=0, invalid=96777 0076: dt=2.000000, rms=0.592 (0.007%), neg=0, invalid=96777 0077: dt=0.700000, rms=0.592 (0.001%), neg=0, invalid=96777 0078: dt=0.700000, rms=0.592 (0.000%), neg=0, invalid=96777 0079: dt=0.700000, rms=0.592 (-0.006%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.592, neg=0, invalid=96777 0080: dt=0.000000, rms=0.592 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.650, neg=0, invalid=96777 0081: dt=5.217893, rms=0.632 (2.803%), neg=0, invalid=96777 0082: dt=2.421053, rms=0.631 (0.100%), neg=0, invalid=96777 0083: dt=2.421053, rms=0.631 (-0.029%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.631, neg=0, invalid=96777 0084: dt=0.000000, rms=0.631 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.686, neg=0, invalid=96777 0085: dt=1.085714, rms=0.682 (0.545%), neg=0, invalid=96777 0086: dt=1.926380, rms=0.678 (0.700%), neg=0, invalid=96777 0087: dt=0.448000, rms=0.677 (0.052%), neg=0, invalid=96777 0088: dt=0.448000, rms=0.677 (0.031%), neg=0, invalid=96777 0089: dt=0.448000, rms=0.677 (0.020%), neg=0, invalid=96777 0090: dt=0.448000, rms=0.677 (-0.018%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.677, neg=0, invalid=96777 0091: dt=1.295455, rms=0.676 (0.173%), neg=0, invalid=96777 0092: dt=0.004000, rms=0.676 (0.001%), neg=0, invalid=96777 0093: dt=0.004000, rms=0.676 (0.000%), neg=0, invalid=96777 0094: dt=0.004000, rms=0.676 (-0.000%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.637, neg=0, invalid=96777 0095: dt=0.448000, rms=0.622 (2.355%), neg=0, invalid=96777 0096: dt=0.000000, rms=0.622 (0.008%), neg=0, invalid=96777 0097: dt=0.050000, rms=0.622 (-0.340%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.622, neg=0, invalid=96777 0098: dt=0.000000, rms=0.622 (0.000%), neg=0, invalid=96777 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.11339 (17) Left_Lateral_Ventricle (4): linear fit = 0.55 x + 0.0 (1546 voxels, overlap=0.005) Left_Lateral_Ventricle (4): linear fit = 0.55 x + 0.0 (1546 voxels, peak = 13), gca=13.1 gca peak = 0.14022 (22) mri peak = 0.11937 (17) Right_Lateral_Ventricle (43): linear fit = 0.68 x + 0.0 (720 voxels, overlap=0.208) Right_Lateral_Ventricle (43): linear fit = 0.68 x + 0.0 (720 voxels, peak = 15), gca=14.9 gca peak = 0.24234 (100) mri peak = 0.09836 (98) Right_Pallidum (52): linear fit = 0.96 x + 0.0 (448 voxels, overlap=0.780) Right_Pallidum (52): linear fit = 0.96 x + 0.0 (448 voxels, peak = 96), gca=96.5 gca peak = 0.19192 (97) mri peak = 0.08027 (86) Left_Pallidum (13): linear fit = 0.88 x + 0.0 (295 voxels, overlap=0.097) Left_Pallidum (13): linear fit = 0.88 x + 0.0 (295 voxels, peak = 85), gca=84.9 gca peak = 0.24007 (63) mri peak = 0.06510 (74) Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (878 voxels, overlap=0.709) Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (878 voxels, peak = 72), gca=71.5 gca peak = 0.29892 (64) mri peak = 0.09758 (68) Left_Hippocampus (17): linear fit = 1.05 x + 0.0 (775 voxels, overlap=0.874) Left_Hippocampus (17): linear fit = 1.05 x + 0.0 (775 voxels, peak = 68), gca=67.5 gca peak = 0.12541 (104) mri peak = 0.08794 (106) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (77538 voxels, overlap=0.812) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (77538 voxels, peak = 106), gca=105.6 gca peak = 0.13686 (104) mri peak = 0.09464 (108) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (78054 voxels, overlap=0.772) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (78054 voxels, peak = 107), gca=106.6 gca peak = 0.11691 (63) mri peak = 0.04233 (63) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (24187 voxels, overlap=0.997) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (24187 voxels, peak = 62), gca=62.1 gca peak = 0.13270 (63) mri peak = 0.04409 (63) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (25940 voxels, overlap=0.997) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (25940 voxels, peak = 63), gca=63.0 gca peak = 0.15182 (70) mri peak = 0.10241 (81) Right_Caudate (50): linear fit = 1.08 x + 0.0 (442 voxels, overlap=0.451) Right_Caudate (50): linear fit = 1.08 x + 0.0 (442 voxels, peak = 75), gca=75.2 gca peak = 0.14251 (76) mri peak = 0.08777 (84) Left_Caudate (11): linear fit = 1.04 x + 0.0 (782 voxels, overlap=0.551) Left_Caudate (11): linear fit = 1.04 x + 0.0 (782 voxels, peak = 79), gca=79.4 gca peak = 0.12116 (60) mri peak = 0.03916 (60) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (27500 voxels, overlap=0.977) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (27500 voxels, peak = 62), gca=61.5 gca peak = 0.12723 (61) mri peak = 0.04462 (61) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (29316 voxels, overlap=0.982) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (29316 voxels, peak = 63), gca=62.5 gca peak = 0.22684 (88) mri peak = 0.08484 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (9023 voxels, overlap=0.689) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (9023 voxels, peak = 94), gca=93.7 gca peak = 0.21067 (87) mri peak = 0.10361 (92) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (8511 voxels, overlap=0.731) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (8511 voxels, peak = 92), gca=91.8 gca peak = 0.25455 (62) mri peak = 0.08931 (71) Left_Amygdala (18): linear fit = 1.12 x + 0.0 (383 voxels, overlap=0.156) Left_Amygdala (18): linear fit = 1.12 x + 0.0 (383 voxels, peak = 69), gca=69.1 gca peak = 0.39668 (62) mri peak = 0.12531 (68) Right_Amygdala (54): linear fit = 1.11 x + 0.0 (399 voxels, overlap=0.387) Right_Amygdala (54): linear fit = 1.11 x + 0.0 (399 voxels, peak = 69), gca=68.5 gca peak = 0.10129 (93) mri peak = 0.06667 (104) Left_Thalamus_Proper (10): linear fit = 1.12 x + 0.0 (5640 voxels, overlap=0.514) Left_Thalamus_Proper (10): linear fit = 1.12 x + 0.0 (5640 voxels, peak = 104), gca=103.7 gca peak = 0.12071 (89) mri peak = 0.06343 (94) Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (4143 voxels, overlap=0.783) Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (4143 voxels, peak = 93), gca=93.0 gca peak = 0.13716 (82) mri peak = 0.05825 (89) Left_Putamen (12): linear fit = 1.07 x + 0.0 (2265 voxels, overlap=0.876) Left_Putamen (12): linear fit = 1.07 x + 0.0 (2265 voxels, peak = 87), gca=87.3 gca peak = 0.15214 (84) mri peak = 0.05826 (89) Right_Putamen (51): linear fit = 1.05 x + 0.0 (2545 voxels, overlap=0.916) Right_Putamen (51): linear fit = 1.05 x + 0.0 (2545 voxels, peak = 89), gca=88.6 gca peak = 0.08983 (85) mri peak = 0.06586 (92) Brain_Stem (16): linear fit = 1.09 x + 0.0 (13471 voxels, overlap=0.666) Brain_Stem (16): linear fit = 1.09 x + 0.0 (13471 voxels, peak = 92), gca=92.2 gca peak = 0.11809 (92) mri peak = 0.07624 (101) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (917 voxels, overlap=0.555) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (917 voxels, peak = 101), gca=100.7 gca peak = 0.12914 (94) mri peak = 0.08480 (101) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (1213 voxels, overlap=0.423) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (1213 voxels, peak = 102), gca=102.0 gca peak = 0.21100 (36) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13542 (27) mri peak = 0.18261 (20) Fourth_Ventricle (15): linear fit = 0.71 x + 0.0 (269 voxels, overlap=0.149) Fourth_Ventricle (15): linear fit = 0.71 x + 0.0 (269 voxels, peak = 19), gca=19.3 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21802 (40) gca peak Third_Ventricle = 0.21100 (36) gca peak CSF = 0.17123 (45) gca peak Left_Accumbens_area = 0.25875 (69) gca peak Left_undetermined = 0.96240 (36) gca peak Left_vessel = 0.33262 (65) gca peak Left_choroid_plexus = 0.09846 (46) gca peak Right_Inf_Lat_Vent = 0.28113 (34) gca peak Right_Accumbens_area = 0.27120 (72) gca peak Right_vessel = 0.61915 (60) gca peak Right_choroid_plexus = 0.12775 (51) gca peak Fifth_Ventricle = 0.45329 (44) gca peak WM_hypointensities = 0.11729 (81) gca peak non_WM_hypointensities = 0.10912 (56) gca peak Optic_Chiasm = 0.33287 (75) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 1.07 x + 0.0 estimating mean wm scale to be 1.02 x + 0.0 estimating mean csf scale to be 0.64 x + 0.0 saving intensity scales to talairach.label_intensities.txt **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.633, neg=0, invalid=96777 0099: dt=129.472000, rms=0.628 (0.774%), neg=0, invalid=96777 0100: dt=129.472000, rms=0.626 (0.238%), neg=0, invalid=96777 0101: dt=129.472000, rms=0.625 (0.202%), neg=0, invalid=96777 0102: dt=110.976000, rms=0.624 (0.125%), neg=0, invalid=96777 0103: dt=129.472000, rms=0.623 (0.140%), neg=0, invalid=96777 0104: dt=110.976000, rms=0.623 (0.088%), neg=0, invalid=96777 0105: dt=129.472000, rms=0.622 (0.104%), neg=0, invalid=96777 0106: dt=92.480000, rms=0.622 (0.065%), neg=0, invalid=96777 0107: dt=129.472000, rms=0.621 (0.088%), neg=0, invalid=96777 0108: dt=73.984000, rms=0.621 (0.051%), neg=0, invalid=96777 0109: dt=129.472000, rms=0.621 (0.071%), neg=0, invalid=96777 0110: dt=110.976000, rms=0.620 (0.041%), neg=0, invalid=96777 0111: dt=110.976000, rms=0.620 (0.060%), neg=0, invalid=96777 0112: dt=110.976000, rms=0.619 (0.085%), neg=0, invalid=96777 0113: dt=110.976000, rms=0.619 (0.098%), neg=0, invalid=96777 0114: dt=110.976000, rms=0.618 (0.120%), neg=0, invalid=96777 0115: dt=110.976000, rms=0.617 (0.125%), neg=0, invalid=96777 0116: dt=110.976000, rms=0.617 (0.099%), neg=0, invalid=96777 0117: dt=110.976000, rms=0.616 (0.101%), neg=0, invalid=96777 0118: dt=110.976000, rms=0.616 (0.088%), neg=0, invalid=96777 0119: dt=110.976000, rms=0.615 (0.107%), neg=0, invalid=96777 0120: dt=110.976000, rms=0.614 (0.091%), neg=0, invalid=96777 0121: dt=110.976000, rms=0.614 (0.081%), neg=0, invalid=96777 0122: dt=110.976000, rms=0.613 (0.086%), neg=0, invalid=96777 0123: dt=110.976000, rms=0.613 (0.080%), neg=0, invalid=96777 0124: dt=110.976000, rms=0.612 (0.094%), neg=0, invalid=96777 0125: dt=110.976000, rms=0.612 (0.092%), neg=0, invalid=96777 0126: dt=110.976000, rms=0.611 (0.092%), neg=0, invalid=96777 0127: dt=110.976000, rms=0.611 (0.068%), neg=0, invalid=96777 0128: dt=110.976000, rms=0.610 (0.068%), neg=0, invalid=96777 0129: dt=110.976000, rms=0.610 (0.058%), neg=0, invalid=96777 0130: dt=110.976000, rms=0.610 (0.064%), neg=0, invalid=96777 0131: dt=110.976000, rms=0.609 (0.070%), neg=0, invalid=96777 0132: dt=110.976000, rms=0.609 (0.047%), neg=0, invalid=96777 0133: dt=110.976000, rms=0.608 (0.064%), neg=0, invalid=96777 0134: dt=110.976000, rms=0.608 (0.040%), neg=0, invalid=96777 0135: dt=110.976000, rms=0.608 (0.057%), neg=0, invalid=96777 0136: dt=110.976000, rms=0.607 (0.054%), neg=0, invalid=96777 0137: dt=110.976000, rms=0.607 (0.051%), neg=0, invalid=96777 0138: dt=110.976000, rms=0.607 (0.042%), neg=0, invalid=96777 0139: dt=110.976000, rms=0.607 (0.060%), neg=0, invalid=96777 0140: dt=110.976000, rms=0.606 (0.055%), neg=0, invalid=96777 0141: dt=110.976000, rms=0.606 (0.035%), neg=0, invalid=96777 0142: dt=110.976000, rms=0.606 (0.044%), neg=0, invalid=96777 0143: dt=110.976000, rms=0.605 (0.044%), neg=0, invalid=96777 0144: dt=110.976000, rms=0.605 (0.051%), neg=0, invalid=96777 0145: dt=110.976000, rms=0.605 (0.036%), neg=0, invalid=96777 0146: dt=110.976000, rms=0.605 (0.057%), neg=0, invalid=96777 0147: dt=110.976000, rms=0.604 (0.046%), neg=0, invalid=96777 0148: dt=110.976000, rms=0.604 (0.041%), neg=0, invalid=96777 0149: dt=110.976000, rms=0.604 (0.032%), neg=0, invalid=96777 0150: dt=110.976000, rms=0.604 (0.033%), neg=0, invalid=96777 0151: dt=110.976000, rms=0.603 (0.037%), neg=0, invalid=96777 0152: dt=110.976000, rms=0.603 (0.039%), neg=0, invalid=96777 0153: dt=110.976000, rms=0.603 (0.033%), neg=0, invalid=96777 0154: dt=110.976000, rms=0.603 (0.040%), neg=0, invalid=96777 0155: dt=110.976000, rms=0.603 (0.034%), neg=0, invalid=96777 0156: dt=110.976000, rms=0.602 (0.029%), neg=0, invalid=96777 0157: dt=110.976000, rms=0.602 (0.023%), neg=0, invalid=96777 0158: dt=110.976000, rms=0.602 (0.028%), neg=0, invalid=96777 0159: dt=110.976000, rms=0.602 (0.034%), neg=0, invalid=96777 0160: dt=110.976000, rms=0.602 (0.038%), neg=0, invalid=96777 0161: dt=110.976000, rms=0.601 (0.032%), neg=0, invalid=96777 0162: dt=110.976000, rms=0.601 (0.027%), neg=0, invalid=96777 0163: dt=110.976000, rms=0.601 (0.022%), neg=0, invalid=96777 0164: dt=110.976000, rms=0.601 (0.018%), neg=0, invalid=96777 0165: dt=129.472000, rms=0.601 (0.009%), neg=0, invalid=96777 0166: dt=129.472000, rms=0.601 (0.000%), neg=0, invalid=96777 0167: dt=129.472000, rms=0.601 (0.006%), neg=0, invalid=96777 0168: dt=129.472000, rms=0.601 (0.009%), neg=0, invalid=96777 0169: dt=129.472000, rms=0.601 (0.006%), neg=0, invalid=96777 0170: dt=129.472000, rms=0.601 (0.006%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.601, neg=0, invalid=96777 0171: dt=295.936000, rms=0.600 (0.167%), neg=0, invalid=96777 0172: dt=110.976000, rms=0.600 (0.058%), neg=0, invalid=96777 0173: dt=129.472000, rms=0.599 (0.036%), neg=0, invalid=96777 0174: dt=129.472000, rms=0.599 (0.021%), neg=0, invalid=96777 0175: dt=129.472000, rms=0.599 (0.046%), neg=0, invalid=96777 0176: dt=129.472000, rms=0.599 (0.041%), neg=0, invalid=96777 0177: dt=129.472000, rms=0.598 (0.064%), neg=0, invalid=96777 0178: dt=129.472000, rms=0.598 (0.035%), neg=0, invalid=96777 0179: dt=129.472000, rms=0.598 (0.059%), neg=0, invalid=96777 0180: dt=129.472000, rms=0.598 (0.016%), neg=0, invalid=96777 0181: dt=129.472000, rms=0.597 (0.059%), neg=0, invalid=96777 0182: dt=129.472000, rms=0.597 (0.024%), neg=0, invalid=96777 0183: dt=129.472000, rms=0.597 (0.030%), neg=0, invalid=96777 0184: dt=129.472000, rms=0.597 (0.028%), neg=0, invalid=96777 0185: dt=129.472000, rms=0.597 (0.021%), neg=0, invalid=96777 0186: dt=129.472000, rms=0.597 (0.011%), neg=0, invalid=96777 0187: dt=129.472000, rms=0.596 (0.021%), neg=0, invalid=96777 0188: dt=129.472000, rms=0.596 (0.013%), neg=0, invalid=96777 0189: dt=129.472000, rms=0.596 (0.008%), neg=0, invalid=96777 0190: dt=129.472000, rms=0.596 (0.018%), neg=0, invalid=96777 0191: dt=129.472000, rms=0.596 (0.012%), neg=0, invalid=96777 0192: dt=129.472000, rms=0.596 (0.011%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.597, neg=0, invalid=96777 0193: dt=124.416000, rms=0.594 (0.501%), neg=0, invalid=96777 0194: dt=103.680000, rms=0.591 (0.472%), neg=0, invalid=96777 0195: dt=25.920000, rms=0.589 (0.423%), neg=0, invalid=96777 0196: dt=145.152000, rms=0.586 (0.430%), neg=0, invalid=96777 0197: dt=31.104000, rms=0.584 (0.386%), neg=0, invalid=96777 0198: dt=36.288000, rms=0.583 (0.175%), neg=0, invalid=96777 0199: dt=82.944000, rms=0.581 (0.260%), neg=0, invalid=96777 0200: dt=25.920000, rms=0.580 (0.196%), neg=0, invalid=96777 0201: dt=145.152000, rms=0.578 (0.349%), neg=0, invalid=96777 0202: dt=20.736000, rms=0.577 (0.233%), neg=0, invalid=96777 0203: dt=580.608000, rms=0.570 (1.103%), neg=0, invalid=96777 0204: dt=20.736000, rms=0.568 (0.485%), neg=0, invalid=96777 0205: dt=82.944000, rms=0.567 (0.204%), neg=0, invalid=96777 0206: dt=36.288000, rms=0.566 (0.075%), neg=0, invalid=96777 0207: dt=82.944000, rms=0.565 (0.142%), neg=0, invalid=96777 0208: dt=25.920000, rms=0.565 (0.079%), neg=0, invalid=96777 0209: dt=248.832000, rms=0.563 (0.280%), neg=0, invalid=96777 0210: dt=20.736000, rms=0.563 (0.118%), neg=0, invalid=96777 0211: dt=82.944000, rms=0.562 (0.102%), neg=0, invalid=96777 0212: dt=36.288000, rms=0.561 (0.106%), neg=0, invalid=96777 0213: dt=31.104000, rms=0.561 (0.021%), neg=0, invalid=96777 0214: dt=31.104000, rms=0.561 (0.059%), neg=0, invalid=96777 0215: dt=31.104000, rms=0.561 (0.081%), neg=0, invalid=96777 0216: dt=31.104000, rms=0.560 (0.102%), neg=0, invalid=96777 0217: dt=31.104000, rms=0.559 (0.113%), neg=0, invalid=96777 0218: dt=31.104000, rms=0.558 (0.151%), neg=0, invalid=96777 0219: dt=31.104000, rms=0.557 (0.183%), neg=0, invalid=96777 0220: dt=31.104000, rms=0.556 (0.181%), neg=0, invalid=96777 0221: dt=31.104000, rms=0.555 (0.179%), neg=0, invalid=96777 0222: dt=31.104000, rms=0.555 (0.167%), neg=0, invalid=96777 0223: dt=31.104000, rms=0.554 (0.182%), neg=0, invalid=96777 0224: dt=31.104000, rms=0.552 (0.184%), neg=0, invalid=96777 0225: dt=31.104000, rms=0.551 (0.181%), neg=0, invalid=96777 0226: dt=31.104000, rms=0.551 (0.175%), neg=0, invalid=96777 0227: dt=31.104000, rms=0.550 (0.155%), neg=0, invalid=96777 0228: dt=31.104000, rms=0.549 (0.141%), neg=0, invalid=96777 0229: dt=31.104000, rms=0.548 (0.147%), neg=0, invalid=96777 0230: dt=31.104000, rms=0.547 (0.127%), neg=0, invalid=96777 0231: dt=31.104000, rms=0.547 (0.107%), neg=0, invalid=96777 0232: dt=31.104000, rms=0.546 (0.097%), neg=0, invalid=96777 0233: dt=31.104000, rms=0.546 (0.116%), neg=0, invalid=96777 0234: dt=31.104000, rms=0.545 (0.119%), neg=0, invalid=96777 0235: dt=31.104000, rms=0.544 (0.110%), neg=0, invalid=96777 0236: dt=31.104000, rms=0.544 (0.088%), neg=0, invalid=96777 0237: dt=31.104000, rms=0.543 (0.092%), neg=0, invalid=96777 0238: dt=31.104000, rms=0.543 (0.089%), neg=0, invalid=96777 0239: dt=31.104000, rms=0.542 (0.097%), neg=0, invalid=96777 0240: dt=31.104000, rms=0.542 (0.097%), neg=0, invalid=96777 0241: dt=31.104000, rms=0.542 (0.069%), neg=0, invalid=96777 0242: dt=31.104000, rms=0.541 (0.084%), neg=0, invalid=96777 0243: dt=31.104000, rms=0.541 (0.081%), neg=0, invalid=96777 0244: dt=31.104000, rms=0.540 (0.082%), neg=0, invalid=96777 0245: dt=31.104000, rms=0.540 (0.089%), neg=0, invalid=96777 0246: dt=31.104000, rms=0.539 (0.065%), neg=0, invalid=96777 0247: dt=31.104000, rms=0.539 (0.079%), neg=0, invalid=96777 0248: dt=31.104000, rms=0.539 (0.077%), neg=0, invalid=96777 0249: dt=31.104000, rms=0.538 (0.070%), neg=0, invalid=96777 0250: dt=31.104000, rms=0.538 (0.054%), neg=0, invalid=96777 0251: dt=31.104000, rms=0.537 (0.070%), neg=0, invalid=96777 0252: dt=31.104000, rms=0.537 (0.066%), neg=0, invalid=96777 0253: dt=31.104000, rms=0.537 (0.063%), neg=0, invalid=96777 0254: dt=31.104000, rms=0.537 (0.050%), neg=0, invalid=96777 0255: dt=31.104000, rms=0.536 (0.046%), neg=0, invalid=96777 0256: dt=31.104000, rms=0.536 (0.045%), neg=0, invalid=96777 0257: dt=31.104000, rms=0.536 (0.043%), neg=0, invalid=96777 0258: dt=31.104000, rms=0.535 (0.054%), neg=0, invalid=96777 0259: dt=31.104000, rms=0.535 (0.059%), neg=0, invalid=96777 0260: dt=31.104000, rms=0.535 (0.048%), neg=0, invalid=96777 0261: dt=31.104000, rms=0.535 (0.032%), neg=0, invalid=96777 0262: dt=31.104000, rms=0.535 (0.031%), neg=0, invalid=96777 0263: dt=31.104000, rms=0.534 (0.053%), neg=0, invalid=96777 0264: dt=31.104000, rms=0.534 (0.049%), neg=0, invalid=96777 0265: dt=31.104000, rms=0.534 (0.033%), neg=0, invalid=96777 0266: dt=31.104000, rms=0.534 (0.023%), neg=0, invalid=96777 0267: dt=31.104000, rms=0.534 (0.038%), neg=0, invalid=96777 0268: dt=31.104000, rms=0.533 (0.044%), neg=0, invalid=96777 0269: dt=31.104000, rms=0.533 (0.041%), neg=0, invalid=96777 0270: dt=31.104000, rms=0.533 (0.037%), neg=0, invalid=96777 0271: dt=31.104000, rms=0.533 (0.024%), neg=0, invalid=96777 0272: dt=31.104000, rms=0.533 (0.035%), neg=0, invalid=96777 0273: dt=31.104000, rms=0.532 (0.028%), neg=0, invalid=96777 0274: dt=31.104000, rms=0.532 (0.030%), neg=0, invalid=96777 0275: dt=31.104000, rms=0.532 (0.039%), neg=0, invalid=96777 0276: dt=31.104000, rms=0.532 (0.039%), neg=0, invalid=96777 0277: dt=31.104000, rms=0.532 (0.035%), neg=0, invalid=96777 0278: dt=31.104000, rms=0.532 (0.025%), neg=0, invalid=96777 0279: dt=31.104000, rms=0.531 (0.018%), neg=0, invalid=96777 0280: dt=31.104000, rms=0.531 (0.010%), neg=0, invalid=96777 0281: dt=36.288000, rms=0.531 (0.025%), neg=0, invalid=96777 0282: dt=20.736000, rms=0.531 (0.002%), neg=0, invalid=96777 0283: dt=20.736000, rms=0.531 (0.012%), neg=0, invalid=96777 0284: dt=20.736000, rms=0.531 (0.006%), neg=0, invalid=96777 0285: dt=20.736000, rms=0.531 (0.005%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.531, neg=0, invalid=96777 0286: dt=145.152000, rms=0.529 (0.394%), neg=0, invalid=96777 0287: dt=36.288000, rms=0.529 (0.097%), neg=0, invalid=96777 0288: dt=36.288000, rms=0.528 (0.042%), neg=0, invalid=96777 0289: dt=36.288000, rms=0.528 (0.023%), neg=0, invalid=96777 0290: dt=36.288000, rms=0.528 (0.054%), neg=0, invalid=96777 0291: dt=36.288000, rms=0.527 (0.079%), neg=0, invalid=96777 0292: dt=36.288000, rms=0.527 (0.081%), neg=0, invalid=96777 0293: dt=36.288000, rms=0.527 (0.095%), neg=0, invalid=96777 0294: dt=36.288000, rms=0.526 (0.081%), neg=0, invalid=96777 0295: dt=36.288000, rms=0.526 (0.080%), neg=0, invalid=96777 0296: dt=36.288000, rms=0.525 (0.073%), neg=0, invalid=96777 0297: dt=36.288000, rms=0.525 (0.065%), neg=0, invalid=96777 0298: dt=36.288000, rms=0.525 (0.056%), neg=0, invalid=96777 0299: dt=36.288000, rms=0.524 (0.052%), neg=0, invalid=96777 0300: dt=36.288000, rms=0.524 (0.048%), neg=0, invalid=96777 0301: dt=36.288000, rms=0.524 (0.044%), neg=0, invalid=96777 0302: dt=36.288000, rms=0.524 (0.035%), neg=0, invalid=96777 0303: dt=36.288000, rms=0.523 (0.057%), neg=0, invalid=96777 0304: dt=36.288000, rms=0.523 (0.041%), neg=0, invalid=96777 0305: dt=36.288000, rms=0.523 (0.028%), neg=0, invalid=96777 0306: dt=36.288000, rms=0.523 (0.044%), neg=0, invalid=96777 0307: dt=36.288000, rms=0.523 (0.050%), neg=0, invalid=96777 0308: dt=36.288000, rms=0.522 (0.029%), neg=0, invalid=96777 0309: dt=36.288000, rms=0.522 (0.038%), neg=0, invalid=96777 0310: dt=36.288000, rms=0.522 (0.029%), neg=0, invalid=96777 0311: dt=36.288000, rms=0.522 (0.032%), neg=0, invalid=96777 0312: dt=36.288000, rms=0.522 (0.033%), neg=0, invalid=96777 0313: dt=36.288000, rms=0.521 (0.052%), neg=0, invalid=96777 0314: dt=36.288000, rms=0.521 (0.036%), neg=0, invalid=96777 0315: dt=36.288000, rms=0.521 (0.039%), neg=0, invalid=96777 0316: dt=36.288000, rms=0.521 (0.035%), neg=0, invalid=96777 0317: dt=36.288000, rms=0.521 (0.021%), neg=0, invalid=96777 0318: dt=36.288000, rms=0.521 (0.021%), neg=0, invalid=96777 0319: dt=36.288000, rms=0.521 (0.027%), neg=0, invalid=96777 0320: dt=36.288000, rms=0.520 (0.040%), neg=0, invalid=96777 0321: dt=36.288000, rms=0.520 (0.020%), neg=0, invalid=96777 0322: dt=36.288000, rms=0.520 (0.022%), neg=0, invalid=96777 0323: dt=36.288000, rms=0.520 (0.033%), neg=0, invalid=96777 0324: dt=36.288000, rms=0.520 (0.019%), neg=0, invalid=96777 0325: dt=36.288000, rms=0.520 (0.025%), neg=0, invalid=96777 0326: dt=36.288000, rms=0.520 (0.033%), neg=0, invalid=96777 0327: dt=36.288000, rms=0.519 (0.031%), neg=0, invalid=96777 0328: dt=36.288000, rms=0.519 (0.023%), neg=0, invalid=96777 0329: dt=36.288000, rms=0.519 (0.018%), neg=0, invalid=96777 0330: dt=15.552000, rms=0.519 (0.003%), neg=0, invalid=96777 0331: dt=15.552000, rms=0.519 (0.008%), neg=0, invalid=96777 0332: dt=15.552000, rms=0.519 (0.003%), neg=0, invalid=96777 0333: dt=15.552000, rms=0.519 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.527, neg=0, invalid=96777 0334: dt=25.600000, rms=0.526 (0.199%), neg=0, invalid=96777 0335: dt=44.800000, rms=0.524 (0.306%), neg=0, invalid=96777 0336: dt=32.000000, rms=0.522 (0.303%), neg=0, invalid=96777 0337: dt=9.600000, rms=0.522 (0.161%), neg=0, invalid=96777 0338: dt=25.600000, rms=0.520 (0.219%), neg=0, invalid=96777 0339: dt=7.607843, rms=0.520 (0.125%), neg=0, invalid=96777 0340: dt=44.800000, rms=0.518 (0.281%), neg=0, invalid=96777 0341: dt=8.936937, rms=0.517 (0.188%), neg=0, invalid=96777 0342: dt=38.400000, rms=0.516 (0.227%), neg=0, invalid=96777 0343: dt=7.796610, rms=0.515 (0.155%), neg=0, invalid=96777 0344: dt=38.400000, rms=0.514 (0.210%), neg=0, invalid=96777 0345: dt=8.323232, rms=0.514 (0.138%), neg=0, invalid=96777 0346: dt=25.600000, rms=0.513 (0.122%), neg=0, invalid=96777 0347: dt=9.600000, rms=0.512 (0.103%), neg=0, invalid=96777 0348: dt=11.200000, rms=0.512 (0.082%), neg=0, invalid=96777 0349: dt=38.400000, rms=0.511 (0.149%), neg=0, invalid=96777 0350: dt=7.472527, rms=0.511 (0.090%), neg=0, invalid=96777 0351: dt=179.200000, rms=0.508 (0.493%), neg=0, invalid=96777 0352: dt=11.970803, rms=0.506 (0.402%), neg=0, invalid=96777 0353: dt=9.600000, rms=0.506 (0.089%), neg=0, invalid=96777 0354: dt=38.400000, rms=0.505 (0.089%), neg=0, invalid=96777 0355: dt=11.200000, rms=0.505 (0.072%), neg=0, invalid=96777 0356: dt=11.200000, rms=0.505 (0.062%), neg=0, invalid=96777 0357: dt=11.200000, rms=0.504 (0.037%), neg=0, invalid=96777 0358: dt=11.200000, rms=0.504 (0.047%), neg=0, invalid=96777 0359: dt=11.200000, rms=0.504 (0.073%), neg=0, invalid=96777 0360: dt=11.200000, rms=0.503 (0.085%), neg=0, invalid=96777 0361: dt=11.200000, rms=0.503 (0.107%), neg=0, invalid=96777 0362: dt=11.200000, rms=0.502 (0.142%), neg=0, invalid=96777 0363: dt=11.200000, rms=0.501 (0.156%), neg=0, invalid=96777 0364: dt=11.200000, rms=0.501 (0.164%), neg=0, invalid=96777 0365: dt=11.200000, rms=0.500 (0.170%), neg=0, invalid=96777 0366: dt=11.200000, rms=0.499 (0.163%), neg=0, invalid=96777 0367: dt=11.200000, rms=0.498 (0.160%), neg=0, invalid=96777 0368: dt=11.200000, rms=0.497 (0.156%), neg=0, invalid=96777 0369: dt=11.200000, rms=0.497 (0.167%), neg=0, invalid=96777 0370: dt=11.200000, rms=0.496 (0.151%), neg=0, invalid=96777 0371: dt=11.200000, rms=0.495 (0.149%), neg=0, invalid=96777 0372: dt=11.200000, rms=0.494 (0.134%), neg=0, invalid=96777 0373: dt=11.200000, rms=0.494 (0.130%), neg=0, invalid=96777 0374: dt=11.200000, rms=0.493 (0.127%), neg=0, invalid=96777 0375: dt=11.200000, rms=0.493 (0.114%), neg=0, invalid=96777 0376: dt=11.200000, rms=0.492 (0.110%), neg=0, invalid=96777 0377: dt=11.200000, rms=0.491 (0.110%), neg=0, invalid=96777 0378: dt=11.200000, rms=0.491 (0.103%), neg=0, invalid=96777 0379: dt=11.200000, rms=0.491 (0.085%), neg=0, invalid=96777 0380: dt=11.200000, rms=0.490 (0.081%), neg=0, invalid=96777 0381: dt=11.200000, rms=0.490 (0.086%), neg=0, invalid=96777 0382: dt=11.200000, rms=0.489 (0.074%), neg=0, invalid=96777 0383: dt=11.200000, rms=0.489 (0.061%), neg=0, invalid=96777 0384: dt=11.200000, rms=0.489 (0.051%), neg=0, invalid=96777 0385: dt=11.200000, rms=0.489 (0.058%), neg=0, invalid=96777 0386: dt=11.200000, rms=0.488 (0.072%), neg=0, invalid=96777 0387: dt=11.200000, rms=0.488 (0.061%), neg=0, invalid=96777 0388: dt=11.200000, rms=0.488 (0.045%), neg=0, invalid=96777 0389: dt=11.200000, rms=0.487 (0.052%), neg=0, invalid=96777 0390: dt=11.200000, rms=0.487 (0.034%), neg=0, invalid=96777 0391: dt=11.200000, rms=0.487 (0.028%), neg=0, invalid=96777 0392: dt=11.200000, rms=0.487 (0.015%), neg=0, invalid=96777 0393: dt=11.200000, rms=0.487 (0.039%), neg=0, invalid=96777 0394: dt=11.200000, rms=0.487 (0.063%), neg=0, invalid=96777 0395: dt=11.200000, rms=0.486 (0.045%), neg=0, invalid=96777 0396: dt=11.200000, rms=0.486 (0.032%), neg=0, invalid=96777 0397: dt=11.200000, rms=0.486 (0.028%), neg=0, invalid=96777 0398: dt=11.200000, rms=0.486 (0.016%), neg=0, invalid=96777 0399: dt=11.200000, rms=0.486 (0.011%), neg=0, invalid=96777 0400: dt=25.600000, rms=0.486 (0.046%), neg=0, invalid=96777 0401: dt=6.400000, rms=0.486 (0.008%), neg=0, invalid=96777 0402: dt=6.400000, rms=0.486 (0.001%), neg=0, invalid=96777 0403: dt=6.400000, rms=0.486 (0.003%), neg=0, invalid=96777 0404: dt=6.400000, rms=0.486 (0.001%), neg=0, invalid=96777 0405: dt=6.400000, rms=0.486 (0.002%), neg=0, invalid=96777 0406: dt=6.400000, rms=0.486 (0.006%), neg=0, invalid=96777 0407: dt=6.400000, rms=0.486 (0.010%), neg=0, invalid=96777 0408: dt=6.400000, rms=0.486 (0.002%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.486, neg=0, invalid=96777 0409: dt=38.400000, rms=0.484 (0.279%), neg=0, invalid=96777 0410: dt=11.200000, rms=0.484 (0.124%), neg=0, invalid=96777 0411: dt=44.800000, rms=0.483 (0.114%), neg=0, invalid=96777 0412: dt=11.200000, rms=0.483 (0.039%), neg=0, invalid=96777 0413: dt=11.200000, rms=0.483 (0.022%), neg=0, invalid=96777 0414: dt=11.200000, rms=0.483 (0.031%), neg=0, invalid=96777 0415: dt=11.200000, rms=0.482 (0.021%), neg=0, invalid=96777 0416: dt=11.200000, rms=0.482 (0.033%), neg=0, invalid=96777 0417: dt=11.200000, rms=0.482 (0.028%), neg=0, invalid=96777 0418: dt=11.200000, rms=0.482 (0.018%), neg=0, invalid=96777 0419: dt=11.200000, rms=0.482 (-0.001%), neg=0, invalid=96777 0420: dt=19.200000, rms=0.482 (0.008%), neg=0, invalid=96777 0421: dt=11.200000, rms=0.482 (0.019%), neg=0, invalid=96777 0422: dt=19.200000, rms=0.482 (0.005%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.502, neg=0, invalid=96777 0423: dt=0.000000, rms=0.502 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.502, neg=0, invalid=96777 0424: dt=0.000000, rms=0.502 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.541, neg=0, invalid=96777 0425: dt=1.336735, rms=0.537 (0.766%), neg=0, invalid=96777 0426: dt=0.384000, rms=0.537 (0.027%), neg=0, invalid=96777 0427: dt=0.384000, rms=0.537 (-0.013%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.537, neg=0, invalid=96777 0428: dt=0.832000, rms=0.536 (0.116%), neg=0, invalid=96777 0429: dt=0.227273, rms=0.536 (0.007%), neg=0, invalid=96777 0430: dt=0.227273, rms=0.536 (-0.004%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.497, neg=0, invalid=96777 0431: dt=0.448000, rms=0.483 (2.929%), neg=0, invalid=96777 0432: dt=0.448000, rms=0.480 (0.553%), neg=0, invalid=96777 0433: dt=0.448000, rms=0.479 (0.361%), neg=0, invalid=96777 0434: dt=0.448000, rms=0.477 (0.232%), neg=0, invalid=96777 0435: dt=0.448000, rms=0.477 (0.170%), neg=0, invalid=96777 0436: dt=0.448000, rms=0.476 (0.122%), neg=0, invalid=96777 0437: dt=0.800000, rms=0.475 (0.166%), neg=0, invalid=96777 0438: dt=0.112000, rms=0.475 (0.024%), neg=0, invalid=96777 0439: dt=0.112000, rms=0.475 (0.020%), neg=0, invalid=96777 0440: dt=0.112000, rms=0.475 (0.031%), neg=0, invalid=96777 0441: dt=0.112000, rms=0.475 (0.040%), neg=0, invalid=96777 0442: dt=0.112000, rms=0.474 (0.048%), neg=0, invalid=96777 0443: dt=0.112000, rms=0.474 (0.050%), neg=0, invalid=96777 0444: dt=0.112000, rms=0.474 (0.056%), neg=0, invalid=96777 0445: dt=0.112000, rms=0.474 (0.059%), neg=0, invalid=96777 0446: dt=0.112000, rms=0.473 (0.053%), neg=0, invalid=96777 0447: dt=0.112000, rms=0.473 (0.046%), neg=0, invalid=96777 0448: dt=0.112000, rms=0.473 (0.046%), neg=0, invalid=96777 0449: dt=0.112000, rms=0.473 (0.038%), neg=0, invalid=96777 0450: dt=0.112000, rms=0.473 (0.035%), neg=0, invalid=96777 0451: dt=0.112000, rms=0.472 (0.029%), neg=0, invalid=96777 0452: dt=0.112000, rms=0.472 (0.020%), neg=0, invalid=96777 0453: dt=0.112000, rms=0.472 (0.018%), neg=0, invalid=96777 0454: dt=0.112000, rms=0.472 (0.001%), neg=0, invalid=96777 0455: dt=0.112000, rms=0.472 (-0.002%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.472, neg=0, invalid=96777 0456: dt=0.448000, rms=0.468 (0.989%), neg=0, invalid=96777 0457: dt=0.384000, rms=0.468 (0.002%), neg=0, invalid=96777 0458: dt=0.384000, rms=0.468 (0.002%), neg=0, invalid=96777 0459: dt=0.384000, rms=0.468 (-0.016%), neg=0, invalid=96777 label assignment complete, 0 changed (0.00%) ********************************************************************************************* ********************************************************************************************* ********************************************************************************************* ********************* ALLOWING NEGATIVE NODES IN DEFORMATION ******************************** ********************************************************************************************* ********************************************************************************************* ********************************************************************************************* **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.465, neg=0, invalid=96777 0460: dt=0.000000, rms=0.465 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.465, neg=0, invalid=96777 0461: dt=129.472000, rms=0.465 (0.062%), neg=0, invalid=96777 0462: dt=110.976000, rms=0.465 (0.033%), neg=0, invalid=96777 0463: dt=110.976000, rms=0.465 (0.012%), neg=0, invalid=96777 0464: dt=110.976000, rms=0.465 (0.036%), neg=0, invalid=96777 0465: dt=110.976000, rms=0.465 (0.031%), neg=0, invalid=96777 0466: dt=110.976000, rms=0.464 (0.025%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.465, neg=0, invalid=96777 0467: dt=25.920000, rms=0.464 (0.028%), neg=0, invalid=96777 0468: dt=25.920000, rms=0.464 (0.008%), neg=0, invalid=96777 0469: dt=25.920000, rms=0.464 (0.011%), neg=0, invalid=96777 0470: dt=25.920000, rms=0.464 (-0.007%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.464, neg=0, invalid=96777 0471: dt=145.152000, rms=0.462 (0.430%), neg=0, invalid=96777 0472: dt=36.288000, rms=0.462 (0.135%), neg=0, invalid=96777 0473: dt=36.288000, rms=0.461 (0.050%), neg=0, invalid=96777 0474: dt=36.288000, rms=0.461 (0.069%), neg=0, invalid=96777 0475: dt=36.288000, rms=0.461 (0.089%), neg=0, invalid=96777 0476: dt=36.288000, rms=0.460 (0.116%), neg=0, invalid=96777 0477: dt=36.288000, rms=0.460 (0.141%), neg=0, invalid=96777 0478: dt=36.288000, rms=0.459 (0.138%), neg=0, invalid=96777 0479: dt=36.288000, rms=0.458 (0.116%), neg=0, invalid=96777 0480: dt=36.288000, rms=0.458 (0.093%), neg=0, invalid=96777 0481: dt=25.920000, rms=0.458 (0.011%), neg=0, invalid=96777 0482: dt=25.920000, rms=0.458 (0.004%), neg=0, invalid=96777 0483: dt=25.920000, rms=0.458 (0.021%), neg=0, invalid=96777 0484: dt=25.920000, rms=0.458 (0.020%), neg=0, invalid=96777 0485: dt=25.920000, rms=0.458 (0.024%), neg=0, invalid=96777 0486: dt=25.920000, rms=0.457 (0.032%), neg=0, invalid=96777 0487: dt=25.920000, rms=0.457 (0.028%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.458, neg=0, invalid=96777 iter 0, gcam->neg = 4 after 6 iterations, nbhd size=1, neg = 0 0488: dt=32.000000, rms=0.456 (0.361%), neg=0, invalid=96777 0489: dt=11.200000, rms=0.455 (0.157%), neg=0, invalid=96777 0490: dt=11.200000, rms=0.455 (0.163%), neg=0, invalid=96777 0491: dt=11.200000, rms=0.454 (0.203%), neg=0, invalid=96777 0492: dt=11.200000, rms=0.453 (0.228%), neg=0, invalid=96777 0493: dt=11.200000, rms=0.452 (0.209%), neg=0, invalid=96777 0494: dt=11.200000, rms=0.451 (0.220%), neg=0, invalid=96777 0495: dt=11.200000, rms=0.450 (0.187%), neg=0, invalid=96777 0496: dt=11.200000, rms=0.449 (0.175%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0497: dt=11.200000, rms=0.448 (0.186%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0498: dt=11.200000, rms=0.447 (0.210%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0499: dt=11.200000, rms=0.446 (0.192%), neg=0, invalid=96777 0500: dt=11.200000, rms=0.446 (0.180%), neg=0, invalid=96777 0501: dt=11.200000, rms=0.445 (0.156%), neg=0, invalid=96777 0502: dt=11.200000, rms=0.444 (0.182%), neg=0, invalid=96777 0503: dt=11.200000, rms=0.443 (0.139%), neg=0, invalid=96777 0504: dt=11.200000, rms=0.443 (0.129%), neg=0, invalid=96777 0505: dt=11.200000, rms=0.442 (0.116%), neg=0, invalid=96777 0506: dt=11.200000, rms=0.442 (0.116%), neg=0, invalid=96777 0507: dt=11.200000, rms=0.441 (0.090%), neg=0, invalid=96777 0508: dt=8.000000, rms=0.441 (0.025%), neg=0, invalid=96777 0509: dt=8.000000, rms=0.441 (0.017%), neg=0, invalid=96777 0510: dt=8.000000, rms=0.441 (0.029%), neg=0, invalid=96777 0511: dt=8.000000, rms=0.441 (0.027%), neg=0, invalid=96777 0512: dt=8.000000, rms=0.441 (0.028%), neg=0, invalid=96777 0513: dt=8.000000, rms=0.441 (0.033%), neg=0, invalid=96777 0514: dt=8.000000, rms=0.441 (0.023%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.441, neg=0, invalid=96777 0515: dt=44.800000, rms=0.438 (0.660%), neg=0, invalid=96777 0516: dt=11.200000, rms=0.437 (0.125%), neg=0, invalid=96777 0517: dt=11.200000, rms=0.437 (0.075%), neg=0, invalid=96777 0518: dt=11.200000, rms=0.436 (0.097%), neg=0, invalid=96777 0519: dt=11.200000, rms=0.436 (0.129%), neg=0, invalid=96777 0520: dt=11.200000, rms=0.435 (0.123%), neg=0, invalid=96777 0521: dt=11.200000, rms=0.435 (0.102%), neg=0, invalid=96777 0522: dt=11.200000, rms=0.435 (0.029%), neg=0, invalid=96777 0523: dt=11.200000, rms=0.435 (0.020%), neg=0, invalid=96777 0524: dt=11.200000, rms=0.435 (0.028%), neg=0, invalid=96777 0525: dt=11.200000, rms=0.434 (0.041%), neg=0, invalid=96777 0526: dt=11.200000, rms=0.434 (0.036%), neg=0, invalid=96777 0527: dt=11.200000, rms=0.434 (0.046%), neg=0, invalid=96777 0528: dt=11.200000, rms=0.434 (0.055%), neg=0, invalid=96777 0529: dt=11.200000, rms=0.434 (0.050%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.439, neg=0, invalid=96777 0530: dt=0.252000, rms=0.439 (-0.003%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.439, neg=0, invalid=96777 0531: dt=2.880000, rms=0.438 (0.028%), neg=0, invalid=96777 0532: dt=2.304000, rms=0.438 (0.012%), neg=0, invalid=96777 0533: dt=2.304000, rms=0.438 (-0.000%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.447, neg=0, invalid=96777 0534: dt=0.448000, rms=0.447 (0.053%), neg=0, invalid=96777 0535: dt=0.384000, rms=0.447 (0.008%), neg=0, invalid=96777 0536: dt=0.384000, rms=0.447 (-0.008%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.447, neg=0, invalid=96777 0537: dt=1.280000, rms=0.446 (0.135%), neg=0, invalid=96777 0538: dt=0.448000, rms=0.446 (0.015%), neg=0, invalid=96777 0539: dt=0.448000, rms=0.446 (-0.005%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.437, neg=0, invalid=96777 iter 0, gcam->neg = 565 after 11 iterations, nbhd size=1, neg = 0 0540: dt=1.899000, rms=0.404 (7.507%), neg=0, invalid=96777 0541: dt=0.000250, rms=0.404 (0.004%), neg=0, invalid=96777 0542: dt=0.000250, rms=0.404 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.404, neg=0, invalid=96777 0543: dt=0.000750, rms=0.404 (0.001%), neg=0, invalid=96777 0544: dt=0.000000, rms=0.404 (0.001%), neg=0, invalid=96777 0545: dt=0.000000, rms=0.404 (0.000%), neg=0, invalid=96777 label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.390, neg=0, invalid=96777 0546: dt=0.000000, rms=0.391 (-0.189%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.391, neg=0, invalid=96777 0547: dt=32.368000, rms=0.391 (0.003%), neg=0, invalid=96777 0548: dt=32.368000, rms=0.391 (0.001%), neg=0, invalid=96777 0549: dt=32.368000, rms=0.391 (0.001%), neg=0, invalid=96777 0550: dt=32.368000, rms=0.391 (0.000%), neg=0, invalid=96777 0551: dt=32.368000, rms=0.391 (-0.001%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.391, neg=0, invalid=96777 0552: dt=0.000000, rms=0.391 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.391, neg=0, invalid=96777 0553: dt=82.944000, rms=0.391 (0.038%), neg=0, invalid=96777 0554: dt=145.152000, rms=0.390 (0.046%), neg=0, invalid=96777 0555: dt=36.288000, rms=0.390 (0.010%), neg=0, invalid=96777 0556: dt=36.288000, rms=0.390 (0.008%), neg=0, invalid=96777 0557: dt=36.288000, rms=0.390 (0.013%), neg=0, invalid=96777 0558: dt=36.288000, rms=0.390 (0.016%), neg=0, invalid=96777 0559: dt=36.288000, rms=0.390 (0.018%), neg=0, invalid=96777 0560: dt=36.288000, rms=0.390 (0.017%), neg=0, invalid=96777 0561: dt=36.288000, rms=0.390 (0.014%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.391, neg=0, invalid=96777 0562: dt=8.000000, rms=0.391 (0.029%), neg=0, invalid=96777 0563: dt=2.800000, rms=0.391 (0.004%), neg=0, invalid=96777 0564: dt=2.800000, rms=0.391 (0.004%), neg=0, invalid=96777 0565: dt=2.800000, rms=0.391 (0.001%), neg=0, invalid=96777 0566: dt=2.800000, rms=0.391 (-0.013%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.391, neg=0, invalid=96777 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0567: dt=44.800000, rms=0.389 (0.340%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 5 iterations, nbhd size=1, neg = 0 0568: dt=25.600000, rms=0.388 (0.207%), neg=0, invalid=96777 0569: dt=25.600000, rms=0.388 (0.063%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0570: dt=25.600000, rms=0.388 (0.145%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0571: dt=25.600000, rms=0.387 (0.137%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0572: dt=25.600000, rms=0.387 (0.156%), neg=0, invalid=96777 iter 0, gcam->neg = 6 after 6 iterations, nbhd size=1, neg = 0 0573: dt=25.600000, rms=0.386 (0.232%), neg=0, invalid=96777 iter 0, gcam->neg = 7 after 8 iterations, nbhd size=1, neg = 0 0574: dt=25.600000, rms=0.385 (0.148%), neg=0, invalid=96777 iter 0, gcam->neg = 7 after 6 iterations, nbhd size=1, neg = 0 0575: dt=25.600000, rms=0.384 (0.196%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0576: dt=25.600000, rms=0.384 (0.059%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 6 iterations, nbhd size=1, neg = 0 0577: dt=25.600000, rms=0.384 (0.087%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0578: dt=25.600000, rms=0.383 (0.146%), neg=0, invalid=96777 iter 0, gcam->neg = 5 after 7 iterations, nbhd size=1, neg = 0 0579: dt=25.600000, rms=0.383 (0.075%), neg=0, invalid=96777 iter 0, gcam->neg = 6 after 7 iterations, nbhd size=1, neg = 0 0580: dt=25.600000, rms=0.383 (0.047%), neg=0, invalid=96777 0581: dt=32.000000, rms=0.382 (0.136%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 6 iterations, nbhd size=1, neg = 0 0582: dt=38.400000, rms=0.382 (0.082%), neg=0, invalid=96777 0583: dt=38.400000, rms=0.382 (0.046%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 14 iterations, nbhd size=2, neg = 0 0584: dt=38.400000, rms=0.382 (0.022%), neg=0, invalid=96777 iter 0, gcam->neg = 32 after 37 iterations, nbhd size=3, neg = 0 0585: dt=38.400000, rms=0.382 (-0.046%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.385, neg=0, invalid=96777 0586: dt=0.864000, rms=0.385 (0.003%), neg=0, invalid=96777 0587: dt=1.008000, rms=0.385 (0.004%), neg=0, invalid=96777 0588: dt=0.252000, rms=0.385 (0.000%), neg=0, invalid=96777 0589: dt=0.252000, rms=0.385 (0.000%), neg=0, invalid=96777 0590: dt=0.252000, rms=0.385 (-0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.385, neg=0, invalid=96777 iter 0, gcam->neg = 5 after 6 iterations, nbhd size=1, neg = 0 0591: dt=4.032000, rms=0.385 (0.056%), neg=0, invalid=96777 0592: dt=0.576000, rms=0.385 (0.001%), neg=0, invalid=96777 0593: dt=0.576000, rms=0.385 (0.006%), neg=0, invalid=96777 0594: dt=0.576000, rms=0.385 (0.010%), neg=0, invalid=96777 0595: dt=0.576000, rms=0.385 (0.011%), neg=0, invalid=96777 0596: dt=0.576000, rms=0.385 (0.006%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0597: dt=0.576000, rms=0.385 (0.002%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.392, neg=0, invalid=96777 0598: dt=0.000000, rms=0.392 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.392, neg=0, invalid=96777 0599: dt=0.000000, rms=0.392 (0.000%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.381, neg=0, invalid=96777 iter 0, gcam->neg = 616 after 35 iterations, nbhd size=3, neg = 0 0600: dt=1.004587, rms=0.368 (3.234%), neg=0, invalid=96777 0601: dt=0.000078, rms=0.368 (0.001%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0602: dt=0.000078, rms=0.368 (0.000%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0603: dt=0.000078, rms=0.368 (0.000%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0604: dt=0.000078, rms=0.368 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.368, neg=0, invalid=96777 0605: dt=0.000438, rms=0.368 (0.000%), neg=0, invalid=96777 0606: dt=0.000000, rms=0.368 (0.000%), neg=0, invalid=96777 writing output transformation to transforms/talairach.m3z... GCAMwrite registration took 1 hours, 49 minutes and 15 seconds. #-------------------------------------- #@# CA Reg Inv Tue Aug 29 18:13:54 CEST 2017 /root/Scrivania/subjects/ENP30S001A/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z Inverting GCAM Saving inverse #-------------------------------------- #@# Remove Neck Tue Aug 29 18:14:32 CEST 2017 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2008-03-26.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... removing structures at least 25 mm from brain... 11060657 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 0 minutes and 40 seconds. #-------------------------------------- #@# SkullLTA Tue Aug 29 18:15:13 CEST 2017 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull_2.lta ======= NUMBER OF OPENMP THREADS = 1 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 5 using previously computed transform transforms/talairach.lta reading 1 input volumes... logging results to talairach_with_skull_2.log reading '/usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu_noneck.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=10.0 skull bounding box = (46, 59, 24) --> (206, 240, 224) using (99, 119, 124) as brain centroid... mean wm in atlas = 126, using box (79,97,99) --> (118, 141,148) to find MRI wm before smoothing, mri peak at 105 after smoothing, mri peak at 105, scaling input intensities by 1.200 scaling channel 0 by 1.2 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-3.9 (thresh=-3.9) 1.008 0.123 -0.020 -16.612; -0.103 1.119 0.243 -50.631; 0.046 -0.204 0.999 13.847; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 1 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-4.0 (thresh=-4.0) 0.990 0.115 0.013 -17.013; -0.106 1.145 0.215 -52.552; 0.010 -0.174 1.026 12.904; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 0.990 0.115 0.013 -17.013; -0.106 1.145 0.215 -52.552; 0.010 -0.174 1.026 12.904; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 3 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 0.990 0.115 0.013 -17.013; -0.106 1.143 0.214 -52.145; 0.010 -0.174 1.027 12.794; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 0.990 0.115 0.013 -17.013; -0.106 1.143 0.214 -52.145; 0.010 -0.174 1.029 12.576; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3481 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.98977 0.11511 0.01295 -17.01270; -0.10588 1.14264 0.21442 -52.14524; 0.00965 -0.17411 1.02927 12.57591; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 0.98977 0.11511 0.01295 -17.01270; -0.10588 1.14264 0.21442 -52.14524; 0.00965 -0.17411 1.02927 12.57591; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 006: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.990 0.115 0.013 -17.013; -0.106 1.143 0.214 -52.145; 0.010 -0.174 1.029 12.576; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.9 (old=-3.9) transform before final EM align: 0.990 0.115 0.013 -17.013; -0.106 1.143 0.214 -52.145; 0.010 -0.174 1.029 12.576; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 382743 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.98977 0.11511 0.01295 -17.01270; -0.10588 1.14264 0.21442 -52.14524; 0.00965 -0.17411 1.02927 12.57591; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 0.98977 0.11511 0.01295 -17.01270; -0.10588 1.14264 0.21442 -52.14524; 0.00965 -0.17411 1.02927 12.57591; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = 4.4 tol 0.000000 final transform: 0.990 0.115 0.013 -17.013; -0.106 1.143 0.214 -52.145; 0.010 -0.174 1.029 12.576; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull_2.lta... registration took 13 minutes and 20 seconds. #-------------------------------------- #@# SubCort Seg Tue Aug 29 18:28:32 CEST 2017 mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.mgz --diff aseg.manedit.mgz $Id: mri_seg_diff.c,v 1.5 2011/03/02 00:04:24 nicks Exp $ cwd /root/Scrivania/subjects/ENP30S001A/mri cmdline mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.mgz --diff aseg.manedit.mgz sysname Linux hostname Braindata machine x86_64 user root Seg1 aseg.auto.mgz Seg2 aseg.mgz Diff aseg.manedit.mgz InDiff (null) Merged (null) ForceDiff 0 Computing difference between segmentations No difference found. mri_ca_label -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz sysname Linux hostname Braindata machine x86_64 setenv SUBJECTS_DIR /root/Scrivania/subjects cd /root/Scrivania/subjects/ENP30S001A/mri mri_ca_label -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes... reading classifier array from /usr/local/freesurfer/average/RB_all_2008-03-26.gca... reading input volume from norm.mgz... average std[0] = 6.9 reading transform from transforms/talairach.m3z... Atlas used for the 3D morph was /usr/local/freesurfer/average/RB_all_2008-03-26.gca average std = 6.9 using min determinant for regularization = 4.7 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15151 (27) mri peak = 0.10621 (17) Left_Lateral_Ventricle (4): linear fit = 0.67 x + 0.0 (539 voxels, overlap=0.068) Left_Lateral_Ventricle (4): linear fit = 0.67 x + 0.0 (539 voxels, peak = 18), gca=18.0 gca peak = 0.14982 (20) mri peak = 0.14418 (17) Right_Lateral_Ventricle (43): linear fit = 0.71 x + 0.0 (480 voxels, overlap=0.398) Right_Lateral_Ventricle (43): linear fit = 0.71 x + 0.0 (480 voxels, peak = 14), gca=14.3 gca peak = 0.28003 (97) mri peak = 0.14546 (98) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (325 voxels, overlap=1.019) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (325 voxels, peak = 96), gca=95.5 gca peak = 0.18160 (96) mri peak = 0.08548 (88) Left_Pallidum (13): linear fit = 0.94 x + 0.0 (154 voxels, overlap=0.912) Left_Pallidum (13): linear fit = 0.94 x + 0.0 (154 voxels, peak = 91), gca=90.7 gca peak = 0.27536 (62) mri peak = 0.09314 (67) Right_Hippocampus (53): linear fit = 1.07 x + 0.0 (788 voxels, overlap=0.726) Right_Hippocampus (53): linear fit = 1.07 x + 0.0 (788 voxels, peak = 66), gca=66.0 gca peak = 0.32745 (63) mri peak = 0.11444 (68) Left_Hippocampus (17): linear fit = 1.07 x + 0.0 (900 voxels, overlap=1.007) Left_Hippocampus (17): linear fit = 1.07 x + 0.0 (900 voxels, peak = 67), gca=67.1 gca peak = 0.08597 (105) mri peak = 0.08675 (106) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (57425 voxels, overlap=0.743) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (57425 voxels, peak = 107), gca=106.6 gca peak = 0.09209 (106) mri peak = 0.09645 (108) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (58838 voxels, overlap=0.703) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (58838 voxels, peak = 108), gca=107.6 gca peak = 0.07826 (63) mri peak = 0.04755 (63) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (20006 voxels, overlap=0.921) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (20006 voxels, peak = 62), gca=62.1 gca peak = 0.08598 (64) mri peak = 0.04507 (60) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (18139 voxels, overlap=0.940) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (18139 voxels, peak = 63), gca=63.0 gca peak = 0.24164 (71) mri peak = 0.11489 (81) Right_Caudate (50): linear fit = 1.08 x + 0.0 (724 voxels, overlap=0.447) Right_Caudate (50): linear fit = 1.08 x + 0.0 (724 voxels, peak = 76), gca=76.3 gca peak = 0.18227 (75) mri peak = 0.11054 (81) Left_Caudate (11): linear fit = 1.05 x + 0.0 (963 voxels, overlap=0.693) Left_Caudate (11): linear fit = 1.05 x + 0.0 (963 voxels, peak = 79), gca=79.1 gca peak = 0.10629 (62) mri peak = 0.04631 (62) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (22881 voxels, overlap=0.977) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (22881 voxels, peak = 64), gca=63.5 gca peak = 0.11668 (59) mri peak = 0.05203 (64) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (22676 voxels, overlap=0.972) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (22676 voxels, peak = 60), gca=60.5 gca peak = 0.17849 (88) mri peak = 0.11564 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (6188 voxels, overlap=0.722) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (6188 voxels, peak = 93), gca=92.8 gca peak = 0.16819 (86) mri peak = 0.12368 (92) Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (5867 voxels, overlap=0.827) Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (5867 voxels, peak = 90), gca=89.9 gca peak = 0.41688 (64) mri peak = 0.09705 (74) Left_Amygdala (18): linear fit = 1.16 x + 0.0 (287 voxels, overlap=0.056) Left_Amygdala (18): linear fit = 1.16 x + 0.0 (287 voxels, peak = 75), gca=74.6 gca peak = 0.42394 (62) mri peak = 0.11856 (72) Right_Amygdala (54): linear fit = 1.13 x + 0.0 (319 voxels, overlap=0.061) Right_Amygdala (54): linear fit = 1.13 x + 0.0 (319 voxels, peak = 70), gca=70.4 gca peak = 0.10041 (96) mri peak = 0.07555 (97) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (3963 voxels, overlap=0.664) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (3963 voxels, peak = 102), gca=102.2 gca peak = 0.13978 (88) mri peak = 0.08098 (94) Right_Thalamus_Proper (49): linear fit = 1.05 x + 0.0 (3614 voxels, overlap=0.872) Right_Thalamus_Proper (49): linear fit = 1.05 x + 0.0 (3614 voxels, peak = 93), gca=92.8 gca peak = 0.08514 (81) mri peak = 0.07270 (88) Left_Putamen (12): linear fit = 1.03 x + 0.0 (1245 voxels, overlap=0.831) Left_Putamen (12): linear fit = 1.03 x + 0.0 (1245 voxels, peak = 84), gca=83.8 gca peak = 0.09624 (82) mri peak = 0.07603 (85) Right_Putamen (51): linear fit = 1.05 x + 0.0 (1682 voxels, overlap=0.747) Right_Putamen (51): linear fit = 1.05 x + 0.0 (1682 voxels, peak = 87), gca=86.5 gca peak = 0.07543 (88) mri peak = 0.06935 (92) Brain_Stem (16): linear fit = 1.07 x + 0.0 (12279 voxels, overlap=0.687) Brain_Stem (16): linear fit = 1.07 x + 0.0 (12279 voxels, peak = 94), gca=93.7 gca peak = 0.12757 (95) mri peak = 0.07476 (104) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1278 voxels, overlap=0.616) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1278 voxels, peak = 103), gca=103.1 gca peak = 0.17004 (92) mri peak = 0.08651 (101) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (1301 voxels, overlap=0.537) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (1301 voxels, peak = 100), gca=99.8 gca peak = 0.21361 (36) mri peak = 0.11422 (22) gca peak = 0.26069 (23) mri peak = 0.17362 (19) Fourth_Ventricle (15): linear fit = 0.77 x + 0.0 (90 voxels, overlap=0.603) Fourth_Ventricle (15): linear fit = 0.77 x + 0.0 (90 voxels, peak = 18), gca=17.8 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.31795 (35) gca peak Third_Ventricle = 0.21361 (36) gca peak CSF = 0.14367 (38) gca peak Left_Accumbens_area = 0.57033 (70) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65201 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.31129 (32) gca peak Right_Accumbens_area = 0.30219 (72) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.72939 (42) gca peak WM_hypointensities = 0.14821 (82) gca peak non_WM_hypointensities = 0.10354 (53) gca peak Optic_Chiasm = 0.34849 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.07 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 0.72 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.19757 (18) mri peak = 0.10621 (17) Left_Lateral_Ventricle (4): linear fit = 0.95 x + 0.0 (539 voxels, overlap=0.941) Left_Lateral_Ventricle (4): linear fit = 0.95 x + 0.0 (539 voxels, peak = 17), gca=17.2 gca peak = 0.19392 (15) mri peak = 0.14418 (17) Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (480 voxels, overlap=0.887) Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (480 voxels, peak = 15), gca=15.4 gca peak = 0.32703 (96) mri peak = 0.14546 (98) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (325 voxels, overlap=1.010) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (325 voxels, peak = 97), gca=97.4 gca peak = 0.19619 (91) mri peak = 0.08548 (88) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (154 voxels, overlap=1.004) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (154 voxels, peak = 91), gca=91.5 gca peak = 0.24887 (66) mri peak = 0.09314 (67) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (788 voxels, overlap=1.005) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (788 voxels, peak = 66), gca=66.0 gca peak = 0.28946 (67) mri peak = 0.11444 (68) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (900 voxels, overlap=1.003) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (900 voxels, peak = 67), gca=67.0 gca peak = 0.08542 (107) mri peak = 0.08675 (106) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (57425 voxels, overlap=0.780) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (57425 voxels, peak = 106), gca=106.5 gca peak = 0.08742 (107) mri peak = 0.09645 (108) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (58838 voxels, overlap=0.730) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (58838 voxels, peak = 107), gca=107.0 gca peak = 0.07876 (62) mri peak = 0.04755 (63) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (20006 voxels, overlap=0.949) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (20006 voxels, peak = 64), gca=63.5 gca peak = 0.08738 (63) mri peak = 0.04507 (60) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (18139 voxels, overlap=0.960) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (18139 voxels, peak = 62), gca=62.1 gca peak = 0.27738 (79) mri peak = 0.11489 (81) Right_Caudate (50): linear fit = 1.01 x + 0.0 (724 voxels, overlap=1.002) Right_Caudate (50): linear fit = 1.01 x + 0.0 (724 voxels, peak = 80), gca=80.2 gca peak = 0.18126 (79) mri peak = 0.11054 (81) Left_Caudate (11): linear fit = 1.00 x + 0.0 (963 voxels, overlap=0.953) Left_Caudate (11): linear fit = 1.00 x + 0.0 (963 voxels, peak = 79), gca=79.0 gca peak = 0.10281 (63) mri peak = 0.04631 (62) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (22881 voxels, overlap=0.992) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (22881 voxels, peak = 65), gca=64.6 gca peak = 0.12584 (61) mri peak = 0.05203 (64) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (22676 voxels, overlap=0.991) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (22676 voxels, peak = 63), gca=62.5 gca peak = 0.17071 (92) mri peak = 0.11564 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6188 voxels, overlap=0.971) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6188 voxels, peak = 92), gca=91.5 gca peak = 0.15955 (90) mri peak = 0.12368 (92) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5867 voxels, overlap=0.981) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5867 voxels, peak = 90), gca=89.6 gca peak = 0.29786 (74) mri peak = 0.09705 (74) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (287 voxels, overlap=1.004) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (287 voxels, peak = 75), gca=75.1 gca peak = 0.30975 (71) mri peak = 0.11856 (72) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (319 voxels, overlap=1.007) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (319 voxels, peak = 71), gca=71.0 gca peak = 0.11099 (102) mri peak = 0.07555 (97) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3963 voxels, overlap=0.930) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3963 voxels, peak = 103), gca=102.5 gca peak = 0.10579 (93) mri peak = 0.08098 (94) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3614 voxels, overlap=0.912) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3614 voxels, peak = 93), gca=93.5 gca peak = 0.08482 (85) mri peak = 0.07270 (88) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1245 voxels, overlap=0.950) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1245 voxels, peak = 85), gca=84.6 gca peak = 0.10379 (80) mri peak = 0.07603 (85) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1682 voxels, overlap=0.922) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1682 voxels, peak = 79), gca=78.8 gca peak = 0.06628 (88) mri peak = 0.06935 (92) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12279 voxels, overlap=0.844) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12279 voxels, peak = 88), gca=88.0 gca peak = 0.10874 (99) mri peak = 0.07476 (104) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1278 voxels, overlap=0.815) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1278 voxels, peak = 99), gca=99.0 gca peak = 0.17076 (100) mri peak = 0.08651 (101) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1301 voxels, overlap=0.872) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1301 voxels, peak = 100), gca=100.5 gca peak = 0.25515 (27) mri peak = 0.11422 (22) gca peak = 0.27522 (18) mri peak = 0.17362 (19) Fourth_Ventricle (15): linear fit = 0.99 x + 0.0 (90 voxels, overlap=0.767) Fourth_Ventricle (15): linear fit = 0.99 x + 0.0 (90 voxels, peak = 18), gca=17.7 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21381 (38) gca peak Third_Ventricle = 0.25515 (27) gca peak CSF = 0.24868 (28) gca peak Left_Accumbens_area = 0.49915 (74) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65267 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.31109 (34) gca peak Right_Accumbens_area = 0.43827 (77) gca peak Right_vessel = 0.83457 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.45329 (31) gca peak WM_hypointensities = 0.17562 (83) gca peak non_WM_hypointensities = 0.10249 (54) gca peak Optic_Chiasm = 0.34853 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.99 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 19722 gm and wm labels changed (%20 to gray, %80 to white out of all changed labels) 328 hippocampal voxels changed. 2 amygdala voxels changed. pass 1: 76490 changed. image ll: -2.169, PF=1.000 pass 2: 11252 changed. image ll: -2.166, PF=1.000 pass 3: 3466 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 9 minutes and 44 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /root/Scrivania/subjects/ENP30S001A/mri/transforms/cc_up.lta ENP30S001A will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /root/Scrivania/subjects/ENP30S001A/mri/transforms/cc_up.lta reading aseg from /root/Scrivania/subjects/ENP30S001A/mri/aseg.auto_noCCseg.mgz reading norm from /root/Scrivania/subjects/ENP30S001A/mri/norm.mgz 35834 voxels in left wm, 62890 in right wm, xrange [121, 132] searching rotation angles z=[-13 1], y=[-9 5] searching scale 1 Z rot -13.3 searching scale 1 Z rot -13.0 searching scale 1 Z rot -12.8 searching scale 1 Z rot -12.5 searching scale 1 Z rot -12.3 searching scale 1 Z rot -12.0 searching scale 1 Z rot -11.8 searching scale 1 Z rot -11.5 searching scale 1 Z rot -11.3 searching scale 1 Z rot -11.0 searching scale 1 Z rot -10.8 searching scale 1 Z rot -10.5 searching scale 1 Z rot -10.3 searching scale 1 Z rot -10.0 searching scale 1 Z rot -9.8 searching scale 1 Z rot -9.5 searching scale 1 Z rot -9.3 searching scale 1 Z rot -9.0 searching scale 1 Z rot -8.8 searching scale 1 Z rot -8.5 searching scale 1 Z rot -8.3 searching scale 1 Z rot -8.0 searching scale 1 Z rot -7.8 searching scale 1 Z rot -7.5 searching scale 1 Z rot -7.3 searching scale 1 Z rot -7.0 searching scale 1 Z rot -6.8 searching scale 1 Z rot -6.5 searching scale 1 Z rot -6.3 searching scale 1 Z rot -6.0 searching scale 1 Z rot -5.8 searching scale 1 Z rot -5.5 searching scale 1 Z rot -5.3 searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.8 searching scale 1 Z rot -4.5 searching scale 1 Z rot -4.3 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.8 searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.3 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.8 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.3 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.8 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.3 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.8 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.3 searching scale 1 Z rot -0.0 global minimum found at slice 127.0, rotations (-1.78, -6.77) final transformation (x=127.0, yr=-1.775, zr=-6.766): 0.993 0.118 -0.031 -9.362; -0.118 0.993 0.004 17.414; 0.031 -0.000 1.000 9.120; 0.000 0.000 0.000 1.000; updating x range to be [126, 130] in xformed coordinates best xformed slice 128 cc center is found at 128 147 110 eigenvectors: -0.001 -0.006 1.000; -0.132 -0.991 -0.006; 0.991 -0.132 0.000; error in mid anterior detected - correcting... writing aseg with callosum to /root/Scrivania/subjects/ENP30S001A/mri/aseg.auto.mgz... corpus callosum matter segmentation took 0.6 minutes #-------------------------------------- #@# Merge ASeg Tue Aug 29 18:38:57 CEST 2017 cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# Intensity Normalization2 Tue Aug 29 18:38:57 CEST 2017 /root/Scrivania/subjects/ENP30S001A/mri mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 1887 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 70 (70), valley at 31 (31) csf peak at 35, setting threshold to 58 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 70 (70), valley at 32 (32) csf peak at 35, setting threshold to 58 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 2 minutes and 16 seconds. #-------------------------------------------- #@# Mask BFS Tue Aug 29 18:41:14 CEST 2017 /root/Scrivania/subjects/ENP30S001A/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1639089 voxels in mask (pct= 9.77) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Tue Aug 29 18:41:15 CEST 2017 mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /root/Scrivania/subjects/ENP30S001A/mri cmdline mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt sysname Linux hostname Braindata machine x86_64 user root input wm.mgz frame 0 nErode3d 0 nErode2d 0 output wm255.mgz Binarizing based on threshold min 255 max 255 binval 1 binvalnot 0 Found 0 values in range Counting number of voxels Found 0 voxels in final mask mri_binarize done mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /root/Scrivania/subjects/ENP30S001A/mri cmdline mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt sysname Linux hostname Braindata machine x86_64 user root input wm.mgz frame 0 nErode3d 0 nErode2d 0 output wm1.mgz Binarizing based on threshold min 1 max 1 binval 1 binvalnot 0 Found 0 values in range Counting number of voxels Found 0 voxels in final mask mri_binarize done rm wm1.mgz wm255.mgz mri_segment -keep brain.mgz wm.seg.mgz preserving editing changes in output volume... doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (105.0): 104.7 +- 6.3 [80.0 --> 125.0] GM (73.0) : 71.9 +- 9.1 [30.0 --> 96.0] setting bottom of white matter range to 81.1 setting top of gray matter range to 90.2 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... 3925 sparsely connected voxels removed... thickening thin strands.... 20 segments, 4846 filled 76 bright non-wm voxels segmented. 2292 diagonally connected voxels added... white matter segmentation took 1.1 minutes writing output to wm.seg.mgz... mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.35 minutes reading wm segmentation from wm.seg.mgz... 14 voxels added to wm to prevent paths from MTL structures to cortex 1866 additional wm voxels added 0 additional wm voxels added SEG EDIT: 30991 voxels turned on, 47286 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 105 new 105 115,126,128 old 105 new 105 writing edited volume to wm.asegedit.mgz.... mri_pretess -keep wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 14 found - 14 modified | TOTAL: 14 pass 2 (xy+): 0 found - 14 modified | TOTAL: 14 pass 1 (xy-): 21 found - 21 modified | TOTAL: 35 pass 2 (xy-): 0 found - 21 modified | TOTAL: 35 pass 1 (yz+): 32 found - 32 modified | TOTAL: 67 pass 2 (yz+): 0 found - 32 modified | TOTAL: 67 pass 1 (yz-): 16 found - 16 modified | TOTAL: 83 pass 2 (yz-): 0 found - 16 modified | TOTAL: 83 pass 1 (xz+): 12 found - 12 modified | TOTAL: 95 pass 2 (xz+): 0 found - 12 modified | TOTAL: 95 pass 1 (xz-): 12 found - 12 modified | TOTAL: 107 pass 2 (xz-): 0 found - 12 modified | TOTAL: 107 Iteration Number : 1 pass 1 (+++): 20 found - 20 modified | TOTAL: 20 pass 2 (+++): 0 found - 20 modified | TOTAL: 20 pass 1 (+++): 11 found - 11 modified | TOTAL: 31 pass 2 (+++): 0 found - 11 modified | TOTAL: 31 pass 1 (+++): 16 found - 16 modified | TOTAL: 47 pass 2 (+++): 0 found - 16 modified | TOTAL: 47 pass 1 (+++): 8 found - 8 modified | TOTAL: 55 pass 2 (+++): 0 found - 8 modified | TOTAL: 55 Iteration Number : 1 pass 1 (++): 57 found - 57 modified | TOTAL: 57 pass 2 (++): 0 found - 57 modified | TOTAL: 57 pass 1 (+-): 66 found - 66 modified | TOTAL: 123 pass 2 (+-): 0 found - 66 modified | TOTAL: 123 pass 1 (--): 71 found - 71 modified | TOTAL: 194 pass 2 (--): 0 found - 71 modified | TOTAL: 194 pass 1 (-+): 61 found - 61 modified | TOTAL: 255 pass 2 (-+): 0 found - 61 modified | TOTAL: 255 Iteration Number : 2 pass 1 (xy+): 4 found - 4 modified | TOTAL: 4 pass 2 (xy+): 0 found - 4 modified | TOTAL: 4 pass 1 (xy-): 0 found - 0 modified | TOTAL: 4 pass 1 (yz+): 4 found - 4 modified | TOTAL: 8 pass 2 (yz+): 0 found - 4 modified | TOTAL: 8 pass 1 (yz-): 2 found - 2 modified | TOTAL: 10 pass 2 (yz-): 0 found - 2 modified | TOTAL: 10 pass 1 (xz+): 4 found - 4 modified | TOTAL: 14 pass 2 (xz+): 0 found - 4 modified | TOTAL: 14 pass 1 (xz-): 5 found - 5 modified | TOTAL: 19 pass 2 (xz-): 0 found - 5 modified | TOTAL: 19 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 2 pass 1 (++): 2 found - 2 modified | TOTAL: 2 pass 2 (++): 0 found - 2 modified | TOTAL: 2 pass 1 (+-): 5 found - 5 modified | TOTAL: 7 pass 2 (+-): 0 found - 5 modified | TOTAL: 7 pass 1 (--): 3 found - 3 modified | TOTAL: 10 pass 2 (--): 0 found - 3 modified | TOTAL: 10 pass 1 (-+): 1 found - 1 modified | TOTAL: 11 pass 2 (-+): 0 found - 1 modified | TOTAL: 11 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 1 found - 1 modified | TOTAL: 2 pass 2 (yz-): 0 found - 1 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 1 found - 1 modified | TOTAL: 1 pass 2 (--): 0 found - 1 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 452 (out of 641267: 0.070485) keeping edits binarizing input wm segmentation... Ambiguous edge configurations... Searching for edits to keep ... kept 0 WM ON voxels kept 0 WM OFF voxels mri_pretess done #-------------------------------------------- #@# Fill Tue Aug 29 18:42:52 CEST 2017 /root/Scrivania/subjects/ENP30S001A/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 1.008 0.123 -0.020 -16.612; -0.103 1.119 0.243 -50.631; 0.046 -0.204 0.999 13.847; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.008 0.123 -0.020 -16.612; -0.103 1.119 0.243 -50.631; 0.046 -0.204 0.999 13.847; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1435 (min = 350, max = 1400), aspect = 0.43 (min = 0.10, max = 0.75) need search nearby using seed (125, 109, 93), TAL = (3.0, -35.0, 19.0) talairach voxel to voxel transform 0.980 -0.100 0.044 10.635; 0.096 0.846 -0.204 47.233; -0.026 0.178 0.957 -4.682; 0.000 0.000 0.000 1.000; segmentation indicates cc at (125, 109, 93) --> (3.0, -35.0, 19.0) done. writing output to filled.mgz... filling took 0.5 minutes talairach cc position changed to (3.00, -35.00, 19.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(21.00, -35.00, 19.00) SRC: (108.70, 130.72, 100.99) search lh wm seed point around talairach space (-15.00, -35.00, 19.00), SRC: (143.98, 134.16, 100.07) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Tue Aug 29 18:43:23 CEST 2017 /root/Scrivania/subjects/ENP30S001A/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 3 found - 3 modified | TOTAL: 3 pass 2 (yz+): 0 found - 3 modified | TOTAL: 3 pass 1 (yz-): 1 found - 1 modified | TOTAL: 4 pass 2 (yz-): 0 found - 1 modified | TOTAL: 4 pass 1 (xz+): 0 found - 0 modified | TOTAL: 4 pass 1 (xz-): 1 found - 1 modified | TOTAL: 5 pass 2 (xz-): 0 found - 1 modified | TOTAL: 5 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 5 (out of 311038: 0.001608) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 40: 240 vertices, 301 faces slice 50: 5017 vertices, 5273 faces slice 60: 14697 vertices, 15073 faces slice 70: 26857 vertices, 27315 faces slice 80: 39435 vertices, 39879 faces slice 90: 51347 vertices, 51735 faces slice 100: 63743 vertices, 64174 faces slice 110: 75955 vertices, 76387 faces slice 120: 87780 vertices, 88161 faces slice 130: 98924 vertices, 99342 faces slice 140: 110269 vertices, 110710 faces slice 150: 120356 vertices, 120693 faces slice 160: 129325 vertices, 129654 faces slice 170: 136817 vertices, 137075 faces slice 180: 143299 vertices, 143547 faces slice 190: 148357 vertices, 148522 faces slice 200: 150098 vertices, 150132 faces slice 210: 150098 vertices, 150132 faces slice 220: 150098 vertices, 150132 faces slice 230: 150098 vertices, 150132 faces slice 240: 150098 vertices, 150132 faces slice 250: 150098 vertices, 150132 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 150098 voxel in cpt #1: X=-34 [v=150098,e=450396,f=300264] located at (-26.846394, -17.426208, -7.505356) For the whole surface: X=-34 [v=150098,e=450396,f=300264] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Tue Aug 29 18:43:27 CEST 2017 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /root/Scrivania/subjects/ENP30S001A/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Tue Aug 29 18:43:30 CEST 2017 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /root/Scrivania/subjects/ENP30S001A/scripts avg radius = 48.0 mm, total surface area = 78883 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.4 minutes Not saving sulc step 000: RMS=0.100 (target=0.015) step 005: RMS=0.072 (target=0.015) step 010: RMS=0.054 (target=0.015) step 015: RMS=0.046 (target=0.015) step 020: RMS=0.040 (target=0.015) step 025: RMS=0.036 (target=0.015) step 030: RMS=0.033 (target=0.015) step 035: RMS=0.031 (target=0.015) step 040: RMS=0.030 (target=0.015) step 045: RMS=0.028 (target=0.015) step 050: RMS=0.028 (target=0.015) step 055: RMS=0.027 (target=0.015) step 060: RMS=0.027 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Tue Aug 29 18:43:51 CEST 2017 /root/Scrivania/subjects/ENP30S001A/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.96 +- 0.55 (0.00-->6.23) (max @ vno 112361 --> 113534) face area 0.03 +- 0.03 (-0.19-->0.67) scaling brain by 0.316... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.685, avgs=0 005/300: dt: 0.9000, rms radial error=175.428, avgs=0 010/300: dt: 0.9000, rms radial error=174.877, avgs=0 015/300: dt: 0.9000, rms radial error=174.153, avgs=0 020/300: dt: 0.9000, rms radial error=173.328, avgs=0 025/300: dt: 0.9000, rms radial error=172.447, avgs=0 030/300: dt: 0.9000, rms radial error=171.533, avgs=0 035/300: dt: 0.9000, rms radial error=170.603, avgs=0 040/300: dt: 0.9000, rms radial error=169.665, avgs=0 045/300: dt: 0.9000, rms radial error=168.724, avgs=0 050/300: dt: 0.9000, rms radial error=167.784, avgs=0 055/300: dt: 0.9000, rms radial error=166.846, avgs=0 060/300: dt: 0.9000, rms radial error=165.912, avgs=0 065/300: dt: 0.9000, rms radial error=164.982, avgs=0 070/300: dt: 0.9000, rms radial error=164.056, avgs=0 075/300: dt: 0.9000, rms radial error=163.135, avgs=0 080/300: dt: 0.9000, rms radial error=162.219, avgs=0 085/300: dt: 0.9000, rms radial error=161.307, avgs=0 090/300: dt: 0.9000, rms radial error=160.400, avgs=0 095/300: dt: 0.9000, rms radial error=159.499, avgs=0 100/300: dt: 0.9000, rms radial error=158.602, avgs=0 105/300: dt: 0.9000, rms radial error=157.711, avgs=0 110/300: dt: 0.9000, rms radial error=156.824, avgs=0 115/300: dt: 0.9000, rms radial error=155.942, avgs=0 120/300: dt: 0.9000, rms radial error=155.065, avgs=0 125/300: dt: 0.9000, rms radial error=154.193, avgs=0 130/300: dt: 0.9000, rms radial error=153.325, avgs=0 135/300: dt: 0.9000, rms radial error=152.463, avgs=0 140/300: dt: 0.9000, rms radial error=151.605, avgs=0 145/300: dt: 0.9000, rms radial error=150.751, avgs=0 150/300: dt: 0.9000, rms radial error=149.903, avgs=0 155/300: dt: 0.9000, rms radial error=149.059, avgs=0 160/300: dt: 0.9000, rms radial error=148.219, avgs=0 165/300: dt: 0.9000, rms radial error=147.385, avgs=0 170/300: dt: 0.9000, rms radial error=146.555, avgs=0 175/300: dt: 0.9000, rms radial error=145.729, avgs=0 180/300: dt: 0.9000, rms radial error=144.908, avgs=0 185/300: dt: 0.9000, rms radial error=144.092, avgs=0 190/300: dt: 0.9000, rms radial error=143.280, avgs=0 195/300: dt: 0.9000, rms radial error=142.473, avgs=0 200/300: dt: 0.9000, rms radial error=141.670, avgs=0 205/300: dt: 0.9000, rms radial error=140.872, avgs=0 210/300: dt: 0.9000, rms radial error=140.078, avgs=0 215/300: dt: 0.9000, rms radial error=139.289, avgs=0 220/300: dt: 0.9000, rms radial error=138.504, avgs=0 225/300: dt: 0.9000, rms radial error=137.723, avgs=0 230/300: dt: 0.9000, rms radial error=136.947, avgs=0 235/300: dt: 0.9000, rms radial error=136.174, avgs=0 240/300: dt: 0.9000, rms radial error=135.407, avgs=0 245/300: dt: 0.9000, rms radial error=134.643, avgs=0 250/300: dt: 0.9000, rms radial error=133.885, avgs=0 255/300: dt: 0.9000, rms radial error=133.130, avgs=0 260/300: dt: 0.9000, rms radial error=132.379, avgs=0 265/300: dt: 0.9000, rms radial error=131.632, avgs=0 270/300: dt: 0.9000, rms radial error=130.890, avgs=0 275/300: dt: 0.9000, rms radial error=130.151, avgs=0 280/300: dt: 0.9000, rms radial error=129.418, avgs=0 285/300: dt: 0.9000, rms radial error=128.688, avgs=0 290/300: dt: 0.9000, rms radial error=127.963, avgs=0 295/300: dt: 0.9000, rms radial error=127.242, avgs=0 300/300: dt: 0.9000, rms radial error=126.524, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 17474.52 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00014 epoch 2 (K=40.0), pass 1, starting sse = 2884.86 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00003 epoch 3 (K=160.0), pass 1, starting sse = 282.40 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/12 = 0.00590 epoch 4 (K=640.0), pass 1, starting sse = 17.74 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.11/14 = 0.00754 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.05 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Tue Aug 29 18:46:53 CEST 2017 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /root/Scrivania/subjects/ENP30S001A/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 ENP30S001A lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ before topology correction, eno=-34 (nv=150098, nf=300264, ne=450396, g=18) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 8 iterations marking ambiguous vertices... 5420 ambiguous faces found in tessellation segmenting defects... 19 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 8 into 6 18 defects to be corrected 0 vertices coincident reading input surface /root/Scrivania/subjects/ENP30S001A/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.1187 (-4.5593) -vertex loglikelihood: -6.1454 (-3.0727) -normal dot loglikelihood: -3.6411 (-3.6411) -quad curv loglikelihood: -6.5283 (-3.2641) Total Loglikelihood : -25.4335 CORRECTING DEFECT 0 (vertices=16, convex hull=54) After retessellation of defect 0, euler #=-16 (147015,440266,293235) : difference with theory (-15) = 1 CORRECTING DEFECT 1 (vertices=311, convex hull=227) After retessellation of defect 1, euler #=-15 (147025,440411,293371) : difference with theory (-14) = 1 CORRECTING DEFECT 2 (vertices=13, convex hull=28) After retessellation of defect 2, euler #=-14 (147028,440428,293386) : difference with theory (-13) = 1 CORRECTING DEFECT 3 (vertices=254, convex hull=151) After retessellation of defect 3, euler #=-13 (147114,440766,293639) : difference with theory (-12) = 1 CORRECTING DEFECT 4 (vertices=338, convex hull=99) After retessellation of defect 4, euler #=-12 (147139,440878,293727) : difference with theory (-11) = 1 CORRECTING DEFECT 5 (vertices=5, convex hull=27) After retessellation of defect 5, euler #=-11 (147141,440892,293740) : difference with theory (-10) = 1 CORRECTING DEFECT 6 (vertices=725, convex hull=456) After retessellation of defect 6, euler #=-9 (147313,441641,294319) : difference with theory (-9) = 0 CORRECTING DEFECT 7 (vertices=64, convex hull=113) After retessellation of defect 7, euler #=-8 (147330,441741,294403) : difference with theory (-8) = 0 CORRECTING DEFECT 8 (vertices=40, convex hull=63) After retessellation of defect 8, euler #=-7 (147347,441815,294461) : difference with theory (-7) = 0 CORRECTING DEFECT 9 (vertices=30, convex hull=57) After retessellation of defect 9, euler #=-6 (147365,441893,294522) : difference with theory (-6) = 0 CORRECTING DEFECT 10 (vertices=161, convex hull=74) After retessellation of defect 10, euler #=-5 (147385,441979,294589) : difference with theory (-5) = 0 CORRECTING DEFECT 11 (vertices=88, convex hull=33) After retessellation of defect 11, euler #=-4 (147395,442019,294620) : difference with theory (-4) = 0 CORRECTING DEFECT 12 (vertices=19, convex hull=44) After retessellation of defect 12, euler #=-3 (147404,442063,294656) : difference with theory (-3) = 0 CORRECTING DEFECT 13 (vertices=855, convex hull=139) After retessellation of defect 13, euler #=-2 (147444,442250,294804) : difference with theory (-2) = 0 CORRECTING DEFECT 14 (vertices=13, convex hull=33) After retessellation of defect 14, euler #=-1 (147447,442267,294819) : difference with theory (-1) = 0 CORRECTING DEFECT 15 (vertices=66, convex hull=32) After retessellation of defect 15, euler #=0 (147452,442294,294842) : difference with theory (0) = 0 CORRECTING DEFECT 16 (vertices=75, convex hull=128) After retessellation of defect 16, euler #=1 (147499,442486,294988) : difference with theory (1) = 0 CORRECTING DEFECT 17 (vertices=17, convex hull=20) After retessellation of defect 17, euler #=2 (147504,442506,295004) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.22 (0.11-->9.97) (max @ vno 54443 --> 60501) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.22 (0.11-->9.97) (max @ vno 54443 --> 60501) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 65 mutations (34.4%), 124 crossovers (65.6%), 320 vertices were eliminated building final representation... 2594 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=147504, nf=295004, ne=442506, g=0) writing corrected surface to /root/Scrivania/subjects/ENP30S001A/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 16.4 minutes 0 defective edges removing intersecting faces 000: 266 intersecting 001: 13 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 147504 - 442506 + 295004 = 2 --> 0 holes F =2V-4: 295004 = 295008-4 (0) 2E=3F: 885012 = 885012 (0) total defect index = 0 /root/Scrivania/subjects/ENP30S001A/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 51 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Tue Aug 29 19:03:20 CEST 2017 /root/Scrivania/subjects/ENP30S001A/scripts mris_make_surfaces -noaparc -mgz -T1 brain.finalsurfs ENP30S001A lh not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /root/Scrivania/subjects/ENP30S001A/mri/filled.mgz... reading volume /root/Scrivania/subjects/ENP30S001A/mri/brain.finalsurfs.mgz... reading volume /root/Scrivania/subjects/ENP30S001A/mri/wm.mgz... 15082 bright wm thresholded. 257 bright non-wm voxels segmented. reading original surface position from /root/Scrivania/subjects/ENP30S001A/surf/lh.orig... computing class statistics... border white: 279213 voxels (1.66%) border gray 305834 voxels (1.82%) WM (95.0): 96.2 +- 8.0 [70.0 --> 110.0] GM (82.0) : 80.5 +- 11.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 58.3 (was 70) setting MAX_BORDER_WHITE to 113.0 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 46.5 (was 40) setting MAX_GRAY to 97.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.1 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 34.8 (was 40) repositioning cortical surface to gray/white boundary reading volume /root/Scrivania/subjects/ENP30S001A/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.03-->5.11) (max @ vno 147215 --> 147225) face area 0.28 +- 0.12 (0.00-->4.41) mean absolute distance = 0.72 +- 0.92 3158 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=70 mean inside = 95.4, mean outside = 76.9 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group mean border=81.6, 63 (63) missing vertices, mean dist 0.2 [0.6 (%38.5)->0.8 (%61.5))] %67 local maxima, %28 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=Brain, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.25 (0.11-->5.56) (max @ vno 61866 --> 70213) face area 0.28 +- 0.13 (0.00-->6.01) mean absolute distance = 0.36 +- 0.60 2966 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5657202.0, rms=10.37 001: dt: 0.5000, sse=6295746.5, rms=7.264 (0.000%) 002: dt: 0.5000, sse=6680853.5, rms=5.396 (0.000%) 003: dt: 0.5000, sse=7001209.0, rms=4.303 (0.000%) 004: dt: 0.5000, sse=7266023.0, rms=3.652 (0.000%) 005: dt: 0.5000, sse=7439146.5, rms=3.382 (0.000%) 006: dt: 0.5000, sse=7540030.0, rms=3.209 (0.000%) rms = 3.18, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=7586327.5, rms=3.183 (0.000%) 008: dt: 0.2500, sse=4553411.0, rms=2.071 (0.000%) 009: dt: 0.2500, sse=4131929.8, rms=1.782 (0.000%) 010: dt: 0.2500, sse=3965712.2, rms=1.710 (0.000%) rms = 1.68, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=3908679.0, rms=1.676 (0.000%) rms = 1.64, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=3844914.5, rms=1.641 (0.000%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=84.6, 66 (36) missing vertices, mean dist -0.2 [0.4 (%71.6)->0.2 (%28.4))] %77 local maxima, %18 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=Brain, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.24 (0.06-->5.69) (max @ vno 61866 --> 70213) face area 0.35 +- 0.16 (0.00-->8.23) mean absolute distance = 0.25 +- 0.36 3616 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4533491.0, rms=4.76 013: dt: 0.5000, sse=4869790.0, rms=3.016 (0.000%) 014: dt: 0.5000, sse=5351834.0, rms=2.934 (0.000%) 015: dt: 0.5000, sse=5945726.0, rms=2.811 (0.000%) rms = 3.09, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=4769637.5, rms=1.935 (0.000%) 017: dt: 0.2500, sse=4371681.0, rms=1.530 (0.000%) 018: dt: 0.2500, sse=4226138.5, rms=1.406 (0.000%) rms = 1.39, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=4156737.2, rms=1.388 (0.000%) rms = 1.35, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=4108307.5, rms=1.354 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group mean border=87.2, 49 (16) missing vertices, mean dist -0.1 [0.3 (%73.9)->0.2 (%26.1))] %87 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=Brain, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.24 (0.08-->5.74) (max @ vno 61866 --> 70213) face area 0.33 +- 0.16 (0.00-->8.32) mean absolute distance = 0.20 +- 0.29 3258 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4361166.0, rms=3.43 021: dt: 0.5000, sse=4636350.0, rms=2.533 (0.000%) rms = 2.78, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=4330722.5, rms=1.774 (0.000%) 023: dt: 0.2500, sse=4220126.5, rms=1.366 (0.000%) 024: dt: 0.2500, sse=4199025.0, rms=1.247 (0.000%) rms = 1.24, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=4164955.8, rms=1.245 (0.000%) rms = 1.22, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=4127032.5, rms=1.218 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group mean border=88.1, 36 (6) missing vertices, mean dist -0.0 [0.2 (%58.9)->0.2 (%41.1))] %89 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=Brain, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /root/Scrivania/subjects/ENP30S001A/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=4143982.5, rms=1.63 rms = 1.68, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=4199977.5, rms=1.167 (0.000%) 028: dt: 0.2500, sse=4331419.5, rms=0.922 (0.000%) rms = 0.95, time step reduction 2 of 3 to 0.125... rms = 0.92, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=4329852.5, rms=0.922 (0.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 10 non-cortical segments detected only using segment with 1859 vertices erasing segment 1 (vno[0] = 92979) erasing segment 2 (vno[0] = 105518) erasing segment 3 (vno[0] = 108730) erasing segment 4 (vno[0] = 108850) erasing segment 5 (vno[0] = 111033) erasing segment 6 (vno[0] = 112129) erasing segment 7 (vno[0] = 116319) erasing segment 8 (vno[0] = 117171) erasing segment 9 (vno[0] = 147408) writing cortex label to /root/Scrivania/subjects/ENP30S001A/label/lh.cortex.label... writing curvature file /root/Scrivania/subjects/ENP30S001A/surf/lh.curv writing smoothed area to lh.area writing curvature file /root/Scrivania/subjects/ENP30S001A/surf/lh.area vertex spacing 0.88 +- 0.24 (0.08-->5.76) (max @ vno 61866 --> 70213) face area 0.33 +- 0.16 (0.00-->8.18) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... smoothing surface for 5 iterations... mean border=59.8, 57 (57) missing vertices, mean dist 1.7 [0.2 (%0.0)->2.4 (%100.0))] %20 local maxima, %45 large gradients and %30 min vals, 1962 gradients ignored tol=1.0e-04, sigma=2.0, host=Brain, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=25543636.0, rms=28.38 001: dt: 0.5000, sse=19441656.0, rms=24.277 (0.000%) 002: dt: 0.5000, sse=14907747.0, rms=20.745 (0.000%) 003: dt: 0.5000, sse=11703384.0, rms=17.777 (0.000%) 004: dt: 0.5000, sse=9613071.0, rms=15.318 (0.000%) 005: dt: 0.5000, sse=8222695.5, rms=13.315 (0.000%) 006: dt: 0.5000, sse=7359229.5, rms=11.672 (0.000%) 007: dt: 0.5000, sse=6819032.5, rms=10.212 (0.000%) 008: dt: 0.5000, sse=6524053.0, rms=8.846 (0.000%) 009: dt: 0.5000, sse=6316680.5, rms=7.540 (0.000%) 010: dt: 0.5000, sse=6258585.5, rms=6.337 (0.000%) 011: dt: 0.5000, sse=6311766.0, rms=5.357 (0.000%) 012: dt: 0.5000, sse=6463550.0, rms=4.687 (0.000%) 013: dt: 0.5000, sse=6660345.5, rms=4.288 (0.000%) 014: dt: 0.5000, sse=6717485.5, rms=4.037 (0.000%) 015: dt: 0.5000, sse=6826577.5, rms=3.904 (0.000%) 016: dt: 0.5000, sse=6821763.0, rms=3.798 (0.000%) rms = 3.76, time step reduction 1 of 3 to 0.250... 017: dt: 0.5000, sse=6889647.0, rms=3.757 (0.000%) 018: dt: 0.2500, sse=4698488.0, rms=2.954 (0.000%) 019: dt: 0.2500, sse=4505496.0, rms=2.726 (0.000%) rms = 2.69, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=4381880.5, rms=2.686 (0.000%) 021: dt: 0.1250, sse=4165291.0, rms=2.545 (0.000%) rms = 2.52, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=4134977.8, rms=2.525 (0.000%) positioning took 1.5 minutes mean border=57.4, 1035 (15) missing vertices, mean dist 0.1 [0.2 (%45.1)->0.5 (%54.9))] %38 local maxima, %34 large gradients and %24 min vals, 679 gradients ignored tol=1.0e-04, sigma=1.0, host=Brain, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4821551.0, rms=4.87 023: dt: 0.5000, sse=4970073.5, rms=3.754 (0.000%) 024: dt: 0.5000, sse=6358176.0, rms=3.693 (0.000%) rms = 3.75, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=5224813.0, rms=2.911 (0.000%) 026: dt: 0.2500, sse=4772492.5, rms=2.586 (0.000%) 027: dt: 0.2500, sse=4732135.0, rms=2.515 (0.000%) rms = 2.49, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=4692478.5, rms=2.490 (0.000%) 029: dt: 0.1250, sse=4516331.0, rms=2.335 (0.000%) rms = 2.31, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=4499261.5, rms=2.313 (0.000%) positioning took 0.6 minutes mean border=55.7, 1397 (13) missing vertices, mean dist 0.1 [0.2 (%39.9)->0.3 (%60.1))] %51 local maxima, %21 large gradients and %23 min vals, 736 gradients ignored tol=1.0e-04, sigma=0.5, host=Brain, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4683497.0, rms=3.35 rms = 3.49, time step reduction 1 of 3 to 0.250... 031: dt: 0.2500, sse=4496808.5, rms=2.792 (0.000%) 032: dt: 0.2500, sse=4486482.0, rms=2.455 (0.000%) 033: dt: 0.2500, sse=4679203.5, rms=2.367 (0.000%) rms = 2.35, time step reduction 2 of 3 to 0.125... 034: dt: 0.2500, sse=4710668.0, rms=2.354 (0.000%) 035: dt: 0.1250, sse=4578261.0, rms=2.235 (0.000%) rms = 2.22, time step reduction 3 of 3 to 0.062... 036: dt: 0.1250, sse=4588261.5, rms=2.216 (0.000%) positioning took 0.5 minutes mean border=54.8, 2958 (13) missing vertices, mean dist 0.0 [0.2 (%45.4)->0.3 (%54.6))] %55 local maxima, %16 large gradients and %22 min vals, 625 gradients ignored tol=1.0e-04, sigma=0.2, host=Brain, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /root/Scrivania/subjects/ENP30S001A/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=4627021.0, rms=2.52 rms = 3.06, time step reduction 1 of 3 to 0.250... 037: dt: 0.2500, sse=4527738.0, rms=2.305 (0.000%) 038: dt: 0.2500, sse=4683505.5, rms=2.241 (0.000%) rms = 2.23, time step reduction 2 of 3 to 0.125... 039: dt: 0.2500, sse=4742968.0, rms=2.227 (0.000%) 040: dt: 0.1250, sse=4663334.5, rms=2.142 (0.000%) rms = 2.13, time step reduction 3 of 3 to 0.062... 041: dt: 0.1250, sse=4669977.0, rms=2.128 (0.000%) positioning took 0.4 minutes writing curvature file /root/Scrivania/subjects/ENP30S001A/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /root/Scrivania/subjects/ENP30S001A/surf/lh.area.pial vertex spacing 0.97 +- 0.39 (0.08-->8.02) (max @ vno 54443 --> 54444) face area 0.38 +- 0.27 (0.00-->9.50) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 147504 vertices processed 25000 of 147504 vertices processed 50000 of 147504 vertices processed 75000 of 147504 vertices processed 100000 of 147504 vertices processed 125000 of 147504 vertices processed 0 of 147504 vertices processed 25000 of 147504 vertices processed 50000 of 147504 vertices processed 75000 of 147504 vertices processed 100000 of 147504 vertices processed 125000 of 147504 vertices processed thickness calculation complete, 540:705 truncations. 34277 vertices at 0 distance 105816 vertices at 1 distance 90224 vertices at 2 distance 35317 vertices at 3 distance 11366 vertices at 4 distance 3668 vertices at 5 distance 1200 vertices at 6 distance 403 vertices at 7 distance 104 vertices at 8 distance 47 vertices at 9 distance 51 vertices at 10 distance 25 vertices at 11 distance 15 vertices at 12 distance 19 vertices at 13 distance 13 vertices at 14 distance 3 vertices at 15 distance 12 vertices at 16 distance 4 vertices at 17 distance 4 vertices at 18 distance 6 vertices at 19 distance 6 vertices at 20 distance writing curvature file /root/Scrivania/subjects/ENP30S001A/surf/lh.thickness positioning took 7.6 minutes #-------------------------------------------- #@# Smooth2 lh Tue Aug 29 19:10:53 CEST 2017 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /root/Scrivania/subjects/ENP30S001A/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 lh Tue Aug 29 19:10:56 CEST 2017 /root/Scrivania/subjects/ENP30S001A/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 48.3 mm, total surface area = 88495 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.114 (target=0.015) step 005: RMS=0.078 (target=0.015) step 010: RMS=0.056 (target=0.015) step 015: RMS=0.046 (target=0.015) step 020: RMS=0.038 (target=0.015) step 025: RMS=0.031 (target=0.015) step 030: RMS=0.027 (target=0.015) step 035: RMS=0.023 (target=0.015) step 040: RMS=0.020 (target=0.015) step 045: RMS=0.018 (target=0.015) step 050: RMS=0.016 (target=0.015) inflation complete. inflation took 0.3 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 189 vertices thresholded to be in k1 ~ [-0.20 1.60], k2 ~ [-0.10 0.06] total integrated curvature = 0.591*4pi (7.424) --> 0 handles ICI = 1.8, FI = 11.5, variation=195.206 104 vertices thresholded to be in [-0.01 0.01] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 104 vertices thresholded to be in [-0.11 0.37] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.015, std = 0.025 done. #----------------------------------------- #@# Curvature Stats lh Tue Aug 29 19:12:12 CEST 2017 /root/Scrivania/subjects/ENP30S001A/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm ENP30S001A lh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/lh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ ENP30S001A/lh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 274 ] Gb_filter = 0 WARN: S lookup min: -0.235098 WARN: S explicit min: 0.000000 vertex = 910 #-------------------------------------------- #@# Tessellate rh Tue Aug 29 19:12:15 CEST 2017 /root/Scrivania/subjects/ENP30S001A/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 2 found - 2 modified | TOTAL: 3 pass 2 (xy-): 0 found - 2 modified | TOTAL: 3 pass 1 (yz+): 1 found - 1 modified | TOTAL: 4 pass 2 (yz+): 0 found - 1 modified | TOTAL: 4 pass 1 (yz-): 1 found - 1 modified | TOTAL: 5 pass 2 (yz-): 0 found - 1 modified | TOTAL: 5 pass 1 (xz+): 1 found - 1 modified | TOTAL: 6 pass 2 (xz+): 0 found - 1 modified | TOTAL: 6 pass 1 (xz-): 4 found - 4 modified | TOTAL: 10 pass 2 (xz-): 0 found - 4 modified | TOTAL: 10 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 2 found - 2 modified | TOTAL: 3 pass 2 (--): 0 found - 2 modified | TOTAL: 3 pass 1 (-+): 3 found - 3 modified | TOTAL: 6 pass 2 (-+): 0 found - 3 modified | TOTAL: 6 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 16 (out of 306836: 0.005215) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 50: 1741 vertices, 1865 faces slice 60: 8006 vertices, 8296 faces slice 70: 17928 vertices, 18288 faces slice 80: 29254 vertices, 29637 faces slice 90: 40592 vertices, 40993 faces slice 100: 52403 vertices, 52788 faces slice 110: 64349 vertices, 64762 faces slice 120: 76555 vertices, 76977 faces slice 130: 88923 vertices, 89377 faces slice 140: 100892 vertices, 101335 faces slice 150: 111863 vertices, 112236 faces slice 160: 121972 vertices, 122349 faces slice 170: 130708 vertices, 131005 faces slice 180: 138064 vertices, 138334 faces slice 190: 144573 vertices, 144824 faces slice 200: 148115 vertices, 148184 faces slice 210: 148266 vertices, 148304 faces slice 220: 148266 vertices, 148304 faces slice 230: 148266 vertices, 148304 faces slice 240: 148266 vertices, 148304 faces slice 250: 148266 vertices, 148304 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 148266 voxel in cpt #1: X=-38 [v=148266,e=444912,f=296608] located at (29.803556, -10.062510, 0.052271) For the whole surface: X=-38 [v=148266,e=444912,f=296608] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Tue Aug 29 19:12:19 CEST 2017 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /root/Scrivania/subjects/ENP30S001A/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 rh Tue Aug 29 19:12:22 CEST 2017 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /root/Scrivania/subjects/ENP30S001A/scripts avg radius = 47.3 mm, total surface area = 77888 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.4 minutes Not saving sulc step 000: RMS=0.099 (target=0.015) step 005: RMS=0.072 (target=0.015) step 010: RMS=0.052 (target=0.015) step 015: RMS=0.044 (target=0.015) step 020: RMS=0.037 (target=0.015) step 025: RMS=0.033 (target=0.015) step 030: RMS=0.030 (target=0.015) step 035: RMS=0.027 (target=0.015) step 040: RMS=0.026 (target=0.015) step 045: RMS=0.025 (target=0.015) step 050: RMS=0.024 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.022 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere rh Tue Aug 29 19:12:43 CEST 2017 /root/Scrivania/subjects/ENP30S001A/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.97 +- 0.53 (0.00-->6.32) (max @ vno 58132 --> 59359) face area 0.03 +- 0.03 (-0.19-->0.51) scaling brain by 0.318... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.914, avgs=0 005/300: dt: 0.9000, rms radial error=175.655, avgs=0 010/300: dt: 0.9000, rms radial error=175.098, avgs=0 015/300: dt: 0.9000, rms radial error=174.368, avgs=0 020/300: dt: 0.9000, rms radial error=173.537, avgs=0 025/300: dt: 0.9000, rms radial error=172.647, avgs=0 030/300: dt: 0.9000, rms radial error=171.725, avgs=0 035/300: dt: 0.9000, rms radial error=170.791, avgs=0 040/300: dt: 0.9000, rms radial error=169.850, avgs=0 045/300: dt: 0.9000, rms radial error=168.906, avgs=0 050/300: dt: 0.9000, rms radial error=167.962, avgs=0 055/300: dt: 0.9000, rms radial error=167.021, avgs=0 060/300: dt: 0.9000, rms radial error=166.084, avgs=0 065/300: dt: 0.9000, rms radial error=165.151, avgs=0 070/300: dt: 0.9000, rms radial error=164.223, avgs=0 075/300: dt: 0.9000, rms radial error=163.299, avgs=0 080/300: dt: 0.9000, rms radial error=162.380, avgs=0 085/300: dt: 0.9000, rms radial error=161.467, avgs=0 090/300: dt: 0.9000, rms radial error=160.558, avgs=0 095/300: dt: 0.9000, rms radial error=159.654, avgs=0 100/300: dt: 0.9000, rms radial error=158.755, avgs=0 105/300: dt: 0.9000, rms radial error=157.861, avgs=0 110/300: dt: 0.9000, rms radial error=156.972, avgs=0 115/300: dt: 0.9000, rms radial error=156.088, avgs=0 120/300: dt: 0.9000, rms radial error=155.208, avgs=0 125/300: dt: 0.9000, rms radial error=154.334, avgs=0 130/300: dt: 0.9000, rms radial error=153.465, avgs=0 135/300: dt: 0.9000, rms radial error=152.600, avgs=0 140/300: dt: 0.9000, rms radial error=151.740, avgs=0 145/300: dt: 0.9000, rms radial error=150.885, avgs=0 150/300: dt: 0.9000, rms radial error=150.035, avgs=0 155/300: dt: 0.9000, rms radial error=149.189, avgs=0 160/300: dt: 0.9000, rms radial error=148.348, avgs=0 165/300: dt: 0.9000, rms radial error=147.513, avgs=0 170/300: dt: 0.9000, rms radial error=146.681, avgs=0 175/300: dt: 0.9000, rms radial error=145.855, avgs=0 180/300: dt: 0.9000, rms radial error=145.033, avgs=0 185/300: dt: 0.9000, rms radial error=144.215, avgs=0 190/300: dt: 0.9000, rms radial error=143.402, avgs=0 195/300: dt: 0.9000, rms radial error=142.594, avgs=0 200/300: dt: 0.9000, rms radial error=141.790, avgs=0 205/300: dt: 0.9000, rms radial error=140.991, avgs=0 210/300: dt: 0.9000, rms radial error=140.196, avgs=0 215/300: dt: 0.9000, rms radial error=139.406, avgs=0 220/300: dt: 0.9000, rms radial error=138.620, avgs=0 225/300: dt: 0.9000, rms radial error=137.839, avgs=0 230/300: dt: 0.9000, rms radial error=137.062, avgs=0 235/300: dt: 0.9000, rms radial error=136.289, avgs=0 240/300: dt: 0.9000, rms radial error=135.521, avgs=0 245/300: dt: 0.9000, rms radial error=134.757, avgs=0 250/300: dt: 0.9000, rms radial error=133.998, avgs=0 255/300: dt: 0.9000, rms radial error=133.242, avgs=0 260/300: dt: 0.9000, rms radial error=132.491, avgs=0 265/300: dt: 0.9000, rms radial error=131.745, avgs=0 270/300: dt: 0.9000, rms radial error=131.002, avgs=0 275/300: dt: 0.9000, rms radial error=130.263, avgs=0 280/300: dt: 0.9000, rms radial error=129.529, avgs=0 285/300: dt: 0.9000, rms radial error=128.799, avgs=0 290/300: dt: 0.9000, rms radial error=128.073, avgs=0 295/300: dt: 0.9000, rms radial error=127.351, avgs=0 300/300: dt: 0.9000, rms radial error=126.633, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 17188.96 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00014 epoch 2 (K=40.0), pass 1, starting sse = 2770.32 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00003 epoch 3 (K=160.0), pass 1, starting sse = 255.64 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.08/11 = 0.00712 epoch 4 (K=640.0), pass 1, starting sse = 14.72 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.13/16 = 0.00796 final writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.05 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology rh Tue Aug 29 19:15:45 CEST 2017 cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated /root/Scrivania/subjects/ENP30S001A/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 ENP30S001A rh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ before topology correction, eno=-38 (nv=148266, nf=296608, ne=444912, g=20) 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 6 iterations marking ambiguous vertices... 4017 ambiguous faces found in tessellation segmenting defects... 17 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 10 into 9 16 defects to be corrected 0 vertices coincident reading input surface /root/Scrivania/subjects/ENP30S001A/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.1666 (-4.5833) -vertex loglikelihood: -6.1626 (-3.0813) -normal dot loglikelihood: -3.6725 (-3.6725) -quad curv loglikelihood: -6.5927 (-3.2963) Total Loglikelihood : -25.5943 CORRECTING DEFECT 0 (vertices=65, convex hull=108) After retessellation of defect 0, euler #=-14 (145942,437112,291156) : difference with theory (-13) = 1 CORRECTING DEFECT 1 (vertices=38, convex hull=84) After retessellation of defect 1, euler #=-13 (145959,437196,291224) : difference with theory (-12) = 1 CORRECTING DEFECT 2 (vertices=23, convex hull=55) After retessellation of defect 2, euler #=-12 (145970,437250,291268) : difference with theory (-11) = 1 CORRECTING DEFECT 3 (vertices=20, convex hull=33) After retessellation of defect 3, euler #=-11 (145974,437275,291290) : difference with theory (-10) = 1 CORRECTING DEFECT 4 (vertices=127, convex hull=116) After retessellation of defect 4, euler #=-10 (145992,437377,291375) : difference with theory (-9) = 1 CORRECTING DEFECT 5 (vertices=33, convex hull=49) After retessellation of defect 5, euler #=-9 (146002,437423,291412) : difference with theory (-8) = 1 CORRECTING DEFECT 6 (vertices=22, convex hull=20) After retessellation of defect 6, euler #=-8 (146006,437442,291428) : difference with theory (-7) = 1 CORRECTING DEFECT 7 (vertices=7, convex hull=27) After retessellation of defect 7, euler #=-7 (146009,437459,291443) : difference with theory (-6) = 1 CORRECTING DEFECT 8 (vertices=5, convex hull=27) After retessellation of defect 8, euler #=-6 (146011,437472,291455) : difference with theory (-5) = 1 CORRECTING DEFECT 9 (vertices=949, convex hull=468) After retessellation of defect 9, euler #=-4 (146276,438502,292222) : difference with theory (-4) = 0 CORRECTING DEFECT 10 (vertices=30, convex hull=62) After retessellation of defect 10, euler #=-3 (146293,438581,292285) : difference with theory (-3) = 0 CORRECTING DEFECT 11 (vertices=73, convex hull=29) After retessellation of defect 11, euler #=-2 (146300,438613,292311) : difference with theory (-2) = 0 CORRECTING DEFECT 12 (vertices=195, convex hull=83) After retessellation of defect 12, euler #=-1 (146318,438706,292387) : difference with theory (-1) = 0 CORRECTING DEFECT 13 (vertices=676, convex hull=329) After retessellation of defect 13, euler #=0 (146436,439229,292793) : difference with theory (0) = 0 CORRECTING DEFECT 14 (vertices=73, convex hull=128) normal vector of length zero at vertex 148223 with 3 faces After retessellation of defect 14, euler #=1 (146488,439443,292956) : difference with theory (1) = 0 CORRECTING DEFECT 15 (vertices=19, convex hull=44) After retessellation of defect 15, euler #=2 (146494,439476,292984) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.22 (0.08-->10.07) (max @ vno 57834 --> 57844) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.22 (0.08-->10.07) (max @ vno 57834 --> 57844) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 69 mutations (37.9%), 113 crossovers (62.1%), 162 vertices were eliminated building final representation... 1772 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=146494, nf=292984, ne=439476, g=0) writing corrected surface to /root/Scrivania/subjects/ENP30S001A/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 9.4 minutes 0 defective edges removing intersecting faces 000: 190 intersecting 001: 6 intersecting 002: 2 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 146494 - 439476 + 292984 = 2 --> 0 holes F =2V-4: 292984 = 292988-4 (0) 2E=3F: 878952 = 878952 (0) total defect index = 0 /root/Scrivania/subjects/ENP30S001A/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 60 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Tue Aug 29 19:25:15 CEST 2017 /root/Scrivania/subjects/ENP30S001A/scripts mris_make_surfaces -noaparc -mgz -T1 brain.finalsurfs ENP30S001A rh not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /root/Scrivania/subjects/ENP30S001A/mri/filled.mgz... reading volume /root/Scrivania/subjects/ENP30S001A/mri/brain.finalsurfs.mgz... reading volume /root/Scrivania/subjects/ENP30S001A/mri/wm.mgz... 15270 bright wm thresholded. 253 bright non-wm voxels segmented. reading original surface position from /root/Scrivania/subjects/ENP30S001A/surf/rh.orig... computing class statistics... border white: 279213 voxels (1.66%) border gray 305834 voxels (1.82%) WM (95.0): 96.2 +- 8.0 [70.0 --> 110.0] GM (82.0) : 80.5 +- 11.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 59.2 (was 70) setting MAX_BORDER_WHITE to 113.0 (was 105) setting MIN_BORDER_WHITE to 71.0 (was 85) setting MAX_CSF to 47.5 (was 40) setting MAX_GRAY to 97.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 65.1 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 35.7 (was 40) repositioning cortical surface to gray/white boundary reading volume /root/Scrivania/subjects/ENP30S001A/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.04-->4.93) (max @ vno 115644 --> 146363) face area 0.28 +- 0.12 (0.00-->3.16) mean absolute distance = 0.72 +- 0.94 3175 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=71 mean inside = 95.4, mean outside = 76.9 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group mean border=81.7, 44 (44) missing vertices, mean dist 0.2 [0.7 (%38.7)->0.8 (%61.3))] %63 local maxima, %32 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=Brain, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.25 (0.09-->7.17) (max @ vno 146363 --> 105868) face area 0.28 +- 0.13 (0.00-->3.99) mean absolute distance = 0.35 +- 0.62 2794 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5702343.0, rms=10.46 001: dt: 0.5000, sse=6405871.0, rms=7.318 (0.000%) 002: dt: 0.5000, sse=6826688.5, rms=5.434 (0.000%) 003: dt: 0.5000, sse=7166785.5, rms=4.323 (0.000%) 004: dt: 0.5000, sse=7463928.5, rms=3.664 (0.000%) 005: dt: 0.5000, sse=7598569.5, rms=3.406 (0.000%) 006: dt: 0.5000, sse=7705287.5, rms=3.236 (0.000%) rms = 3.22, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=7724298.0, rms=3.216 (0.000%) 008: dt: 0.2500, sse=4660595.5, rms=2.092 (0.000%) 009: dt: 0.2500, sse=4222490.5, rms=1.798 (0.000%) 010: dt: 0.2500, sse=4037516.8, rms=1.727 (0.000%) rms = 1.69, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=3981314.8, rms=1.690 (0.000%) rms = 1.65, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=3912573.2, rms=1.653 (0.000%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=84.7, 50 (27) missing vertices, mean dist -0.2 [0.4 (%71.8)->0.2 (%28.2))] %74 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=Brain, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.24 (0.10-->7.62) (max @ vno 146363 --> 105868) face area 0.35 +- 0.16 (0.00-->5.36) mean absolute distance = 0.25 +- 0.39 3400 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4544403.0, rms=4.50 013: dt: 0.5000, sse=4911992.5, rms=2.799 (0.000%) rms = 2.85, time step reduction 1 of 3 to 0.250... 014: dt: 0.2500, sse=4552014.5, rms=2.210 (0.000%) 015: dt: 0.2500, sse=4360258.0, rms=1.699 (0.000%) 016: dt: 0.2500, sse=4265820.5, rms=1.489 (0.000%) 017: dt: 0.2500, sse=4205783.0, rms=1.427 (0.000%) rms = 1.40, time step reduction 2 of 3 to 0.125... 018: dt: 0.2500, sse=4178903.5, rms=1.398 (0.000%) rms = 1.37, time step reduction 3 of 3 to 0.062... 019: dt: 0.1250, sse=4130657.8, rms=1.370 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=87.3, 34 (24) missing vertices, mean dist -0.2 [0.3 (%74.1)->0.2 (%25.9))] %85 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=Brain, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.24 (0.06-->7.81) (max @ vno 146363 --> 105868) face area 0.34 +- 0.16 (0.00-->5.50) mean absolute distance = 0.20 +- 0.29 2761 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4372754.0, rms=3.38 020: dt: 0.5000, sse=4658310.0, rms=2.480 (0.000%) rms = 2.77, time step reduction 1 of 3 to 0.250... 021: dt: 0.2500, sse=4366053.0, rms=1.737 (0.000%) 022: dt: 0.2500, sse=4271424.0, rms=1.355 (0.000%) 023: dt: 0.2500, sse=4252276.0, rms=1.251 (0.000%) rms = 1.25, time step reduction 2 of 3 to 0.125... rms = 1.24, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=4226660.0, rms=1.236 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=88.2, 30 (17) missing vertices, mean dist -0.0 [0.2 (%58.0)->0.2 (%42.0))] %88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=Brain, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /root/Scrivania/subjects/ENP30S001A/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=4242564.0, rms=1.61 rms = 1.75, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=4273110.5, rms=1.149 (0.000%) 026: dt: 0.2500, sse=4404211.5, rms=0.936 (0.000%) rms = 0.96, time step reduction 2 of 3 to 0.125... rms = 0.93, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=4402747.0, rms=0.935 (0.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 19 non-cortical segments detected only using segment with 2202 vertices erasing segment 1 (vno[0] = 62620) erasing segment 2 (vno[0] = 92515) erasing segment 3 (vno[0] = 94741) erasing segment 4 (vno[0] = 95898) erasing segment 5 (vno[0] = 95914) erasing segment 6 (vno[0] = 102530) erasing segment 7 (vno[0] = 103624) erasing segment 8 (vno[0] = 103688) erasing segment 9 (vno[0] = 103728) erasing segment 10 (vno[0] = 104751) erasing segment 11 (vno[0] = 104822) erasing segment 12 (vno[0] = 106808) erasing segment 13 (vno[0] = 107794) erasing segment 14 (vno[0] = 109732) erasing segment 15 (vno[0] = 111591) erasing segment 16 (vno[0] = 111600) erasing segment 17 (vno[0] = 111619) erasing segment 18 (vno[0] = 111654) writing cortex label to /root/Scrivania/subjects/ENP30S001A/label/rh.cortex.label... writing curvature file /root/Scrivania/subjects/ENP30S001A/surf/rh.curv writing smoothed area to rh.area writing curvature file /root/Scrivania/subjects/ENP30S001A/surf/rh.area vertex spacing 0.89 +- 0.25 (0.06-->7.87) (max @ vno 105868 --> 146363) face area 0.33 +- 0.16 (0.00-->5.42) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... smoothing surface for 5 iterations... mean border=60.5, 38 (38) missing vertices, mean dist 1.7 [0.1 (%0.0)->2.3 (%100.0))] %22 local maxima, %47 large gradients and %26 min vals, 2197 gradients ignored tol=1.0e-04, sigma=2.0, host=Brain, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=24539720.0, rms=27.79 001: dt: 0.5000, sse=18647480.0, rms=23.718 (0.000%) 002: dt: 0.5000, sse=14287355.0, rms=20.215 (0.000%) 003: dt: 0.5000, sse=11284376.0, rms=17.302 (0.000%) 004: dt: 0.5000, sse=9317794.0, rms=14.879 (0.000%) 005: dt: 0.5000, sse=8024025.5, rms=12.890 (0.000%) 006: dt: 0.5000, sse=7175750.5, rms=11.253 (0.000%) 007: dt: 0.5000, sse=6657254.5, rms=9.798 (0.000%) 008: dt: 0.5000, sse=6366998.0, rms=8.468 (0.000%) 009: dt: 0.5000, sse=6185964.0, rms=7.222 (0.000%) 010: dt: 0.5000, sse=6137974.0, rms=6.101 (0.000%) 011: dt: 0.5000, sse=6207756.0, rms=5.199 (0.000%) 012: dt: 0.5000, sse=6282500.0, rms=4.569 (0.000%) 013: dt: 0.5000, sse=6451894.0, rms=4.184 (0.000%) 014: dt: 0.5000, sse=6508639.5, rms=3.928 (0.000%) 015: dt: 0.5000, sse=6616787.5, rms=3.790 (0.000%) 016: dt: 0.5000, sse=6596986.0, rms=3.695 (0.000%) rms = 3.66, time step reduction 1 of 3 to 0.250... 017: dt: 0.5000, sse=6679531.0, rms=3.661 (0.000%) 018: dt: 0.2500, sse=4492114.0, rms=2.857 (0.000%) 019: dt: 0.2500, sse=4287860.5, rms=2.629 (0.000%) rms = 2.59, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=4171476.8, rms=2.591 (0.000%) 021: dt: 0.1250, sse=3977533.8, rms=2.449 (0.000%) rms = 2.43, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=3951687.8, rms=2.431 (0.000%) positioning took 1.5 minutes mean border=57.6, 740 (11) missing vertices, mean dist 0.2 [0.2 (%43.6)->0.5 (%56.4))] %41 local maxima, %35 large gradients and %20 min vals, 606 gradients ignored tol=1.0e-04, sigma=1.0, host=Brain, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4768926.0, rms=5.29 023: dt: 0.5000, sse=4797700.5, rms=3.869 (0.000%) 024: dt: 0.5000, sse=6160785.5, rms=3.720 (0.000%) rms = 3.78, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=5046288.0, rms=2.916 (0.000%) 026: dt: 0.2500, sse=4597392.5, rms=2.574 (0.000%) 027: dt: 0.2500, sse=4552962.5, rms=2.495 (0.000%) rms = 2.48, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=4524732.5, rms=2.475 (0.000%) 029: dt: 0.1250, sse=4341472.5, rms=2.296 (0.000%) rms = 2.27, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=4323674.0, rms=2.270 (0.000%) positioning took 0.6 minutes mean border=55.7, 950 (3) missing vertices, mean dist 0.1 [0.2 (%37.9)->0.3 (%62.1))] %54 local maxima, %22 large gradients and %19 min vals, 660 gradients ignored tol=1.0e-04, sigma=0.5, host=Brain, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4546630.5, rms=3.52 rms = 3.53, time step reduction 1 of 3 to 0.250... 031: dt: 0.2500, sse=4351162.0, rms=2.900 (0.000%) 032: dt: 0.2500, sse=4324523.0, rms=2.468 (0.000%) 033: dt: 0.2500, sse=4493762.0, rms=2.366 (0.000%) rms = 2.35, time step reduction 2 of 3 to 0.125... 034: dt: 0.2500, sse=4545132.5, rms=2.354 (0.000%) 035: dt: 0.1250, sse=4408806.0, rms=2.218 (0.000%) rms = 2.19, time step reduction 3 of 3 to 0.062... 036: dt: 0.1250, sse=4412772.5, rms=2.195 (0.000%) positioning took 0.5 minutes mean border=54.8, 2296 (2) missing vertices, mean dist 0.0 [0.2 (%44.0)->0.3 (%56.0))] %59 local maxima, %17 large gradients and %19 min vals, 534 gradients ignored tol=1.0e-04, sigma=0.2, host=Brain, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /root/Scrivania/subjects/ENP30S001A/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=4454894.0, rms=2.53 rms = 3.08, time step reduction 1 of 3 to 0.250... 037: dt: 0.2500, sse=4351642.0, rms=2.274 (0.000%) 038: dt: 0.2500, sse=4487932.5, rms=2.176 (0.000%) rms = 2.16, time step reduction 2 of 3 to 0.125... 039: dt: 0.2500, sse=4553325.5, rms=2.159 (0.000%) 040: dt: 0.1250, sse=4474079.5, rms=2.062 (0.000%) rms = 2.04, time step reduction 3 of 3 to 0.062... 041: dt: 0.1250, sse=4481417.0, rms=2.045 (0.000%) positioning took 0.4 minutes writing curvature file /root/Scrivania/subjects/ENP30S001A/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /root/Scrivania/subjects/ENP30S001A/surf/rh.area.pial vertex spacing 0.98 +- 0.40 (0.10-->8.78) (max @ vno 95909 --> 95896) face area 0.38 +- 0.27 (0.00-->7.96) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 146494 vertices processed 25000 of 146494 vertices processed 50000 of 146494 vertices processed 75000 of 146494 vertices processed 100000 of 146494 vertices processed 125000 of 146494 vertices processed 0 of 146494 vertices processed 25000 of 146494 vertices processed 50000 of 146494 vertices processed 75000 of 146494 vertices processed 100000 of 146494 vertices processed 125000 of 146494 vertices processed thickness calculation complete, 468:642 truncations. 35696 vertices at 0 distance 105049 vertices at 1 distance 88664 vertices at 2 distance 35183 vertices at 3 distance 11107 vertices at 4 distance 3442 vertices at 5 distance 1051 vertices at 6 distance 356 vertices at 7 distance 139 vertices at 8 distance 51 vertices at 9 distance 30 vertices at 10 distance 20 vertices at 11 distance 14 vertices at 12 distance 20 vertices at 13 distance 11 vertices at 14 distance 17 vertices at 15 distance 17 vertices at 16 distance 10 vertices at 17 distance 6 vertices at 18 distance 3 vertices at 19 distance 6 vertices at 20 distance writing curvature file /root/Scrivania/subjects/ENP30S001A/surf/rh.thickness positioning took 7.4 minutes #-------------------------------------------- #@# Smooth2 rh Tue Aug 29 19:32:37 CEST 2017 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /root/Scrivania/subjects/ENP30S001A/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 rh Tue Aug 29 19:32:39 CEST 2017 /root/Scrivania/subjects/ENP30S001A/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 47.4 mm, total surface area = 87954 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.114 (target=0.015) step 005: RMS=0.077 (target=0.015) step 010: RMS=0.055 (target=0.015) step 015: RMS=0.045 (target=0.015) step 020: RMS=0.037 (target=0.015) step 025: RMS=0.031 (target=0.015) step 030: RMS=0.025 (target=0.015) step 035: RMS=0.021 (target=0.015) step 040: RMS=0.018 (target=0.015) step 045: RMS=0.016 (target=0.015) inflation complete. inflation took 0.3 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 274 vertices thresholded to be in k1 ~ [-0.23 0.35], k2 ~ [-0.09 0.06] total integrated curvature = 0.547*4pi (6.879) --> 0 handles ICI = 1.9, FI = 14.3, variation=235.521 138 vertices thresholded to be in [-0.01 0.01] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 142 vertices thresholded to be in [-0.12 0.18] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.015, std = 0.028 done. #----------------------------------------- #@# Curvature Stats rh Tue Aug 29 19:33:54 CEST 2017 /root/Scrivania/subjects/ENP30S001A/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm ENP30S001A rh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/rh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ ENP30S001A/rh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 252 ] Gb_filter = 0 WARN: S lookup min: -0.036446 WARN: S explicit min: 0.000000 vertex = 321 #-------------------------------------------- #@# ASeg Stats Tue Aug 29 19:33:57 CEST 2017 INFO: mri_segstats will not calculate Supratentorial due to missing ribbon.mgz file /root/Scrivania/subjects/ENP30S001A mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/freesurfer/ASegStatsLUT.txt --subject ENP30S001A $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/freesurfer/ASegStatsLUT.txt --subject ENP30S001A sysname Linux hostname Braindata machine x86_64 user root UseRobust 0 atlas_icv (eTIV) = 1682783 mm^3 (det: 1.157669 ) mghRead(/root/Scrivania/subjects/ENP30S001A/mri/ribbon.mgz, -1): could not open file Computing euler number orig.nofix lheno = -34, rheno = -38 orig.nofix lhholes = 18, rhholes = 20 Loading mri/aseg.mgz Getting Brain Volume Statistics Linux Braindata 3.19.0-15-generic #15-Ubuntu SMP Thu Apr 16 23:32:37 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux recon-all -s ENP30S001A exited with ERRORS at Tue Aug 29 19:34:03 CEST 2017 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all Wed Sep 6 09:18:48 CEST 2017 /root/Scrivania/subjects/ENP30S001A /usr/local/freesurfer/bin/recon-all -s ENP30S001A -autorecon2 subjid ENP30S001A setenv SUBJECTS_DIR /root/Scrivania/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux Braindata 3.19.0-15-generic #15-Ubuntu SMP Thu Apr 16 23:32:37 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 128307 maxlocks unlimited maxsignal 128307 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 32869864 11623548 21246316 66956 290280 10337808 -/+ buffers/cache: 995460 31874404 Swap: 33472508 0 33472508 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/09/06-07:18:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/09/06-07:18:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/09/06-07:18:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/09/06-07:18:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/09/06-07:18:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/09/06-07:18:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/09/06-07:18:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/09/06-07:18:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/09/06-07:18:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/09/06-07:18:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/09/06-07:18:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/09/06-07:18:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/09/06-07:18:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/09/06-07:18:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/09/06-07:18:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/09/06-07:18:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/09/06-07:18:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/09/06-07:18:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/09/06-07:18:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/09/06-07:18:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/09/06-07:18:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/09/06-07:18:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/09/06-07:18:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/09/06-07:18:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/09/06-07:18:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/09/06-07:18:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/09/06-07:18:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/09/06-07:18:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/09/06-07:18:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/09/06-07:18:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/09/06-07:18:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/09/06-07:18:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/09/06-07:18:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/09/06-07:18:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/09/06-07:18:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/09/06-07:18:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/09/06-07:18:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/09/06-07:18:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: root Machine: Braindata Platform: Linux PlatformVersion: 3.19.0-15-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #------------------------------------- #@# EM Registration Wed Sep 6 09:18:52 CEST 2017 /root/Scrivania/subjects/ENP30S001A/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta ======= NUMBER OF OPENMP THREADS = 1 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 14.9 or > 790.2 total sample mean = 84.4 (994 zeros) ************************************************ spacing=8, using 2772 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2772, passno 0, spacing 8 resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=22.9 skull bounding box = (57, 77, 42) --> (195, 207, 201) using (103, 120, 122) as brain centroid... mean wm in atlas = 107, using box (86,104,102) --> (119, 135,141) to find MRI wm before smoothing, mri peak at 105 after smoothing, mri peak at 105, scaling input intensities by 1.019 scaling channel 0 by 1.01905 initial log_p = -4.3 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.028454 @ (-9.091, -27.273, -9.091) max log p = -3.788519 @ (4.545, 4.545, -4.545) max log p = -3.679009 @ (2.273, 6.818, 2.273) max log p = -3.639682 @ (-1.136, -3.409, -1.136) max log p = -3.635263 @ (1.705, 1.705, -0.568) max log p = -3.635263 @ (0.000, 0.000, 0.000) Found translation: (-1.7, -17.6, -13.1): log p = -3.635 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.4, old_max_log_p =-3.6 (thresh=-3.6) 0.991 0.145 0.039 -24.993; -0.131 1.101 0.295 -49.604; 0.000 -0.259 0.966 33.789; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.4, old_max_log_p =-3.4 (thresh=-3.4) 0.991 0.145 0.039 -24.993; -0.131 1.101 0.295 -49.604; 0.000 -0.259 0.966 33.789; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.2, old_max_log_p =-3.4 (thresh=-3.4) 1.012 0.127 -0.036 -14.850; -0.100 1.092 0.255 -49.625; 0.065 -0.223 1.011 13.540; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2) 1.012 0.127 -0.036 -14.850; -0.104 1.120 0.226 -49.632; 0.061 -0.184 1.000 9.900; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2) 1.010 0.123 -0.020 -16.949; -0.103 1.119 0.243 -50.632; 0.046 -0.203 0.993 14.381; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2) 1.008 0.123 -0.020 -16.612; -0.103 1.122 0.243 -51.029; 0.046 -0.204 0.995 14.168; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2) 1.008 0.123 -0.020 -16.612; -0.103 1.119 0.243 -50.631; 0.046 -0.204 0.999 13.847; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2) 1.008 0.123 -0.020 -16.612; -0.103 1.119 0.243 -50.631; 0.046 -0.204 0.999 13.847; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2772 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.00784 0.12282 -0.01976 -16.61161; -0.10285 1.11918 0.24274 -50.63125; 0.04595 -0.20448 0.99897 13.84704; 0.00000 0.00000 0.00000 1.00000; nsamples 2772 Quasinewton: input matrix 1.00784 0.12282 -0.01976 -16.61161; -0.10285 1.11918 0.24274 -50.63125; 0.04595 -0.20448 0.99897 13.84704; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.008 0.123 -0.020 -16.612; -0.103 1.119 0.243 -50.631; 0.046 -0.204 0.999 13.847; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.2 (old=-4.3) transform before final EM align: 1.008 0.123 -0.020 -16.612; -0.103 1.119 0.243 -50.631; 0.046 -0.204 0.999 13.847; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 312841 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.00784 0.12282 -0.01976 -16.61161; -0.10285 1.11918 0.24274 -50.63125; 0.04595 -0.20448 0.99897 13.84704; 0.00000 0.00000 0.00000 1.00000; nsamples 312841 Quasinewton: input matrix 1.00784 0.12282 -0.01976 -16.61161; -0.10285 1.11918 0.24274 -50.63125; 0.04595 -0.20448 0.99897 13.84704; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 012: -log(p) = 3.7 tol 0.000000 final transform: 1.008 0.123 -0.020 -16.612; -0.103 1.119 0.243 -50.631; 0.046 -0.204 0.999 13.847; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 15 minutes and 49 seconds. #-------------------------------------- #@# CA Normalize Wed Sep 6 09:34:42 CEST 2017 /root/Scrivania/subjects/ENP30S001A/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=22.9 skull bounding box = (57, 77, 42) --> (195, 207, 202) using (103, 120, 122) as brain centroid... mean wm in atlas = 107, using box (86,104,102) --> (119, 135,141) to find MRI wm before smoothing, mri peak at 105 after smoothing, mri peak at 105, scaling input intensities by 1.019 scaling channel 0 by 1.01905 using 244171 sample points... INFO: compute sample coordinates transform 1.008 0.123 -0.020 -16.612; -0.103 1.119 0.243 -50.631; 0.046 -0.204 0.999 13.847; 0.000 0.000 0.000 1.000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (120, 81, 39) --> (193, 182, 200) Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 147.0 0 of 490 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (61, 79, 39) --> (131, 175, 201) Right_Cerebral_White_Matter: limiting intensities to 94.0 --> 147.0 0 of 251 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (123, 158, 66) --> (170, 200, 118) Left_Cerebellum_White_Matter: limiting intensities to 103.0 --> 147.0 0 of 10 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (75, 158, 64) --> (124, 193, 120) Right_Cerebellum_White_Matter: limiting intensities to 97.0 --> 147.0 0 of 15 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (106, 148, 100) --> (140, 209, 129) Brain_Stem: limiting intensities to 97.0 --> 147.0 0 of 20 (0.0%) samples deleted using 786 total control points for intensity normalization... bias field = 0.991 +- 0.068 1 of 786 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (120, 81, 39) --> (193, 182, 200) Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 139.0 0 of 534 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (61, 79, 39) --> (131, 175, 201) Right_Cerebral_White_Matter: limiting intensities to 93.0 --> 139.0 0 of 275 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (123, 158, 66) --> (170, 200, 118) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 139.0 0 of 68 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (75, 158, 64) --> (124, 193, 120) Right_Cerebellum_White_Matter: limiting intensities to 87.0 --> 139.0 0 of 68 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (106, 148, 100) --> (140, 209, 129) Brain_Stem: limiting intensities to 83.0 --> 139.0 0 of 85 (0.0%) samples deleted using 1030 total control points for intensity normalization... bias field = 1.004 +- 0.061 0 of 1030 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (120, 81, 39) --> (193, 182, 200) Left_Cerebral_White_Matter: limiting intensities to 93.0 --> 139.0 0 of 601 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (61, 79, 39) --> (131, 175, 201) Right_Cerebral_White_Matter: limiting intensities to 93.0 --> 139.0 1 of 367 (0.3%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (123, 158, 66) --> (170, 200, 118) Left_Cerebellum_White_Matter: limiting intensities to 83.0 --> 139.0 0 of 99 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (75, 158, 64) --> (124, 193, 120) Right_Cerebellum_White_Matter: limiting intensities to 81.0 --> 139.0 0 of 74 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (106, 148, 100) --> (140, 209, 129) Brain_Stem: limiting intensities to 75.0 --> 139.0 0 of 182 (0.0%) samples deleted using 1323 total control points for intensity normalization... bias field = 1.004 +- 0.046 0 of 1322 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 5 seconds. #-------------------------------------- #@# CA Reg Wed Sep 6 09:35:46 CEST 2017 /root/Scrivania/subjects/ENP30S001A/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log ======= NUMBER OF OPENMP THREADS = 1 ======= reading input volume 'norm.mgz'... reading GCA '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.19 (predicted orig area = 6.7) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.768, neg=0, invalid=96777 0001: dt=129.472000, rms=0.705 (8.263%), neg=0, invalid=96777 0002: dt=129.472000, rms=0.692 (1.831%), neg=0, invalid=96777 0003: dt=369.920000, rms=0.681 (1.596%), neg=0, invalid=96777 0004: dt=110.976000, rms=0.676 (0.722%), neg=0, invalid=96777 0005: dt=129.472000, rms=0.674 (0.286%), neg=0, invalid=96777 0006: dt=129.472000, rms=0.672 (0.343%), neg=0, invalid=96777 0007: dt=129.472000, rms=0.670 (0.207%), neg=0, invalid=96777 0008: dt=129.472000, rms=0.669 (0.241%), neg=0, invalid=96777 0009: dt=129.472000, rms=0.666 (0.365%), neg=0, invalid=96777 0010: dt=129.472000, rms=0.664 (0.373%), neg=0, invalid=96777 0011: dt=129.472000, rms=0.661 (0.451%), neg=0, invalid=96777 0012: dt=129.472000, rms=0.658 (0.392%), neg=0, invalid=96777 0013: dt=129.472000, rms=0.656 (0.346%), neg=0, invalid=96777 0014: dt=129.472000, rms=0.654 (0.290%), neg=0, invalid=96777 0015: dt=129.472000, rms=0.653 (0.230%), neg=0, invalid=96777 0016: dt=129.472000, rms=0.651 (0.287%), neg=0, invalid=96777 0017: dt=129.472000, rms=0.649 (0.246%), neg=0, invalid=96777 0018: dt=129.472000, rms=0.647 (0.279%), neg=0, invalid=96777 0019: dt=129.472000, rms=0.646 (0.242%), neg=0, invalid=96777 0020: dt=129.472000, rms=0.644 (0.297%), neg=0, invalid=96777 0021: dt=129.472000, rms=0.642 (0.229%), neg=0, invalid=96777 0022: dt=129.472000, rms=0.641 (0.180%), neg=0, invalid=96777 0023: dt=129.472000, rms=0.640 (0.197%), neg=0, invalid=96777 0024: dt=129.472000, rms=0.639 (0.189%), neg=0, invalid=96777 0025: dt=129.472000, rms=0.638 (0.152%), neg=0, invalid=96777 0026: dt=129.472000, rms=0.637 (0.125%), neg=0, invalid=96777 0027: dt=129.472000, rms=0.636 (0.137%), neg=0, invalid=96777 0028: dt=129.472000, rms=0.635 (0.116%), neg=0, invalid=96777 0029: dt=129.472000, rms=0.635 (0.106%), neg=0, invalid=96777 0030: dt=517.888000, rms=0.635 (0.031%), neg=0, invalid=96777 0031: dt=517.888000, rms=0.634 (0.001%), neg=0, invalid=96777 0032: dt=517.888000, rms=0.635 (-0.597%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.635, neg=0, invalid=96777 0033: dt=129.472000, rms=0.633 (0.186%), neg=0, invalid=96777 0034: dt=517.888000, rms=0.632 (0.137%), neg=0, invalid=96777 0035: dt=517.888000, rms=0.632 (-0.357%), neg=0, invalid=96777 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.637, neg=0, invalid=96777 0036: dt=145.152000, rms=0.630 (1.132%), neg=0, invalid=96777 0037: dt=36.288000, rms=0.627 (0.569%), neg=0, invalid=96777 0038: dt=124.416000, rms=0.621 (0.861%), neg=0, invalid=96777 0039: dt=20.736000, rms=0.618 (0.454%), neg=0, invalid=96777 0040: dt=145.152000, rms=0.616 (0.464%), neg=0, invalid=96777 0041: dt=36.288000, rms=0.612 (0.584%), neg=0, invalid=96777 0042: dt=31.104000, rms=0.611 (0.135%), neg=0, invalid=96777 0043: dt=31.104000, rms=0.610 (0.203%), neg=0, invalid=96777 0044: dt=31.104000, rms=0.608 (0.265%), neg=0, invalid=96777 0045: dt=31.104000, rms=0.606 (0.345%), neg=0, invalid=96777 0046: dt=31.104000, rms=0.604 (0.404%), neg=0, invalid=96777 0047: dt=31.104000, rms=0.601 (0.467%), neg=0, invalid=96777 0048: dt=31.104000, rms=0.598 (0.506%), neg=0, invalid=96777 0049: dt=31.104000, rms=0.595 (0.493%), neg=0, invalid=96777 0050: dt=31.104000, rms=0.592 (0.449%), neg=0, invalid=96777 0051: dt=31.104000, rms=0.590 (0.379%), neg=0, invalid=96777 0052: dt=31.104000, rms=0.588 (0.384%), neg=0, invalid=96777 0053: dt=31.104000, rms=0.586 (0.355%), neg=0, invalid=96777 0054: dt=31.104000, rms=0.584 (0.311%), neg=0, invalid=96777 0055: dt=31.104000, rms=0.582 (0.247%), neg=0, invalid=96777 0056: dt=31.104000, rms=0.581 (0.226%), neg=0, invalid=96777 0057: dt=31.104000, rms=0.580 (0.237%), neg=0, invalid=96777 0058: dt=31.104000, rms=0.578 (0.217%), neg=0, invalid=96777 0059: dt=31.104000, rms=0.577 (0.168%), neg=0, invalid=96777 0060: dt=31.104000, rms=0.577 (0.139%), neg=0, invalid=96777 0061: dt=31.104000, rms=0.576 (0.137%), neg=0, invalid=96777 0062: dt=31.104000, rms=0.575 (0.116%), neg=0, invalid=96777 0063: dt=31.104000, rms=0.575 (0.112%), neg=0, invalid=96777 0064: dt=31.104000, rms=0.574 (0.008%), neg=0, invalid=96777 0065: dt=31.104000, rms=0.574 (0.013%), neg=0, invalid=96777 0066: dt=31.104000, rms=0.574 (0.028%), neg=0, invalid=96777 0067: dt=31.104000, rms=0.574 (0.020%), neg=0, invalid=96777 0068: dt=31.104000, rms=0.574 (0.016%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.574, neg=0, invalid=96777 0069: dt=124.416000, rms=0.573 (0.233%), neg=0, invalid=96777 0070: dt=36.288000, rms=0.572 (0.074%), neg=0, invalid=96777 0071: dt=36.288000, rms=0.572 (0.018%), neg=0, invalid=96777 0072: dt=36.288000, rms=0.572 (0.030%), neg=0, invalid=96777 0073: dt=36.288000, rms=0.572 (0.036%), neg=0, invalid=96777 0074: dt=36.288000, rms=0.572 (0.009%), neg=0, invalid=96777 0075: dt=36.288000, rms=0.572 (-0.016%), neg=0, invalid=96777 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.592, neg=0, invalid=96777 0076: dt=2.000000, rms=0.592 (0.007%), neg=0, invalid=96777 0077: dt=0.700000, rms=0.592 (0.001%), neg=0, invalid=96777 0078: dt=0.700000, rms=0.592 (0.000%), neg=0, invalid=96777 0079: dt=0.700000, rms=0.592 (-0.006%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.592, neg=0, invalid=96777 0080: dt=0.000000, rms=0.592 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.650, neg=0, invalid=96777 0081: dt=5.217893, rms=0.632 (2.803%), neg=0, invalid=96777 0082: dt=2.421053, rms=0.631 (0.100%), neg=0, invalid=96777 0083: dt=2.421053, rms=0.631 (-0.029%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.631, neg=0, invalid=96777 0084: dt=0.000000, rms=0.631 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.686, neg=0, invalid=96777 0085: dt=1.085714, rms=0.682 (0.545%), neg=0, invalid=96777 0086: dt=1.926380, rms=0.678 (0.700%), neg=0, invalid=96777 0087: dt=0.448000, rms=0.677 (0.052%), neg=0, invalid=96777 0088: dt=0.448000, rms=0.677 (0.031%), neg=0, invalid=96777 0089: dt=0.448000, rms=0.677 (0.020%), neg=0, invalid=96777 0090: dt=0.448000, rms=0.677 (-0.018%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.677, neg=0, invalid=96777 0091: dt=1.295455, rms=0.676 (0.173%), neg=0, invalid=96777 0092: dt=0.004000, rms=0.676 (0.001%), neg=0, invalid=96777 0093: dt=0.004000, rms=0.676 (0.000%), neg=0, invalid=96777 0094: dt=0.004000, rms=0.676 (-0.000%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.637, neg=0, invalid=96777 0095: dt=0.448000, rms=0.622 (2.355%), neg=0, invalid=96777 0096: dt=0.000000, rms=0.622 (0.008%), neg=0, invalid=96777 0097: dt=0.050000, rms=0.622 (-0.340%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.622, neg=0, invalid=96777 0098: dt=0.000000, rms=0.622 (0.000%), neg=0, invalid=96777 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.11339 (17) Left_Lateral_Ventricle (4): linear fit = 0.55 x + 0.0 (1546 voxels, overlap=0.005) Left_Lateral_Ventricle (4): linear fit = 0.55 x + 0.0 (1546 voxels, peak = 13), gca=13.1 gca peak = 0.14022 (22) mri peak = 0.11937 (17) Right_Lateral_Ventricle (43): linear fit = 0.68 x + 0.0 (720 voxels, overlap=0.208) Right_Lateral_Ventricle (43): linear fit = 0.68 x + 0.0 (720 voxels, peak = 15), gca=14.9 gca peak = 0.24234 (100) mri peak = 0.09836 (98) Right_Pallidum (52): linear fit = 0.96 x + 0.0 (448 voxels, overlap=0.780) Right_Pallidum (52): linear fit = 0.96 x + 0.0 (448 voxels, peak = 96), gca=96.5 gca peak = 0.19192 (97) mri peak = 0.08027 (86) Left_Pallidum (13): linear fit = 0.88 x + 0.0 (295 voxels, overlap=0.097) Left_Pallidum (13): linear fit = 0.88 x + 0.0 (295 voxels, peak = 85), gca=84.9 gca peak = 0.24007 (63) mri peak = 0.06510 (74) Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (878 voxels, overlap=0.709) Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (878 voxels, peak = 72), gca=71.5 gca peak = 0.29892 (64) mri peak = 0.09758 (68) Left_Hippocampus (17): linear fit = 1.05 x + 0.0 (775 voxels, overlap=0.874) Left_Hippocampus (17): linear fit = 1.05 x + 0.0 (775 voxels, peak = 68), gca=67.5 gca peak = 0.12541 (104) mri peak = 0.08794 (106) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (77538 voxels, overlap=0.812) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (77538 voxels, peak = 106), gca=105.6 gca peak = 0.13686 (104) mri peak = 0.09464 (108) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (78054 voxels, overlap=0.772) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (78054 voxels, peak = 107), gca=106.6 gca peak = 0.11691 (63) mri peak = 0.04233 (63) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (24187 voxels, overlap=0.997) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (24187 voxels, peak = 62), gca=62.1 gca peak = 0.13270 (63) mri peak = 0.04409 (63) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (25940 voxels, overlap=0.997) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (25940 voxels, peak = 63), gca=63.0 gca peak = 0.15182 (70) mri peak = 0.10241 (81) Right_Caudate (50): linear fit = 1.08 x + 0.0 (442 voxels, overlap=0.451) Right_Caudate (50): linear fit = 1.08 x + 0.0 (442 voxels, peak = 75), gca=75.2 gca peak = 0.14251 (76) mri peak = 0.08777 (84) Left_Caudate (11): linear fit = 1.04 x + 0.0 (782 voxels, overlap=0.551) Left_Caudate (11): linear fit = 1.04 x + 0.0 (782 voxels, peak = 79), gca=79.4 gca peak = 0.12116 (60) mri peak = 0.03916 (60) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (27500 voxels, overlap=0.977) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (27500 voxels, peak = 62), gca=61.5 gca peak = 0.12723 (61) mri peak = 0.04462 (61) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (29316 voxels, overlap=0.982) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (29316 voxels, peak = 63), gca=62.5 gca peak = 0.22684 (88) mri peak = 0.08484 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (9023 voxels, overlap=0.689) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (9023 voxels, peak = 94), gca=93.7 gca peak = 0.21067 (87) mri peak = 0.10361 (92) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (8511 voxels, overlap=0.731) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (8511 voxels, peak = 92), gca=91.8 gca peak = 0.25455 (62) mri peak = 0.08931 (71) Left_Amygdala (18): linear fit = 1.12 x + 0.0 (383 voxels, overlap=0.156) Left_Amygdala (18): linear fit = 1.12 x + 0.0 (383 voxels, peak = 69), gca=69.1 gca peak = 0.39668 (62) mri peak = 0.12531 (68) Right_Amygdala (54): linear fit = 1.11 x + 0.0 (399 voxels, overlap=0.387) Right_Amygdala (54): linear fit = 1.11 x + 0.0 (399 voxels, peak = 69), gca=68.5 gca peak = 0.10129 (93) mri peak = 0.06667 (104) Left_Thalamus_Proper (10): linear fit = 1.12 x + 0.0 (5640 voxels, overlap=0.514) Left_Thalamus_Proper (10): linear fit = 1.12 x + 0.0 (5640 voxels, peak = 104), gca=103.7 gca peak = 0.12071 (89) mri peak = 0.06343 (94) Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (4143 voxels, overlap=0.783) Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (4143 voxels, peak = 93), gca=93.0 gca peak = 0.13716 (82) mri peak = 0.05825 (89) Left_Putamen (12): linear fit = 1.07 x + 0.0 (2265 voxels, overlap=0.876) Left_Putamen (12): linear fit = 1.07 x + 0.0 (2265 voxels, peak = 87), gca=87.3 gca peak = 0.15214 (84) mri peak = 0.05826 (89) Right_Putamen (51): linear fit = 1.05 x + 0.0 (2545 voxels, overlap=0.916) Right_Putamen (51): linear fit = 1.05 x + 0.0 (2545 voxels, peak = 89), gca=88.6 gca peak = 0.08983 (85) mri peak = 0.06586 (92) Brain_Stem (16): linear fit = 1.09 x + 0.0 (13471 voxels, overlap=0.666) Brain_Stem (16): linear fit = 1.09 x + 0.0 (13471 voxels, peak = 92), gca=92.2 gca peak = 0.11809 (92) mri peak = 0.07624 (101) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (917 voxels, overlap=0.555) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (917 voxels, peak = 101), gca=100.7 gca peak = 0.12914 (94) mri peak = 0.08480 (101) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (1213 voxels, overlap=0.423) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (1213 voxels, peak = 102), gca=102.0 gca peak = 0.21100 (36) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13542 (27) mri peak = 0.18261 (20) Fourth_Ventricle (15): linear fit = 0.71 x + 0.0 (269 voxels, overlap=0.149) Fourth_Ventricle (15): linear fit = 0.71 x + 0.0 (269 voxels, peak = 19), gca=19.3 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21802 (40) gca peak Third_Ventricle = 0.21100 (36) gca peak CSF = 0.17123 (45) gca peak Left_Accumbens_area = 0.25875 (69) gca peak Left_undetermined = 0.96240 (36) gca peak Left_vessel = 0.33262 (65) gca peak Left_choroid_plexus = 0.09846 (46) gca peak Right_Inf_Lat_Vent = 0.28113 (34) gca peak Right_Accumbens_area = 0.27120 (72) gca peak Right_vessel = 0.61915 (60) gca peak Right_choroid_plexus = 0.12775 (51) gca peak Fifth_Ventricle = 0.45329 (44) gca peak WM_hypointensities = 0.11729 (81) gca peak non_WM_hypointensities = 0.10912 (56) gca peak Optic_Chiasm = 0.33287 (75) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 1.07 x + 0.0 estimating mean wm scale to be 1.02 x + 0.0 estimating mean csf scale to be 0.64 x + 0.0 saving intensity scales to talairach.label_intensities.txt **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.633, neg=0, invalid=96777 0099: dt=129.472000, rms=0.628 (0.774%), neg=0, invalid=96777 0100: dt=129.472000, rms=0.626 (0.238%), neg=0, invalid=96777 0101: dt=129.472000, rms=0.625 (0.202%), neg=0, invalid=96777 0102: dt=110.976000, rms=0.624 (0.125%), neg=0, invalid=96777 0103: dt=129.472000, rms=0.623 (0.140%), neg=0, invalid=96777 0104: dt=110.976000, rms=0.623 (0.088%), neg=0, invalid=96777 0105: dt=129.472000, rms=0.622 (0.104%), neg=0, invalid=96777 0106: dt=92.480000, rms=0.622 (0.065%), neg=0, invalid=96777 0107: dt=129.472000, rms=0.621 (0.088%), neg=0, invalid=96777 0108: dt=73.984000, rms=0.621 (0.051%), neg=0, invalid=96777 0109: dt=129.472000, rms=0.621 (0.071%), neg=0, invalid=96777 0110: dt=110.976000, rms=0.620 (0.041%), neg=0, invalid=96777 0111: dt=110.976000, rms=0.620 (0.060%), neg=0, invalid=96777 0112: dt=110.976000, rms=0.619 (0.085%), neg=0, invalid=96777 0113: dt=110.976000, rms=0.619 (0.098%), neg=0, invalid=96777 0114: dt=110.976000, rms=0.618 (0.120%), neg=0, invalid=96777 0115: dt=110.976000, rms=0.617 (0.125%), neg=0, invalid=96777 0116: dt=110.976000, rms=0.617 (0.099%), neg=0, invalid=96777 0117: dt=110.976000, rms=0.616 (0.101%), neg=0, invalid=96777 0118: dt=110.976000, rms=0.616 (0.088%), neg=0, invalid=96777 0119: dt=110.976000, rms=0.615 (0.107%), neg=0, invalid=96777 0120: dt=110.976000, rms=0.614 (0.091%), neg=0, invalid=96777 0121: dt=110.976000, rms=0.614 (0.081%), neg=0, invalid=96777 0122: dt=110.976000, rms=0.613 (0.086%), neg=0, invalid=96777 0123: dt=110.976000, rms=0.613 (0.080%), neg=0, invalid=96777 0124: dt=110.976000, rms=0.612 (0.094%), neg=0, invalid=96777 0125: dt=110.976000, rms=0.612 (0.092%), neg=0, invalid=96777 0126: dt=110.976000, rms=0.611 (0.092%), neg=0, invalid=96777 0127: dt=110.976000, rms=0.611 (0.068%), neg=0, invalid=96777 0128: dt=110.976000, rms=0.610 (0.068%), neg=0, invalid=96777 0129: dt=110.976000, rms=0.610 (0.058%), neg=0, invalid=96777 0130: dt=110.976000, rms=0.610 (0.064%), neg=0, invalid=96777 0131: dt=110.976000, rms=0.609 (0.070%), neg=0, invalid=96777 0132: dt=110.976000, rms=0.609 (0.047%), neg=0, invalid=96777 0133: dt=110.976000, rms=0.608 (0.064%), neg=0, invalid=96777 0134: dt=110.976000, rms=0.608 (0.040%), neg=0, invalid=96777 0135: dt=110.976000, rms=0.608 (0.057%), neg=0, invalid=96777 0136: dt=110.976000, rms=0.607 (0.054%), neg=0, invalid=96777 0137: dt=110.976000, rms=0.607 (0.051%), neg=0, invalid=96777 0138: dt=110.976000, rms=0.607 (0.042%), neg=0, invalid=96777 0139: dt=110.976000, rms=0.607 (0.060%), neg=0, invalid=96777 0140: dt=110.976000, rms=0.606 (0.055%), neg=0, invalid=96777 0141: dt=110.976000, rms=0.606 (0.035%), neg=0, invalid=96777 0142: dt=110.976000, rms=0.606 (0.044%), neg=0, invalid=96777 0143: dt=110.976000, rms=0.605 (0.044%), neg=0, invalid=96777 0144: dt=110.976000, rms=0.605 (0.051%), neg=0, invalid=96777 0145: dt=110.976000, rms=0.605 (0.036%), neg=0, invalid=96777 0146: dt=110.976000, rms=0.605 (0.057%), neg=0, invalid=96777 0147: dt=110.976000, rms=0.604 (0.046%), neg=0, invalid=96777 0148: dt=110.976000, rms=0.604 (0.041%), neg=0, invalid=96777 0149: dt=110.976000, rms=0.604 (0.032%), neg=0, invalid=96777 0150: dt=110.976000, rms=0.604 (0.033%), neg=0, invalid=96777 0151: dt=110.976000, rms=0.603 (0.037%), neg=0, invalid=96777 0152: dt=110.976000, rms=0.603 (0.039%), neg=0, invalid=96777 0153: dt=110.976000, rms=0.603 (0.033%), neg=0, invalid=96777 0154: dt=110.976000, rms=0.603 (0.040%), neg=0, invalid=96777 0155: dt=110.976000, rms=0.603 (0.034%), neg=0, invalid=96777 0156: dt=110.976000, rms=0.602 (0.029%), neg=0, invalid=96777 0157: dt=110.976000, rms=0.602 (0.023%), neg=0, invalid=96777 0158: dt=110.976000, rms=0.602 (0.028%), neg=0, invalid=96777 0159: dt=110.976000, rms=0.602 (0.034%), neg=0, invalid=96777 0160: dt=110.976000, rms=0.602 (0.038%), neg=0, invalid=96777 0161: dt=110.976000, rms=0.601 (0.032%), neg=0, invalid=96777 0162: dt=110.976000, rms=0.601 (0.027%), neg=0, invalid=96777 0163: dt=110.976000, rms=0.601 (0.022%), neg=0, invalid=96777 0164: dt=110.976000, rms=0.601 (0.018%), neg=0, invalid=96777 0165: dt=129.472000, rms=0.601 (0.009%), neg=0, invalid=96777 0166: dt=129.472000, rms=0.601 (0.000%), neg=0, invalid=96777 0167: dt=129.472000, rms=0.601 (0.006%), neg=0, invalid=96777 0168: dt=129.472000, rms=0.601 (0.009%), neg=0, invalid=96777 0169: dt=129.472000, rms=0.601 (0.006%), neg=0, invalid=96777 0170: dt=129.472000, rms=0.601 (0.006%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.601, neg=0, invalid=96777 0171: dt=295.936000, rms=0.600 (0.167%), neg=0, invalid=96777 0172: dt=110.976000, rms=0.600 (0.058%), neg=0, invalid=96777 0173: dt=129.472000, rms=0.599 (0.036%), neg=0, invalid=96777 0174: dt=129.472000, rms=0.599 (0.021%), neg=0, invalid=96777 0175: dt=129.472000, rms=0.599 (0.046%), neg=0, invalid=96777 0176: dt=129.472000, rms=0.599 (0.041%), neg=0, invalid=96777 0177: dt=129.472000, rms=0.598 (0.064%), neg=0, invalid=96777 0178: dt=129.472000, rms=0.598 (0.035%), neg=0, invalid=96777 0179: dt=129.472000, rms=0.598 (0.059%), neg=0, invalid=96777 0180: dt=129.472000, rms=0.598 (0.016%), neg=0, invalid=96777 0181: dt=129.472000, rms=0.597 (0.059%), neg=0, invalid=96777 0182: dt=129.472000, rms=0.597 (0.024%), neg=0, invalid=96777 0183: dt=129.472000, rms=0.597 (0.030%), neg=0, invalid=96777 0184: dt=129.472000, rms=0.597 (0.028%), neg=0, invalid=96777 0185: dt=129.472000, rms=0.597 (0.021%), neg=0, invalid=96777 0186: dt=129.472000, rms=0.597 (0.011%), neg=0, invalid=96777 0187: dt=129.472000, rms=0.596 (0.021%), neg=0, invalid=96777 0188: dt=129.472000, rms=0.596 (0.013%), neg=0, invalid=96777 0189: dt=129.472000, rms=0.596 (0.008%), neg=0, invalid=96777 0190: dt=129.472000, rms=0.596 (0.018%), neg=0, invalid=96777 0191: dt=129.472000, rms=0.596 (0.012%), neg=0, invalid=96777 0192: dt=129.472000, rms=0.596 (0.011%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.597, neg=0, invalid=96777 0193: dt=124.416000, rms=0.594 (0.501%), neg=0, invalid=96777 0194: dt=103.680000, rms=0.591 (0.472%), neg=0, invalid=96777 0195: dt=25.920000, rms=0.589 (0.423%), neg=0, invalid=96777 0196: dt=145.152000, rms=0.586 (0.430%), neg=0, invalid=96777 0197: dt=31.104000, rms=0.584 (0.386%), neg=0, invalid=96777 0198: dt=36.288000, rms=0.583 (0.175%), neg=0, invalid=96777 0199: dt=82.944000, rms=0.581 (0.260%), neg=0, invalid=96777 0200: dt=25.920000, rms=0.580 (0.196%), neg=0, invalid=96777 0201: dt=145.152000, rms=0.578 (0.349%), neg=0, invalid=96777 0202: dt=20.736000, rms=0.577 (0.233%), neg=0, invalid=96777 0203: dt=580.608000, rms=0.570 (1.103%), neg=0, invalid=96777 0204: dt=20.736000, rms=0.568 (0.485%), neg=0, invalid=96777 0205: dt=82.944000, rms=0.567 (0.204%), neg=0, invalid=96777 0206: dt=36.288000, rms=0.566 (0.075%), neg=0, invalid=96777 0207: dt=82.944000, rms=0.565 (0.142%), neg=0, invalid=96777 0208: dt=25.920000, rms=0.565 (0.079%), neg=0, invalid=96777 0209: dt=248.832000, rms=0.563 (0.280%), neg=0, invalid=96777 0210: dt=20.736000, rms=0.563 (0.118%), neg=0, invalid=96777 0211: dt=82.944000, rms=0.562 (0.102%), neg=0, invalid=96777 0212: dt=36.288000, rms=0.561 (0.106%), neg=0, invalid=96777 0213: dt=31.104000, rms=0.561 (0.021%), neg=0, invalid=96777 0214: dt=31.104000, rms=0.561 (0.059%), neg=0, invalid=96777 0215: dt=31.104000, rms=0.561 (0.081%), neg=0, invalid=96777 0216: dt=31.104000, rms=0.560 (0.102%), neg=0, invalid=96777 0217: dt=31.104000, rms=0.559 (0.113%), neg=0, invalid=96777 0218: dt=31.104000, rms=0.558 (0.151%), neg=0, invalid=96777 0219: dt=31.104000, rms=0.557 (0.183%), neg=0, invalid=96777 0220: dt=31.104000, rms=0.556 (0.181%), neg=0, invalid=96777 0221: dt=31.104000, rms=0.555 (0.179%), neg=0, invalid=96777 0222: dt=31.104000, rms=0.555 (0.167%), neg=0, invalid=96777 0223: dt=31.104000, rms=0.554 (0.182%), neg=0, invalid=96777 0224: dt=31.104000, rms=0.552 (0.184%), neg=0, invalid=96777 0225: dt=31.104000, rms=0.551 (0.181%), neg=0, invalid=96777 0226: dt=31.104000, rms=0.551 (0.175%), neg=0, invalid=96777 0227: dt=31.104000, rms=0.550 (0.155%), neg=0, invalid=96777 0228: dt=31.104000, rms=0.549 (0.141%), neg=0, invalid=96777 0229: dt=31.104000, rms=0.548 (0.147%), neg=0, invalid=96777 0230: dt=31.104000, rms=0.547 (0.127%), neg=0, invalid=96777 0231: dt=31.104000, rms=0.547 (0.107%), neg=0, invalid=96777 0232: dt=31.104000, rms=0.546 (0.097%), neg=0, invalid=96777 0233: dt=31.104000, rms=0.546 (0.116%), neg=0, invalid=96777 0234: dt=31.104000, rms=0.545 (0.119%), neg=0, invalid=96777 0235: dt=31.104000, rms=0.544 (0.110%), neg=0, invalid=96777 0236: dt=31.104000, rms=0.544 (0.088%), neg=0, invalid=96777 0237: dt=31.104000, rms=0.543 (0.092%), neg=0, invalid=96777 0238: dt=31.104000, rms=0.543 (0.089%), neg=0, invalid=96777 0239: dt=31.104000, rms=0.542 (0.097%), neg=0, invalid=96777 0240: dt=31.104000, rms=0.542 (0.097%), neg=0, invalid=96777 0241: dt=31.104000, rms=0.542 (0.069%), neg=0, invalid=96777 0242: dt=31.104000, rms=0.541 (0.084%), neg=0, invalid=96777 0243: dt=31.104000, rms=0.541 (0.081%), neg=0, invalid=96777 0244: dt=31.104000, rms=0.540 (0.082%), neg=0, invalid=96777 0245: dt=31.104000, rms=0.540 (0.089%), neg=0, invalid=96777 0246: dt=31.104000, rms=0.539 (0.065%), neg=0, invalid=96777 0247: dt=31.104000, rms=0.539 (0.079%), neg=0, invalid=96777 0248: dt=31.104000, rms=0.539 (0.077%), neg=0, invalid=96777 0249: dt=31.104000, rms=0.538 (0.070%), neg=0, invalid=96777 0250: dt=31.104000, rms=0.538 (0.054%), neg=0, invalid=96777 0251: dt=31.104000, rms=0.537 (0.070%), neg=0, invalid=96777 0252: dt=31.104000, rms=0.537 (0.066%), neg=0, invalid=96777 0253: dt=31.104000, rms=0.537 (0.063%), neg=0, invalid=96777 0254: dt=31.104000, rms=0.537 (0.050%), neg=0, invalid=96777 0255: dt=31.104000, rms=0.536 (0.046%), neg=0, invalid=96777 0256: dt=31.104000, rms=0.536 (0.045%), neg=0, invalid=96777 0257: dt=31.104000, rms=0.536 (0.043%), neg=0, invalid=96777 0258: dt=31.104000, rms=0.535 (0.054%), neg=0, invalid=96777 0259: dt=31.104000, rms=0.535 (0.059%), neg=0, invalid=96777 0260: dt=31.104000, rms=0.535 (0.048%), neg=0, invalid=96777 0261: dt=31.104000, rms=0.535 (0.032%), neg=0, invalid=96777 0262: dt=31.104000, rms=0.535 (0.031%), neg=0, invalid=96777 0263: dt=31.104000, rms=0.534 (0.053%), neg=0, invalid=96777 0264: dt=31.104000, rms=0.534 (0.049%), neg=0, invalid=96777 0265: dt=31.104000, rms=0.534 (0.033%), neg=0, invalid=96777 0266: dt=31.104000, rms=0.534 (0.023%), neg=0, invalid=96777 0267: dt=31.104000, rms=0.534 (0.038%), neg=0, invalid=96777 0268: dt=31.104000, rms=0.533 (0.044%), neg=0, invalid=96777 0269: dt=31.104000, rms=0.533 (0.041%), neg=0, invalid=96777 0270: dt=31.104000, rms=0.533 (0.037%), neg=0, invalid=96777 0271: dt=31.104000, rms=0.533 (0.024%), neg=0, invalid=96777 0272: dt=31.104000, rms=0.533 (0.035%), neg=0, invalid=96777 0273: dt=31.104000, rms=0.532 (0.028%), neg=0, invalid=96777 0274: dt=31.104000, rms=0.532 (0.030%), neg=0, invalid=96777 0275: dt=31.104000, rms=0.532 (0.039%), neg=0, invalid=96777 0276: dt=31.104000, rms=0.532 (0.039%), neg=0, invalid=96777 0277: dt=31.104000, rms=0.532 (0.035%), neg=0, invalid=96777 0278: dt=31.104000, rms=0.532 (0.025%), neg=0, invalid=96777 0279: dt=31.104000, rms=0.531 (0.018%), neg=0, invalid=96777 0280: dt=31.104000, rms=0.531 (0.010%), neg=0, invalid=96777 0281: dt=36.288000, rms=0.531 (0.025%), neg=0, invalid=96777 0282: dt=20.736000, rms=0.531 (0.002%), neg=0, invalid=96777 0283: dt=20.736000, rms=0.531 (0.012%), neg=0, invalid=96777 0284: dt=20.736000, rms=0.531 (0.006%), neg=0, invalid=96777 0285: dt=20.736000, rms=0.531 (0.005%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.531, neg=0, invalid=96777 0286: dt=145.152000, rms=0.529 (0.394%), neg=0, invalid=96777 0287: dt=36.288000, rms=0.529 (0.097%), neg=0, invalid=96777 0288: dt=36.288000, rms=0.528 (0.042%), neg=0, invalid=96777 0289: dt=36.288000, rms=0.528 (0.023%), neg=0, invalid=96777 0290: dt=36.288000, rms=0.528 (0.054%), neg=0, invalid=96777 0291: dt=36.288000, rms=0.527 (0.079%), neg=0, invalid=96777 0292: dt=36.288000, rms=0.527 (0.081%), neg=0, invalid=96777 0293: dt=36.288000, rms=0.527 (0.095%), neg=0, invalid=96777 0294: dt=36.288000, rms=0.526 (0.081%), neg=0, invalid=96777 0295: dt=36.288000, rms=0.526 (0.080%), neg=0, invalid=96777 0296: dt=36.288000, rms=0.525 (0.073%), neg=0, invalid=96777 0297: dt=36.288000, rms=0.525 (0.065%), neg=0, invalid=96777 0298: dt=36.288000, rms=0.525 (0.056%), neg=0, invalid=96777 0299: dt=36.288000, rms=0.524 (0.052%), neg=0, invalid=96777 0300: dt=36.288000, rms=0.524 (0.048%), neg=0, invalid=96777 0301: dt=36.288000, rms=0.524 (0.044%), neg=0, invalid=96777 0302: dt=36.288000, rms=0.524 (0.035%), neg=0, invalid=96777 0303: dt=36.288000, rms=0.523 (0.057%), neg=0, invalid=96777 0304: dt=36.288000, rms=0.523 (0.041%), neg=0, invalid=96777 0305: dt=36.288000, rms=0.523 (0.028%), neg=0, invalid=96777 0306: dt=36.288000, rms=0.523 (0.044%), neg=0, invalid=96777 0307: dt=36.288000, rms=0.523 (0.050%), neg=0, invalid=96777 0308: dt=36.288000, rms=0.522 (0.029%), neg=0, invalid=96777 0309: dt=36.288000, rms=0.522 (0.038%), neg=0, invalid=96777 0310: dt=36.288000, rms=0.522 (0.029%), neg=0, invalid=96777 0311: dt=36.288000, rms=0.522 (0.032%), neg=0, invalid=96777 0312: dt=36.288000, rms=0.522 (0.033%), neg=0, invalid=96777 0313: dt=36.288000, rms=0.521 (0.052%), neg=0, invalid=96777 0314: dt=36.288000, rms=0.521 (0.036%), neg=0, invalid=96777 0315: dt=36.288000, rms=0.521 (0.039%), neg=0, invalid=96777 0316: dt=36.288000, rms=0.521 (0.035%), neg=0, invalid=96777 0317: dt=36.288000, rms=0.521 (0.021%), neg=0, invalid=96777 0318: dt=36.288000, rms=0.521 (0.021%), neg=0, invalid=96777 0319: dt=36.288000, rms=0.521 (0.027%), neg=0, invalid=96777 0320: dt=36.288000, rms=0.520 (0.040%), neg=0, invalid=96777 0321: dt=36.288000, rms=0.520 (0.020%), neg=0, invalid=96777 0322: dt=36.288000, rms=0.520 (0.022%), neg=0, invalid=96777 0323: dt=36.288000, rms=0.520 (0.033%), neg=0, invalid=96777 0324: dt=36.288000, rms=0.520 (0.019%), neg=0, invalid=96777 0325: dt=36.288000, rms=0.520 (0.025%), neg=0, invalid=96777 0326: dt=36.288000, rms=0.520 (0.033%), neg=0, invalid=96777 0327: dt=36.288000, rms=0.519 (0.031%), neg=0, invalid=96777 0328: dt=36.288000, rms=0.519 (0.023%), neg=0, invalid=96777 0329: dt=36.288000, rms=0.519 (0.018%), neg=0, invalid=96777 0330: dt=15.552000, rms=0.519 (0.003%), neg=0, invalid=96777 0331: dt=15.552000, rms=0.519 (0.008%), neg=0, invalid=96777 0332: dt=15.552000, rms=0.519 (0.003%), neg=0, invalid=96777 0333: dt=15.552000, rms=0.519 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.527, neg=0, invalid=96777 0334: dt=25.600000, rms=0.526 (0.199%), neg=0, invalid=96777 0335: dt=44.800000, rms=0.524 (0.306%), neg=0, invalid=96777 0336: dt=32.000000, rms=0.522 (0.303%), neg=0, invalid=96777 0337: dt=9.600000, rms=0.522 (0.161%), neg=0, invalid=96777 0338: dt=25.600000, rms=0.520 (0.219%), neg=0, invalid=96777 0339: dt=7.607843, rms=0.520 (0.125%), neg=0, invalid=96777 0340: dt=44.800000, rms=0.518 (0.281%), neg=0, invalid=96777 0341: dt=8.936937, rms=0.517 (0.188%), neg=0, invalid=96777 0342: dt=38.400000, rms=0.516 (0.227%), neg=0, invalid=96777 0343: dt=7.796610, rms=0.515 (0.155%), neg=0, invalid=96777 0344: dt=38.400000, rms=0.514 (0.210%), neg=0, invalid=96777 0345: dt=8.323232, rms=0.514 (0.138%), neg=0, invalid=96777 0346: dt=25.600000, rms=0.513 (0.122%), neg=0, invalid=96777 0347: dt=9.600000, rms=0.512 (0.103%), neg=0, invalid=96777 0348: dt=11.200000, rms=0.512 (0.082%), neg=0, invalid=96777 0349: dt=38.400000, rms=0.511 (0.149%), neg=0, invalid=96777 0350: dt=7.472527, rms=0.511 (0.090%), neg=0, invalid=96777 0351: dt=179.200000, rms=0.508 (0.493%), neg=0, invalid=96777 0352: dt=11.970803, rms=0.506 (0.402%), neg=0, invalid=96777 0353: dt=9.600000, rms=0.506 (0.089%), neg=0, invalid=96777 0354: dt=38.400000, rms=0.505 (0.089%), neg=0, invalid=96777 0355: dt=11.200000, rms=0.505 (0.072%), neg=0, invalid=96777 0356: dt=11.200000, rms=0.505 (0.062%), neg=0, invalid=96777 0357: dt=11.200000, rms=0.504 (0.037%), neg=0, invalid=96777 0358: dt=11.200000, rms=0.504 (0.047%), neg=0, invalid=96777 0359: dt=11.200000, rms=0.504 (0.073%), neg=0, invalid=96777 0360: dt=11.200000, rms=0.503 (0.085%), neg=0, invalid=96777 0361: dt=11.200000, rms=0.503 (0.107%), neg=0, invalid=96777 0362: dt=11.200000, rms=0.502 (0.142%), neg=0, invalid=96777 0363: dt=11.200000, rms=0.501 (0.156%), neg=0, invalid=96777 0364: dt=11.200000, rms=0.501 (0.164%), neg=0, invalid=96777 0365: dt=11.200000, rms=0.500 (0.170%), neg=0, invalid=96777 0366: dt=11.200000, rms=0.499 (0.163%), neg=0, invalid=96777 0367: dt=11.200000, rms=0.498 (0.160%), neg=0, invalid=96777 0368: dt=11.200000, rms=0.497 (0.156%), neg=0, invalid=96777 0369: dt=11.200000, rms=0.497 (0.167%), neg=0, invalid=96777 0370: dt=11.200000, rms=0.496 (0.151%), neg=0, invalid=96777 0371: dt=11.200000, rms=0.495 (0.149%), neg=0, invalid=96777 0372: dt=11.200000, rms=0.494 (0.134%), neg=0, invalid=96777 0373: dt=11.200000, rms=0.494 (0.130%), neg=0, invalid=96777 0374: dt=11.200000, rms=0.493 (0.127%), neg=0, invalid=96777 0375: dt=11.200000, rms=0.493 (0.114%), neg=0, invalid=96777 0376: dt=11.200000, rms=0.492 (0.110%), neg=0, invalid=96777 0377: dt=11.200000, rms=0.491 (0.110%), neg=0, invalid=96777 0378: dt=11.200000, rms=0.491 (0.103%), neg=0, invalid=96777 0379: dt=11.200000, rms=0.491 (0.085%), neg=0, invalid=96777 0380: dt=11.200000, rms=0.490 (0.081%), neg=0, invalid=96777 0381: dt=11.200000, rms=0.490 (0.086%), neg=0, invalid=96777 0382: dt=11.200000, rms=0.489 (0.074%), neg=0, invalid=96777 0383: dt=11.200000, rms=0.489 (0.061%), neg=0, invalid=96777 0384: dt=11.200000, rms=0.489 (0.051%), neg=0, invalid=96777 0385: dt=11.200000, rms=0.489 (0.058%), neg=0, invalid=96777 0386: dt=11.200000, rms=0.488 (0.072%), neg=0, invalid=96777 0387: dt=11.200000, rms=0.488 (0.061%), neg=0, invalid=96777 0388: dt=11.200000, rms=0.488 (0.045%), neg=0, invalid=96777 0389: dt=11.200000, rms=0.487 (0.052%), neg=0, invalid=96777 0390: dt=11.200000, rms=0.487 (0.034%), neg=0, invalid=96777 0391: dt=11.200000, rms=0.487 (0.028%), neg=0, invalid=96777 0392: dt=11.200000, rms=0.487 (0.015%), neg=0, invalid=96777 0393: dt=11.200000, rms=0.487 (0.039%), neg=0, invalid=96777 0394: dt=11.200000, rms=0.487 (0.063%), neg=0, invalid=96777 0395: dt=11.200000, rms=0.486 (0.045%), neg=0, invalid=96777 0396: dt=11.200000, rms=0.486 (0.032%), neg=0, invalid=96777 0397: dt=11.200000, rms=0.486 (0.028%), neg=0, invalid=96777 0398: dt=11.200000, rms=0.486 (0.016%), neg=0, invalid=96777 0399: dt=11.200000, rms=0.486 (0.011%), neg=0, invalid=96777 0400: dt=25.600000, rms=0.486 (0.046%), neg=0, invalid=96777 0401: dt=6.400000, rms=0.486 (0.008%), neg=0, invalid=96777 0402: dt=6.400000, rms=0.486 (0.001%), neg=0, invalid=96777 0403: dt=6.400000, rms=0.486 (0.003%), neg=0, invalid=96777 0404: dt=6.400000, rms=0.486 (0.001%), neg=0, invalid=96777 0405: dt=6.400000, rms=0.486 (0.002%), neg=0, invalid=96777 0406: dt=6.400000, rms=0.486 (0.006%), neg=0, invalid=96777 0407: dt=6.400000, rms=0.486 (0.010%), neg=0, invalid=96777 0408: dt=6.400000, rms=0.486 (0.002%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.486, neg=0, invalid=96777 0409: dt=38.400000, rms=0.484 (0.279%), neg=0, invalid=96777 0410: dt=11.200000, rms=0.484 (0.124%), neg=0, invalid=96777 0411: dt=44.800000, rms=0.483 (0.114%), neg=0, invalid=96777 0412: dt=11.200000, rms=0.483 (0.039%), neg=0, invalid=96777 0413: dt=11.200000, rms=0.483 (0.022%), neg=0, invalid=96777 0414: dt=11.200000, rms=0.483 (0.031%), neg=0, invalid=96777 0415: dt=11.200000, rms=0.482 (0.021%), neg=0, invalid=96777 0416: dt=11.200000, rms=0.482 (0.033%), neg=0, invalid=96777 0417: dt=11.200000, rms=0.482 (0.028%), neg=0, invalid=96777 0418: dt=11.200000, rms=0.482 (0.018%), neg=0, invalid=96777 0419: dt=11.200000, rms=0.482 (-0.001%), neg=0, invalid=96777 0420: dt=19.200000, rms=0.482 (0.008%), neg=0, invalid=96777 0421: dt=11.200000, rms=0.482 (0.019%), neg=0, invalid=96777 0422: dt=19.200000, rms=0.482 (0.005%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.502, neg=0, invalid=96777 0423: dt=0.000000, rms=0.502 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.502, neg=0, invalid=96777 0424: dt=0.000000, rms=0.502 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.541, neg=0, invalid=96777 0425: dt=1.336735, rms=0.537 (0.766%), neg=0, invalid=96777 0426: dt=0.384000, rms=0.537 (0.027%), neg=0, invalid=96777 0427: dt=0.384000, rms=0.537 (-0.013%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.537, neg=0, invalid=96777 0428: dt=0.832000, rms=0.536 (0.116%), neg=0, invalid=96777 0429: dt=0.227273, rms=0.536 (0.007%), neg=0, invalid=96777 0430: dt=0.227273, rms=0.536 (-0.004%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.497, neg=0, invalid=96777 0431: dt=0.448000, rms=0.483 (2.929%), neg=0, invalid=96777 0432: dt=0.448000, rms=0.480 (0.553%), neg=0, invalid=96777 0433: dt=0.448000, rms=0.479 (0.361%), neg=0, invalid=96777 0434: dt=0.448000, rms=0.477 (0.232%), neg=0, invalid=96777 0435: dt=0.448000, rms=0.477 (0.170%), neg=0, invalid=96777 0436: dt=0.448000, rms=0.476 (0.122%), neg=0, invalid=96777 0437: dt=0.800000, rms=0.475 (0.166%), neg=0, invalid=96777 0438: dt=0.112000, rms=0.475 (0.024%), neg=0, invalid=96777 0439: dt=0.112000, rms=0.475 (0.020%), neg=0, invalid=96777 0440: dt=0.112000, rms=0.475 (0.031%), neg=0, invalid=96777 0441: dt=0.112000, rms=0.475 (0.040%), neg=0, invalid=96777 0442: dt=0.112000, rms=0.474 (0.048%), neg=0, invalid=96777 0443: dt=0.112000, rms=0.474 (0.050%), neg=0, invalid=96777 0444: dt=0.112000, rms=0.474 (0.056%), neg=0, invalid=96777 0445: dt=0.112000, rms=0.474 (0.059%), neg=0, invalid=96777 0446: dt=0.112000, rms=0.473 (0.053%), neg=0, invalid=96777 0447: dt=0.112000, rms=0.473 (0.046%), neg=0, invalid=96777 0448: dt=0.112000, rms=0.473 (0.046%), neg=0, invalid=96777 0449: dt=0.112000, rms=0.473 (0.038%), neg=0, invalid=96777 0450: dt=0.112000, rms=0.473 (0.035%), neg=0, invalid=96777 0451: dt=0.112000, rms=0.472 (0.029%), neg=0, invalid=96777 0452: dt=0.112000, rms=0.472 (0.020%), neg=0, invalid=96777 0453: dt=0.112000, rms=0.472 (0.018%), neg=0, invalid=96777 0454: dt=0.112000, rms=0.472 (0.001%), neg=0, invalid=96777 0455: dt=0.112000, rms=0.472 (-0.002%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.472, neg=0, invalid=96777 0456: dt=0.448000, rms=0.468 (0.989%), neg=0, invalid=96777 0457: dt=0.384000, rms=0.468 (0.002%), neg=0, invalid=96777 0458: dt=0.384000, rms=0.468 (0.002%), neg=0, invalid=96777 0459: dt=0.384000, rms=0.468 (-0.016%), neg=0, invalid=96777 label assignment complete, 0 changed (0.00%) ********************************************************************************************* ********************************************************************************************* ********************************************************************************************* ********************* ALLOWING NEGATIVE NODES IN DEFORMATION ******************************** ********************************************************************************************* ********************************************************************************************* ********************************************************************************************* **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.465, neg=0, invalid=96777 0460: dt=0.000000, rms=0.465 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.465, neg=0, invalid=96777 0461: dt=129.472000, rms=0.465 (0.062%), neg=0, invalid=96777 0462: dt=110.976000, rms=0.465 (0.033%), neg=0, invalid=96777 0463: dt=110.976000, rms=0.465 (0.012%), neg=0, invalid=96777 0464: dt=110.976000, rms=0.465 (0.036%), neg=0, invalid=96777 0465: dt=110.976000, rms=0.465 (0.031%), neg=0, invalid=96777 0466: dt=110.976000, rms=0.464 (0.025%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.465, neg=0, invalid=96777 0467: dt=25.920000, rms=0.464 (0.028%), neg=0, invalid=96777 0468: dt=25.920000, rms=0.464 (0.008%), neg=0, invalid=96777 0469: dt=25.920000, rms=0.464 (0.011%), neg=0, invalid=96777 0470: dt=25.920000, rms=0.464 (-0.007%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.464, neg=0, invalid=96777 0471: dt=145.152000, rms=0.462 (0.430%), neg=0, invalid=96777 0472: dt=36.288000, rms=0.462 (0.135%), neg=0, invalid=96777 0473: dt=36.288000, rms=0.461 (0.050%), neg=0, invalid=96777 0474: dt=36.288000, rms=0.461 (0.069%), neg=0, invalid=96777 0475: dt=36.288000, rms=0.461 (0.089%), neg=0, invalid=96777 0476: dt=36.288000, rms=0.460 (0.116%), neg=0, invalid=96777 0477: dt=36.288000, rms=0.460 (0.141%), neg=0, invalid=96777 0478: dt=36.288000, rms=0.459 (0.138%), neg=0, invalid=96777 0479: dt=36.288000, rms=0.458 (0.116%), neg=0, invalid=96777 0480: dt=36.288000, rms=0.458 (0.093%), neg=0, invalid=96777 0481: dt=25.920000, rms=0.458 (0.011%), neg=0, invalid=96777 0482: dt=25.920000, rms=0.458 (0.004%), neg=0, invalid=96777 0483: dt=25.920000, rms=0.458 (0.021%), neg=0, invalid=96777 0484: dt=25.920000, rms=0.458 (0.020%), neg=0, invalid=96777 0485: dt=25.920000, rms=0.458 (0.024%), neg=0, invalid=96777 0486: dt=25.920000, rms=0.457 (0.032%), neg=0, invalid=96777 0487: dt=25.920000, rms=0.457 (0.028%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.458, neg=0, invalid=96777 iter 0, gcam->neg = 4 after 6 iterations, nbhd size=1, neg = 0 0488: dt=32.000000, rms=0.456 (0.361%), neg=0, invalid=96777 0489: dt=11.200000, rms=0.455 (0.157%), neg=0, invalid=96777 0490: dt=11.200000, rms=0.455 (0.163%), neg=0, invalid=96777 0491: dt=11.200000, rms=0.454 (0.203%), neg=0, invalid=96777 0492: dt=11.200000, rms=0.453 (0.228%), neg=0, invalid=96777 0493: dt=11.200000, rms=0.452 (0.209%), neg=0, invalid=96777 0494: dt=11.200000, rms=0.451 (0.220%), neg=0, invalid=96777 0495: dt=11.200000, rms=0.450 (0.187%), neg=0, invalid=96777 0496: dt=11.200000, rms=0.449 (0.175%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0497: dt=11.200000, rms=0.448 (0.186%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0498: dt=11.200000, rms=0.447 (0.210%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0499: dt=11.200000, rms=0.446 (0.192%), neg=0, invalid=96777 0500: dt=11.200000, rms=0.446 (0.180%), neg=0, invalid=96777 0501: dt=11.200000, rms=0.445 (0.156%), neg=0, invalid=96777 0502: dt=11.200000, rms=0.444 (0.182%), neg=0, invalid=96777 0503: dt=11.200000, rms=0.443 (0.139%), neg=0, invalid=96777 0504: dt=11.200000, rms=0.443 (0.129%), neg=0, invalid=96777 0505: dt=11.200000, rms=0.442 (0.116%), neg=0, invalid=96777 0506: dt=11.200000, rms=0.442 (0.116%), neg=0, invalid=96777 0507: dt=11.200000, rms=0.441 (0.090%), neg=0, invalid=96777 0508: dt=8.000000, rms=0.441 (0.025%), neg=0, invalid=96777 0509: dt=8.000000, rms=0.441 (0.017%), neg=0, invalid=96777 0510: dt=8.000000, rms=0.441 (0.029%), neg=0, invalid=96777 0511: dt=8.000000, rms=0.441 (0.027%), neg=0, invalid=96777 0512: dt=8.000000, rms=0.441 (0.028%), neg=0, invalid=96777 0513: dt=8.000000, rms=0.441 (0.033%), neg=0, invalid=96777 0514: dt=8.000000, rms=0.441 (0.023%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.441, neg=0, invalid=96777 0515: dt=44.800000, rms=0.438 (0.660%), neg=0, invalid=96777 0516: dt=11.200000, rms=0.437 (0.125%), neg=0, invalid=96777 0517: dt=11.200000, rms=0.437 (0.075%), neg=0, invalid=96777 0518: dt=11.200000, rms=0.436 (0.097%), neg=0, invalid=96777 0519: dt=11.200000, rms=0.436 (0.129%), neg=0, invalid=96777 0520: dt=11.200000, rms=0.435 (0.123%), neg=0, invalid=96777 0521: dt=11.200000, rms=0.435 (0.102%), neg=0, invalid=96777 0522: dt=11.200000, rms=0.435 (0.029%), neg=0, invalid=96777 0523: dt=11.200000, rms=0.435 (0.020%), neg=0, invalid=96777 0524: dt=11.200000, rms=0.435 (0.028%), neg=0, invalid=96777 0525: dt=11.200000, rms=0.434 (0.041%), neg=0, invalid=96777 0526: dt=11.200000, rms=0.434 (0.036%), neg=0, invalid=96777 0527: dt=11.200000, rms=0.434 (0.046%), neg=0, invalid=96777 0528: dt=11.200000, rms=0.434 (0.055%), neg=0, invalid=96777 0529: dt=11.200000, rms=0.434 (0.050%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.439, neg=0, invalid=96777 0530: dt=0.252000, rms=0.439 (-0.003%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.439, neg=0, invalid=96777 0531: dt=2.880000, rms=0.438 (0.028%), neg=0, invalid=96777 0532: dt=2.304000, rms=0.438 (0.012%), neg=0, invalid=96777 0533: dt=2.304000, rms=0.438 (-0.000%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.447, neg=0, invalid=96777 0534: dt=0.448000, rms=0.447 (0.053%), neg=0, invalid=96777 0535: dt=0.384000, rms=0.447 (0.008%), neg=0, invalid=96777 0536: dt=0.384000, rms=0.447 (-0.008%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.447, neg=0, invalid=96777 0537: dt=1.280000, rms=0.446 (0.135%), neg=0, invalid=96777 0538: dt=0.448000, rms=0.446 (0.015%), neg=0, invalid=96777 0539: dt=0.448000, rms=0.446 (-0.005%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.437, neg=0, invalid=96777 iter 0, gcam->neg = 565 after 11 iterations, nbhd size=1, neg = 0 0540: dt=1.899000, rms=0.404 (7.507%), neg=0, invalid=96777 0541: dt=0.000250, rms=0.404 (0.004%), neg=0, invalid=96777 0542: dt=0.000250, rms=0.404 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.404, neg=0, invalid=96777 0543: dt=0.000750, rms=0.404 (0.001%), neg=0, invalid=96777 0544: dt=0.000000, rms=0.404 (0.001%), neg=0, invalid=96777 0545: dt=0.000000, rms=0.404 (0.000%), neg=0, invalid=96777 label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.390, neg=0, invalid=96777 0546: dt=0.000000, rms=0.391 (-0.189%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.391, neg=0, invalid=96777 0547: dt=32.368000, rms=0.391 (0.003%), neg=0, invalid=96777 0548: dt=32.368000, rms=0.391 (0.001%), neg=0, invalid=96777 0549: dt=32.368000, rms=0.391 (0.001%), neg=0, invalid=96777 0550: dt=32.368000, rms=0.391 (0.000%), neg=0, invalid=96777 0551: dt=32.368000, rms=0.391 (-0.001%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.391, neg=0, invalid=96777 0552: dt=0.000000, rms=0.391 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.391, neg=0, invalid=96777 0553: dt=82.944000, rms=0.391 (0.038%), neg=0, invalid=96777 0554: dt=145.152000, rms=0.390 (0.046%), neg=0, invalid=96777 0555: dt=36.288000, rms=0.390 (0.010%), neg=0, invalid=96777 0556: dt=36.288000, rms=0.390 (0.008%), neg=0, invalid=96777 0557: dt=36.288000, rms=0.390 (0.013%), neg=0, invalid=96777 0558: dt=36.288000, rms=0.390 (0.016%), neg=0, invalid=96777 0559: dt=36.288000, rms=0.390 (0.018%), neg=0, invalid=96777 0560: dt=36.288000, rms=0.390 (0.017%), neg=0, invalid=96777 0561: dt=36.288000, rms=0.390 (0.014%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.391, neg=0, invalid=96777 0562: dt=8.000000, rms=0.391 (0.029%), neg=0, invalid=96777 0563: dt=2.800000, rms=0.391 (0.004%), neg=0, invalid=96777 0564: dt=2.800000, rms=0.391 (0.004%), neg=0, invalid=96777 0565: dt=2.800000, rms=0.391 (0.001%), neg=0, invalid=96777 0566: dt=2.800000, rms=0.391 (-0.013%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.391, neg=0, invalid=96777 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0567: dt=44.800000, rms=0.389 (0.340%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 5 iterations, nbhd size=1, neg = 0 0568: dt=25.600000, rms=0.388 (0.207%), neg=0, invalid=96777 0569: dt=25.600000, rms=0.388 (0.063%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0570: dt=25.600000, rms=0.388 (0.145%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0571: dt=25.600000, rms=0.387 (0.137%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0572: dt=25.600000, rms=0.387 (0.156%), neg=0, invalid=96777 iter 0, gcam->neg = 6 after 6 iterations, nbhd size=1, neg = 0 0573: dt=25.600000, rms=0.386 (0.232%), neg=0, invalid=96777 iter 0, gcam->neg = 7 after 8 iterations, nbhd size=1, neg = 0 0574: dt=25.600000, rms=0.385 (0.148%), neg=0, invalid=96777 iter 0, gcam->neg = 7 after 6 iterations, nbhd size=1, neg = 0 0575: dt=25.600000, rms=0.384 (0.196%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0576: dt=25.600000, rms=0.384 (0.059%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 6 iterations, nbhd size=1, neg = 0 0577: dt=25.600000, rms=0.384 (0.087%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0578: dt=25.600000, rms=0.383 (0.146%), neg=0, invalid=96777 iter 0, gcam->neg = 5 after 7 iterations, nbhd size=1, neg = 0 0579: dt=25.600000, rms=0.383 (0.075%), neg=0, invalid=96777 iter 0, gcam->neg = 6 after 7 iterations, nbhd size=1, neg = 0 0580: dt=25.600000, rms=0.383 (0.047%), neg=0, invalid=96777 0581: dt=32.000000, rms=0.382 (0.136%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 6 iterations, nbhd size=1, neg = 0 0582: dt=38.400000, rms=0.382 (0.082%), neg=0, invalid=96777 0583: dt=38.400000, rms=0.382 (0.046%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 14 iterations, nbhd size=2, neg = 0 0584: dt=38.400000, rms=0.382 (0.022%), neg=0, invalid=96777 iter 0, gcam->neg = 32 after 37 iterations, nbhd size=3, neg = 0 0585: dt=38.400000, rms=0.382 (-0.046%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.385, neg=0, invalid=96777 0586: dt=0.864000, rms=0.385 (0.003%), neg=0, invalid=96777 0587: dt=1.008000, rms=0.385 (0.004%), neg=0, invalid=96777 0588: dt=0.252000, rms=0.385 (0.000%), neg=0, invalid=96777 0589: dt=0.252000, rms=0.385 (0.000%), neg=0, invalid=96777 0590: dt=0.252000, rms=0.385 (-0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.385, neg=0, invalid=96777 iter 0, gcam->neg = 5 after 6 iterations, nbhd size=1, neg = 0 0591: dt=4.032000, rms=0.385 (0.056%), neg=0, invalid=96777 0592: dt=0.576000, rms=0.385 (0.001%), neg=0, invalid=96777 0593: dt=0.576000, rms=0.385 (0.006%), neg=0, invalid=96777 0594: dt=0.576000, rms=0.385 (0.010%), neg=0, invalid=96777 0595: dt=0.576000, rms=0.385 (0.011%), neg=0, invalid=96777 0596: dt=0.576000, rms=0.385 (0.006%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0597: dt=0.576000, rms=0.385 (0.002%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.392, neg=0, invalid=96777 0598: dt=0.000000, rms=0.392 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.392, neg=0, invalid=96777 0599: dt=0.000000, rms=0.392 (0.000%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.381, neg=0, invalid=96777 iter 0, gcam->neg = 616 after 35 iterations, nbhd size=3, neg = 0 0600: dt=1.004587, rms=0.368 (3.234%), neg=0, invalid=96777 0601: dt=0.000078, rms=0.368 (0.001%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0602: dt=0.000078, rms=0.368 (0.000%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0603: dt=0.000078, rms=0.368 (0.000%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0604: dt=0.000078, rms=0.368 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.368, neg=0, invalid=96777 0605: dt=0.000438, rms=0.368 (0.000%), neg=0, invalid=96777 0606: dt=0.000000, rms=0.368 (0.000%), neg=0, invalid=96777 writing output transformation to transforms/talairach.m3z... GCAMwrite registration took 1 hours, 47 minutes and 54 seconds. #-------------------------------------- #@# CA Reg Inv Wed Sep 6 11:23:41 CEST 2017 /root/Scrivania/subjects/ENP30S001A/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z Inverting GCAM Saving inverse #-------------------------------------- #@# Remove Neck Wed Sep 6 11:24:18 CEST 2017 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2008-03-26.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... removing structures at least 25 mm from brain... 11060657 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 0 minutes and 40 seconds. #-------------------------------------- #@# SkullLTA Wed Sep 6 11:24:58 CEST 2017 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull_2.lta ======= NUMBER OF OPENMP THREADS = 1 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 5 using previously computed transform transforms/talairach.lta reading 1 input volumes... logging results to talairach_with_skull_2.log reading '/usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu_noneck.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=10.0 skull bounding box = (46, 59, 24) --> (206, 240, 224) using (99, 119, 124) as brain centroid... mean wm in atlas = 126, using box (79,97,99) --> (118, 141,148) to find MRI wm before smoothing, mri peak at 105 after smoothing, mri peak at 105, scaling input intensities by 1.200 scaling channel 0 by 1.2 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-3.9 (thresh=-3.9) 1.008 0.123 -0.020 -16.612; -0.103 1.119 0.243 -50.631; 0.046 -0.204 0.999 13.847; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 1 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-4.0 (thresh=-4.0) 0.990 0.115 0.013 -17.013; -0.106 1.145 0.215 -52.552; 0.010 -0.174 1.026 12.904; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 0.990 0.115 0.013 -17.013; -0.106 1.145 0.215 -52.552; 0.010 -0.174 1.026 12.904; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 3 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 0.990 0.115 0.013 -17.013; -0.106 1.143 0.214 -52.145; 0.010 -0.174 1.027 12.794; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 0.990 0.115 0.013 -17.013; -0.106 1.143 0.214 -52.145; 0.010 -0.174 1.029 12.576; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3481 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.98977 0.11511 0.01295 -17.01270; -0.10588 1.14264 0.21442 -52.14524; 0.00965 -0.17411 1.02927 12.57591; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 0.98977 0.11511 0.01295 -17.01270; -0.10588 1.14264 0.21442 -52.14524; 0.00965 -0.17411 1.02927 12.57591; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 006: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.990 0.115 0.013 -17.013; -0.106 1.143 0.214 -52.145; 0.010 -0.174 1.029 12.576; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.9 (old=-3.9) transform before final EM align: 0.990 0.115 0.013 -17.013; -0.106 1.143 0.214 -52.145; 0.010 -0.174 1.029 12.576; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 382743 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.98977 0.11511 0.01295 -17.01270; -0.10588 1.14264 0.21442 -52.14524; 0.00965 -0.17411 1.02927 12.57591; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 0.98977 0.11511 0.01295 -17.01270; -0.10588 1.14264 0.21442 -52.14524; 0.00965 -0.17411 1.02927 12.57591; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = 4.4 tol 0.000000 final transform: 0.990 0.115 0.013 -17.013; -0.106 1.143 0.214 -52.145; 0.010 -0.174 1.029 12.576; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull_2.lta... registration took 13 minutes and 19 seconds. #-------------------------------------- #@# SubCort Seg Wed Sep 6 11:38:17 CEST 2017 mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.mgz --diff aseg.manedit.mgz $Id: mri_seg_diff.c,v 1.5 2011/03/02 00:04:24 nicks Exp $ cwd /root/Scrivania/subjects/ENP30S001A/mri cmdline mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.mgz --diff aseg.manedit.mgz sysname Linux hostname Braindata machine x86_64 user root Seg1 aseg.auto.mgz Seg2 aseg.mgz Diff aseg.manedit.mgz InDiff (null) Merged (null) ForceDiff 0 Computing difference between segmentations No difference found. mri_ca_label -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz sysname Linux hostname Braindata machine x86_64 setenv SUBJECTS_DIR /root/Scrivania/subjects cd /root/Scrivania/subjects/ENP30S001A/mri mri_ca_label -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes... reading classifier array from /usr/local/freesurfer/average/RB_all_2008-03-26.gca... reading input volume from norm.mgz... average std[0] = 6.9 reading transform from transforms/talairach.m3z... Atlas used for the 3D morph was /usr/local/freesurfer/average/RB_all_2008-03-26.gca average std = 6.9 using min determinant for regularization = 4.7 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15151 (27) mri peak = 0.10621 (17) Left_Lateral_Ventricle (4): linear fit = 0.67 x + 0.0 (539 voxels, overlap=0.068) Left_Lateral_Ventricle (4): linear fit = 0.67 x + 0.0 (539 voxels, peak = 18), gca=18.0 gca peak = 0.14982 (20) mri peak = 0.14418 (17) Right_Lateral_Ventricle (43): linear fit = 0.71 x + 0.0 (480 voxels, overlap=0.398) Right_Lateral_Ventricle (43): linear fit = 0.71 x + 0.0 (480 voxels, peak = 14), gca=14.3 gca peak = 0.28003 (97) mri peak = 0.14546 (98) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (325 voxels, overlap=1.019) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (325 voxels, peak = 96), gca=95.5 gca peak = 0.18160 (96) mri peak = 0.08548 (88) Left_Pallidum (13): linear fit = 0.94 x + 0.0 (154 voxels, overlap=0.912) Left_Pallidum (13): linear fit = 0.94 x + 0.0 (154 voxels, peak = 91), gca=90.7 gca peak = 0.27536 (62) mri peak = 0.09314 (67) Right_Hippocampus (53): linear fit = 1.07 x + 0.0 (788 voxels, overlap=0.726) Right_Hippocampus (53): linear fit = 1.07 x + 0.0 (788 voxels, peak = 66), gca=66.0 gca peak = 0.32745 (63) mri peak = 0.11444 (68) Left_Hippocampus (17): linear fit = 1.07 x + 0.0 (900 voxels, overlap=1.007) Left_Hippocampus (17): linear fit = 1.07 x + 0.0 (900 voxels, peak = 67), gca=67.1 gca peak = 0.08597 (105) mri peak = 0.08675 (106) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (57425 voxels, overlap=0.743) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (57425 voxels, peak = 107), gca=106.6 gca peak = 0.09209 (106) mri peak = 0.09645 (108) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (58838 voxels, overlap=0.703) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (58838 voxels, peak = 108), gca=107.6 gca peak = 0.07826 (63) mri peak = 0.04755 (63) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (20006 voxels, overlap=0.921) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (20006 voxels, peak = 62), gca=62.1 gca peak = 0.08598 (64) mri peak = 0.04507 (60) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (18139 voxels, overlap=0.940) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (18139 voxels, peak = 63), gca=63.0 gca peak = 0.24164 (71) mri peak = 0.11489 (81) Right_Caudate (50): linear fit = 1.08 x + 0.0 (724 voxels, overlap=0.447) Right_Caudate (50): linear fit = 1.08 x + 0.0 (724 voxels, peak = 76), gca=76.3 gca peak = 0.18227 (75) mri peak = 0.11054 (81) Left_Caudate (11): linear fit = 1.05 x + 0.0 (963 voxels, overlap=0.693) Left_Caudate (11): linear fit = 1.05 x + 0.0 (963 voxels, peak = 79), gca=79.1 gca peak = 0.10629 (62) mri peak = 0.04631 (62) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (22881 voxels, overlap=0.977) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (22881 voxels, peak = 64), gca=63.5 gca peak = 0.11668 (59) mri peak = 0.05203 (64) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (22676 voxels, overlap=0.972) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (22676 voxels, peak = 60), gca=60.5 gca peak = 0.17849 (88) mri peak = 0.11564 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (6188 voxels, overlap=0.722) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (6188 voxels, peak = 93), gca=92.8 gca peak = 0.16819 (86) mri peak = 0.12368 (92) Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (5867 voxels, overlap=0.827) Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (5867 voxels, peak = 90), gca=89.9 gca peak = 0.41688 (64) mri peak = 0.09705 (74) Left_Amygdala (18): linear fit = 1.16 x + 0.0 (287 voxels, overlap=0.056) Left_Amygdala (18): linear fit = 1.16 x + 0.0 (287 voxels, peak = 75), gca=74.6 gca peak = 0.42394 (62) mri peak = 0.11856 (72) Right_Amygdala (54): linear fit = 1.13 x + 0.0 (319 voxels, overlap=0.061) Right_Amygdala (54): linear fit = 1.13 x + 0.0 (319 voxels, peak = 70), gca=70.4 gca peak = 0.10041 (96) mri peak = 0.07555 (97) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (3963 voxels, overlap=0.664) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (3963 voxels, peak = 102), gca=102.2 gca peak = 0.13978 (88) mri peak = 0.08098 (94) Right_Thalamus_Proper (49): linear fit = 1.05 x + 0.0 (3614 voxels, overlap=0.872) Right_Thalamus_Proper (49): linear fit = 1.05 x + 0.0 (3614 voxels, peak = 93), gca=92.8 gca peak = 0.08514 (81) mri peak = 0.07270 (88) Left_Putamen (12): linear fit = 1.03 x + 0.0 (1245 voxels, overlap=0.831) Left_Putamen (12): linear fit = 1.03 x + 0.0 (1245 voxels, peak = 84), gca=83.8 gca peak = 0.09624 (82) mri peak = 0.07603 (85) Right_Putamen (51): linear fit = 1.05 x + 0.0 (1682 voxels, overlap=0.747) Right_Putamen (51): linear fit = 1.05 x + 0.0 (1682 voxels, peak = 87), gca=86.5 gca peak = 0.07543 (88) mri peak = 0.06935 (92) Brain_Stem (16): linear fit = 1.07 x + 0.0 (12279 voxels, overlap=0.687) Brain_Stem (16): linear fit = 1.07 x + 0.0 (12279 voxels, peak = 94), gca=93.7 gca peak = 0.12757 (95) mri peak = 0.07476 (104) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1278 voxels, overlap=0.616) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1278 voxels, peak = 103), gca=103.1 gca peak = 0.17004 (92) mri peak = 0.08651 (101) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (1301 voxels, overlap=0.537) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (1301 voxels, peak = 100), gca=99.8 gca peak = 0.21361 (36) mri peak = 0.11422 (22) gca peak = 0.26069 (23) mri peak = 0.17362 (19) Fourth_Ventricle (15): linear fit = 0.77 x + 0.0 (90 voxels, overlap=0.603) Fourth_Ventricle (15): linear fit = 0.77 x + 0.0 (90 voxels, peak = 18), gca=17.8 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.31795 (35) gca peak Third_Ventricle = 0.21361 (36) gca peak CSF = 0.14367 (38) gca peak Left_Accumbens_area = 0.57033 (70) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65201 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.31129 (32) gca peak Right_Accumbens_area = 0.30219 (72) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.72939 (42) gca peak WM_hypointensities = 0.14821 (82) gca peak non_WM_hypointensities = 0.10354 (53) gca peak Optic_Chiasm = 0.34849 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.07 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 0.72 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.19757 (18) mri peak = 0.10621 (17) Left_Lateral_Ventricle (4): linear fit = 0.95 x + 0.0 (539 voxels, overlap=0.941) Left_Lateral_Ventricle (4): linear fit = 0.95 x + 0.0 (539 voxels, peak = 17), gca=17.2 gca peak = 0.19392 (15) mri peak = 0.14418 (17) Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (480 voxels, overlap=0.887) Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (480 voxels, peak = 15), gca=15.4 gca peak = 0.32703 (96) mri peak = 0.14546 (98) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (325 voxels, overlap=1.010) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (325 voxels, peak = 97), gca=97.4 gca peak = 0.19619 (91) mri peak = 0.08548 (88) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (154 voxels, overlap=1.004) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (154 voxels, peak = 91), gca=91.5 gca peak = 0.24887 (66) mri peak = 0.09314 (67) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (788 voxels, overlap=1.005) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (788 voxels, peak = 66), gca=66.0 gca peak = 0.28946 (67) mri peak = 0.11444 (68) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (900 voxels, overlap=1.003) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (900 voxels, peak = 67), gca=67.0 gca peak = 0.08542 (107) mri peak = 0.08675 (106) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (57425 voxels, overlap=0.780) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (57425 voxels, peak = 106), gca=106.5 gca peak = 0.08742 (107) mri peak = 0.09645 (108) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (58838 voxels, overlap=0.730) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (58838 voxels, peak = 107), gca=107.0 gca peak = 0.07876 (62) mri peak = 0.04755 (63) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (20006 voxels, overlap=0.949) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (20006 voxels, peak = 64), gca=63.5 gca peak = 0.08738 (63) mri peak = 0.04507 (60) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (18139 voxels, overlap=0.960) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (18139 voxels, peak = 62), gca=62.1 gca peak = 0.27738 (79) mri peak = 0.11489 (81) Right_Caudate (50): linear fit = 1.01 x + 0.0 (724 voxels, overlap=1.002) Right_Caudate (50): linear fit = 1.01 x + 0.0 (724 voxels, peak = 80), gca=80.2 gca peak = 0.18126 (79) mri peak = 0.11054 (81) Left_Caudate (11): linear fit = 1.00 x + 0.0 (963 voxels, overlap=0.953) Left_Caudate (11): linear fit = 1.00 x + 0.0 (963 voxels, peak = 79), gca=79.0 gca peak = 0.10281 (63) mri peak = 0.04631 (62) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (22881 voxels, overlap=0.992) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (22881 voxels, peak = 65), gca=64.6 gca peak = 0.12584 (61) mri peak = 0.05203 (64) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (22676 voxels, overlap=0.991) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (22676 voxels, peak = 63), gca=62.5 gca peak = 0.17071 (92) mri peak = 0.11564 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6188 voxels, overlap=0.971) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6188 voxels, peak = 92), gca=91.5 gca peak = 0.15955 (90) mri peak = 0.12368 (92) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5867 voxels, overlap=0.981) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5867 voxels, peak = 90), gca=89.6 gca peak = 0.29786 (74) mri peak = 0.09705 (74) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (287 voxels, overlap=1.004) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (287 voxels, peak = 75), gca=75.1 gca peak = 0.30975 (71) mri peak = 0.11856 (72) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (319 voxels, overlap=1.007) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (319 voxels, peak = 71), gca=71.0 gca peak = 0.11099 (102) mri peak = 0.07555 (97) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3963 voxels, overlap=0.930) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3963 voxels, peak = 103), gca=102.5 gca peak = 0.10579 (93) mri peak = 0.08098 (94) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3614 voxels, overlap=0.912) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3614 voxels, peak = 93), gca=93.5 gca peak = 0.08482 (85) mri peak = 0.07270 (88) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1245 voxels, overlap=0.950) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1245 voxels, peak = 85), gca=84.6 gca peak = 0.10379 (80) mri peak = 0.07603 (85) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1682 voxels, overlap=0.922) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1682 voxels, peak = 79), gca=78.8 gca peak = 0.06628 (88) mri peak = 0.06935 (92) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12279 voxels, overlap=0.844) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12279 voxels, peak = 88), gca=88.0 gca peak = 0.10874 (99) mri peak = 0.07476 (104) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1278 voxels, overlap=0.815) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1278 voxels, peak = 99), gca=99.0 gca peak = 0.17076 (100) mri peak = 0.08651 (101) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1301 voxels, overlap=0.872) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1301 voxels, peak = 100), gca=100.5 gca peak = 0.25515 (27) mri peak = 0.11422 (22) gca peak = 0.27522 (18) mri peak = 0.17362 (19) Fourth_Ventricle (15): linear fit = 0.99 x + 0.0 (90 voxels, overlap=0.767) Fourth_Ventricle (15): linear fit = 0.99 x + 0.0 (90 voxels, peak = 18), gca=17.7 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21381 (38) gca peak Third_Ventricle = 0.25515 (27) gca peak CSF = 0.24868 (28) gca peak Left_Accumbens_area = 0.49915 (74) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65267 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.31109 (34) gca peak Right_Accumbens_area = 0.43827 (77) gca peak Right_vessel = 0.83457 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.45329 (31) gca peak WM_hypointensities = 0.17562 (83) gca peak non_WM_hypointensities = 0.10249 (54) gca peak Optic_Chiasm = 0.34853 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.99 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 19722 gm and wm labels changed (%20 to gray, %80 to white out of all changed labels) 328 hippocampal voxels changed. 2 amygdala voxels changed. pass 1: 76490 changed. image ll: -2.169, PF=1.000 pass 2: 11252 changed. image ll: -2.166, PF=1.000 pass 3: 3466 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 9 minutes and 41 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /root/Scrivania/subjects/ENP30S001A/mri/transforms/cc_up.lta ENP30S001A will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /root/Scrivania/subjects/ENP30S001A/mri/transforms/cc_up.lta reading aseg from /root/Scrivania/subjects/ENP30S001A/mri/aseg.auto_noCCseg.mgz reading norm from /root/Scrivania/subjects/ENP30S001A/mri/norm.mgz 35834 voxels in left wm, 62890 in right wm, xrange [121, 132] searching rotation angles z=[-13 1], y=[-9 5] searching scale 1 Z rot -13.3 searching scale 1 Z rot -13.0 searching scale 1 Z rot -12.8 searching scale 1 Z rot -12.5 searching scale 1 Z rot -12.3 searching scale 1 Z rot -12.0 searching scale 1 Z rot -11.8 searching scale 1 Z rot -11.5 searching scale 1 Z rot -11.3 searching scale 1 Z rot -11.0 searching scale 1 Z rot -10.8 searching scale 1 Z rot -10.5 searching scale 1 Z rot -10.3 searching scale 1 Z rot -10.0 searching scale 1 Z rot -9.8 searching scale 1 Z rot -9.5 searching scale 1 Z rot -9.3 searching scale 1 Z rot -9.0 searching scale 1 Z rot -8.8 searching scale 1 Z rot -8.5 searching scale 1 Z rot -8.3 searching scale 1 Z rot -8.0 searching scale 1 Z rot -7.8 searching scale 1 Z rot -7.5 searching scale 1 Z rot -7.3 searching scale 1 Z rot -7.0 searching scale 1 Z rot -6.8 searching scale 1 Z rot -6.5 searching scale 1 Z rot -6.3 searching scale 1 Z rot -6.0 searching scale 1 Z rot -5.8 searching scale 1 Z rot -5.5 searching scale 1 Z rot -5.3 searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.8 searching scale 1 Z rot -4.5 searching scale 1 Z rot -4.3 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.8 searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.3 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.8 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.3 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.8 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.3 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.8 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.3 searching scale 1 Z rot -0.0 global minimum found at slice 127.0, rotations (-1.78, -6.77) final transformation (x=127.0, yr=-1.775, zr=-6.766): 0.993 0.118 -0.031 -9.362; -0.118 0.993 0.004 17.414; 0.031 -0.000 1.000 9.120; 0.000 0.000 0.000 1.000; updating x range to be [126, 130] in xformed coordinates best xformed slice 128 cc center is found at 128 147 110 eigenvectors: -0.001 -0.006 1.000; -0.132 -0.991 -0.006; 0.991 -0.132 0.000; error in mid anterior detected - correcting... writing aseg with callosum to /root/Scrivania/subjects/ENP30S001A/mri/aseg.auto.mgz... corpus callosum matter segmentation took 0.6 minutes #-------------------------------------- #@# Merge ASeg Wed Sep 6 11:48:38 CEST 2017 cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# Intensity Normalization2 Wed Sep 6 11:48:38 CEST 2017 /root/Scrivania/subjects/ENP30S001A/mri mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 1887 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 70 (70), valley at 31 (31) csf peak at 35, setting threshold to 58 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 70 (70), valley at 32 (32) csf peak at 35, setting threshold to 58 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 2 minutes and 16 seconds. #-------------------------------------------- #@# Mask BFS Wed Sep 6 11:50:55 CEST 2017 /root/Scrivania/subjects/ENP30S001A/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1639089 voxels in mask (pct= 9.77) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Wed Sep 6 11:50:56 CEST 2017 mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /root/Scrivania/subjects/ENP30S001A/mri cmdline mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt sysname Linux hostname Braindata machine x86_64 user root input wm.mgz frame 0 nErode3d 0 nErode2d 0 output wm255.mgz Binarizing based on threshold min 255 max 255 binval 1 binvalnot 0 Found 0 values in range Counting number of voxels Found 0 voxels in final mask mri_binarize done mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /root/Scrivania/subjects/ENP30S001A/mri cmdline mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt sysname Linux hostname Braindata machine x86_64 user root input wm.mgz frame 0 nErode3d 0 nErode2d 0 output wm1.mgz Binarizing based on threshold min 1 max 1 binval 1 binvalnot 0 Found 0 values in range Counting number of voxels Found 0 voxels in final mask mri_binarize done rm wm1.mgz wm255.mgz mri_segment -keep brain.mgz wm.seg.mgz preserving editing changes in output volume... doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (105.0): 104.7 +- 6.3 [80.0 --> 125.0] GM (73.0) : 71.9 +- 9.1 [30.0 --> 96.0] setting bottom of white matter range to 81.1 setting top of gray matter range to 90.2 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... 3925 sparsely connected voxels removed... thickening thin strands.... 20 segments, 4846 filled 76 bright non-wm voxels segmented. 2292 diagonally connected voxels added... white matter segmentation took 1.1 minutes writing output to wm.seg.mgz... mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.34 minutes reading wm segmentation from wm.seg.mgz... 14 voxels added to wm to prevent paths from MTL structures to cortex 1866 additional wm voxels added 0 additional wm voxels added SEG EDIT: 30991 voxels turned on, 47286 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 105 new 105 115,126,128 old 105 new 105 writing edited volume to wm.asegedit.mgz.... mri_pretess -keep wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 14 found - 14 modified | TOTAL: 14 pass 2 (xy+): 0 found - 14 modified | TOTAL: 14 pass 1 (xy-): 21 found - 21 modified | TOTAL: 35 pass 2 (xy-): 0 found - 21 modified | TOTAL: 35 pass 1 (yz+): 32 found - 32 modified | TOTAL: 67 pass 2 (yz+): 0 found - 32 modified | TOTAL: 67 pass 1 (yz-): 16 found - 16 modified | TOTAL: 83 pass 2 (yz-): 0 found - 16 modified | TOTAL: 83 pass 1 (xz+): 12 found - 12 modified | TOTAL: 95 pass 2 (xz+): 0 found - 12 modified | TOTAL: 95 pass 1 (xz-): 12 found - 12 modified | TOTAL: 107 pass 2 (xz-): 0 found - 12 modified | TOTAL: 107 Iteration Number : 1 pass 1 (+++): 20 found - 20 modified | TOTAL: 20 pass 2 (+++): 0 found - 20 modified | TOTAL: 20 pass 1 (+++): 11 found - 11 modified | TOTAL: 31 pass 2 (+++): 0 found - 11 modified | TOTAL: 31 pass 1 (+++): 16 found - 16 modified | TOTAL: 47 pass 2 (+++): 0 found - 16 modified | TOTAL: 47 pass 1 (+++): 8 found - 8 modified | TOTAL: 55 pass 2 (+++): 0 found - 8 modified | TOTAL: 55 Iteration Number : 1 pass 1 (++): 57 found - 57 modified | TOTAL: 57 pass 2 (++): 0 found - 57 modified | TOTAL: 57 pass 1 (+-): 66 found - 66 modified | TOTAL: 123 pass 2 (+-): 0 found - 66 modified | TOTAL: 123 pass 1 (--): 71 found - 71 modified | TOTAL: 194 pass 2 (--): 0 found - 71 modified | TOTAL: 194 pass 1 (-+): 61 found - 61 modified | TOTAL: 255 pass 2 (-+): 0 found - 61 modified | TOTAL: 255 Iteration Number : 2 pass 1 (xy+): 4 found - 4 modified | TOTAL: 4 pass 2 (xy+): 0 found - 4 modified | TOTAL: 4 pass 1 (xy-): 0 found - 0 modified | TOTAL: 4 pass 1 (yz+): 4 found - 4 modified | TOTAL: 8 pass 2 (yz+): 0 found - 4 modified | TOTAL: 8 pass 1 (yz-): 2 found - 2 modified | TOTAL: 10 pass 2 (yz-): 0 found - 2 modified | TOTAL: 10 pass 1 (xz+): 4 found - 4 modified | TOTAL: 14 pass 2 (xz+): 0 found - 4 modified | TOTAL: 14 pass 1 (xz-): 5 found - 5 modified | TOTAL: 19 pass 2 (xz-): 0 found - 5 modified | TOTAL: 19 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 2 pass 1 (++): 2 found - 2 modified | TOTAL: 2 pass 2 (++): 0 found - 2 modified | TOTAL: 2 pass 1 (+-): 5 found - 5 modified | TOTAL: 7 pass 2 (+-): 0 found - 5 modified | TOTAL: 7 pass 1 (--): 3 found - 3 modified | TOTAL: 10 pass 2 (--): 0 found - 3 modified | TOTAL: 10 pass 1 (-+): 1 found - 1 modified | TOTAL: 11 pass 2 (-+): 0 found - 1 modified | TOTAL: 11 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 1 found - 1 modified | TOTAL: 2 pass 2 (yz-): 0 found - 1 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 1 found - 1 modified | TOTAL: 1 pass 2 (--): 0 found - 1 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 452 (out of 641267: 0.070485) keeping edits binarizing input wm segmentation... Ambiguous edge configurations... Searching for edits to keep ... kept 0 WM ON voxels kept 0 WM OFF voxels mri_pretess done #-------------------------------------------- #@# Fill Wed Sep 6 11:52:31 CEST 2017 /root/Scrivania/subjects/ENP30S001A/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 1.008 0.123 -0.020 -16.612; -0.103 1.119 0.243 -50.631; 0.046 -0.204 0.999 13.847; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.008 0.123 -0.020 -16.612; -0.103 1.119 0.243 -50.631; 0.046 -0.204 0.999 13.847; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1435 (min = 350, max = 1400), aspect = 0.43 (min = 0.10, max = 0.75) need search nearby using seed (125, 109, 93), TAL = (3.0, -35.0, 19.0) talairach voxel to voxel transform 0.980 -0.100 0.044 10.635; 0.096 0.846 -0.204 47.233; -0.026 0.178 0.957 -4.682; 0.000 0.000 0.000 1.000; segmentation indicates cc at (125, 109, 93) --> (3.0, -35.0, 19.0) done. writing output to filled.mgz... filling took 0.5 minutes talairach cc position changed to (3.00, -35.00, 19.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(21.00, -35.00, 19.00) SRC: (108.70, 130.72, 100.99) search lh wm seed point around talairach space (-15.00, -35.00, 19.00), SRC: (143.98, 134.16, 100.07) 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 Wed Sep 6 11:52:59 CEST 2017 /root/Scrivania/subjects/ENP30S001A/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 3 found - 3 modified | TOTAL: 3 pass 2 (yz+): 0 found - 3 modified | TOTAL: 3 pass 1 (yz-): 1 found - 1 modified | TOTAL: 4 pass 2 (yz-): 0 found - 1 modified | TOTAL: 4 pass 1 (xz+): 0 found - 0 modified | TOTAL: 4 pass 1 (xz-): 1 found - 1 modified | TOTAL: 5 pass 2 (xz-): 0 found - 1 modified | TOTAL: 5 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 5 (out of 311038: 0.001608) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 40: 240 vertices, 301 faces slice 50: 5017 vertices, 5273 faces slice 60: 14697 vertices, 15073 faces slice 70: 26857 vertices, 27315 faces slice 80: 39435 vertices, 39879 faces slice 90: 51347 vertices, 51735 faces slice 100: 63743 vertices, 64174 faces slice 110: 75955 vertices, 76387 faces slice 120: 87780 vertices, 88161 faces slice 130: 98924 vertices, 99342 faces slice 140: 110269 vertices, 110710 faces slice 150: 120356 vertices, 120693 faces slice 160: 129325 vertices, 129654 faces slice 170: 136817 vertices, 137075 faces slice 180: 143299 vertices, 143547 faces slice 190: 148357 vertices, 148522 faces slice 200: 150098 vertices, 150132 faces slice 210: 150098 vertices, 150132 faces slice 220: 150098 vertices, 150132 faces slice 230: 150098 vertices, 150132 faces slice 240: 150098 vertices, 150132 faces slice 250: 150098 vertices, 150132 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 150098 voxel in cpt #1: X=-34 [v=150098,e=450396,f=300264] located at (-26.846394, -17.426208, -7.505356) For the whole surface: X=-34 [v=150098,e=450396,f=300264] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Wed Sep 6 11:53:03 CEST 2017 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /root/Scrivania/subjects/ENP30S001A/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Wed Sep 6 11:53:06 CEST 2017 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /root/Scrivania/subjects/ENP30S001A/scripts avg radius = 48.0 mm, total surface area = 78883 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.4 minutes Not saving sulc step 000: RMS=0.100 (target=0.015) step 005: RMS=0.072 (target=0.015) step 010: RMS=0.054 (target=0.015) step 015: RMS=0.046 (target=0.015) step 020: RMS=0.040 (target=0.015) step 025: RMS=0.036 (target=0.015) step 030: RMS=0.033 (target=0.015) step 035: RMS=0.031 (target=0.015) step 040: RMS=0.030 (target=0.015) step 045: RMS=0.028 (target=0.015) step 050: RMS=0.028 (target=0.015) step 055: RMS=0.027 (target=0.015) step 060: RMS=0.027 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Wed Sep 6 11:53:27 CEST 2017 /root/Scrivania/subjects/ENP30S001A/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.96 +- 0.55 (0.00-->6.23) (max @ vno 112361 --> 113534) face area 0.03 +- 0.03 (-0.19-->0.67) scaling brain by 0.316... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.685, avgs=0 005/300: dt: 0.9000, rms radial error=175.428, avgs=0 010/300: dt: 0.9000, rms radial error=174.877, avgs=0 015/300: dt: 0.9000, rms radial error=174.153, avgs=0 020/300: dt: 0.9000, rms radial error=173.328, avgs=0 025/300: dt: 0.9000, rms radial error=172.447, avgs=0 030/300: dt: 0.9000, rms radial error=171.533, avgs=0 035/300: dt: 0.9000, rms radial error=170.603, avgs=0 040/300: dt: 0.9000, rms radial error=169.665, avgs=0 045/300: dt: 0.9000, rms radial error=168.724, avgs=0 050/300: dt: 0.9000, rms radial error=167.784, avgs=0 055/300: dt: 0.9000, rms radial error=166.846, avgs=0 060/300: dt: 0.9000, rms radial error=165.912, avgs=0 065/300: dt: 0.9000, rms radial error=164.982, avgs=0 070/300: dt: 0.9000, rms radial error=164.056, avgs=0 075/300: dt: 0.9000, rms radial error=163.135, avgs=0 080/300: dt: 0.9000, rms radial error=162.219, avgs=0 085/300: dt: 0.9000, rms radial error=161.307, avgs=0 090/300: dt: 0.9000, rms radial error=160.400, avgs=0 095/300: dt: 0.9000, rms radial error=159.499, avgs=0 100/300: dt: 0.9000, rms radial error=158.602, avgs=0 105/300: dt: 0.9000, rms radial error=157.711, avgs=0 110/300: dt: 0.9000, rms radial error=156.824, avgs=0 115/300: dt: 0.9000, rms radial error=155.942, avgs=0 120/300: dt: 0.9000, rms radial error=155.065, avgs=0 125/300: dt: 0.9000, rms radial error=154.193, avgs=0 130/300: dt: 0.9000, rms radial error=153.325, avgs=0 135/300: dt: 0.9000, rms radial error=152.463, avgs=0 140/300: dt: 0.9000, rms radial error=151.605, avgs=0 145/300: dt: 0.9000, rms radial error=150.751, avgs=0 150/300: dt: 0.9000, rms radial error=149.903, avgs=0 155/300: dt: 0.9000, rms radial error=149.059, avgs=0 160/300: dt: 0.9000, rms radial error=148.219, avgs=0 165/300: dt: 0.9000, rms radial error=147.385, avgs=0 170/300: dt: 0.9000, rms radial error=146.555, avgs=0 175/300: dt: 0.9000, rms radial error=145.729, avgs=0 180/300: dt: 0.9000, rms radial error=144.908, avgs=0 185/300: dt: 0.9000, rms radial error=144.092, avgs=0 190/300: dt: 0.9000, rms radial error=143.280, avgs=0 195/300: dt: 0.9000, rms radial error=142.473, avgs=0 200/300: dt: 0.9000, rms radial error=141.670, avgs=0 205/300: dt: 0.9000, rms radial error=140.872, avgs=0 210/300: dt: 0.9000, rms radial error=140.078, avgs=0 215/300: dt: 0.9000, rms radial error=139.289, avgs=0 220/300: dt: 0.9000, rms radial error=138.504, avgs=0 225/300: dt: 0.9000, rms radial error=137.723, avgs=0 230/300: dt: 0.9000, rms radial error=136.947, avgs=0 235/300: dt: 0.9000, rms radial error=136.174, avgs=0 240/300: dt: 0.9000, rms radial error=135.407, avgs=0 245/300: dt: 0.9000, rms radial error=134.643, avgs=0 250/300: dt: 0.9000, rms radial error=133.885, avgs=0 255/300: dt: 0.9000, rms radial error=133.130, avgs=0 260/300: dt: 0.9000, rms radial error=132.379, avgs=0 265/300: dt: 0.9000, rms radial error=131.632, avgs=0 270/300: dt: 0.9000, rms radial error=130.890, avgs=0 275/300: dt: 0.9000, rms radial error=130.151, avgs=0 280/300: dt: 0.9000, rms radial error=129.418, avgs=0 285/300: dt: 0.9000, rms radial error=128.688, avgs=0 290/300: dt: 0.9000, rms radial error=127.963, avgs=0 295/300: dt: 0.9000, rms radial error=127.242, avgs=0 300/300: dt: 0.9000, rms radial error=126.524, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 17474.52 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00014 epoch 2 (K=40.0), pass 1, starting sse = 2884.86 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00003 epoch 3 (K=160.0), pass 1, starting sse = 282.40 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/12 = 0.00590 epoch 4 (K=640.0), pass 1, starting sse = 17.74 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.11/14 = 0.00754 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.05 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Wed Sep 6 11:56:29 CEST 2017 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /root/Scrivania/subjects/ENP30S001A/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 ENP30S001A lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ before topology correction, eno=-34 (nv=150098, nf=300264, ne=450396, g=18) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 8 iterations marking ambiguous vertices... 5420 ambiguous faces found in tessellation segmenting defects... 19 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 8 into 6 18 defects to be corrected 0 vertices coincident reading input surface /root/Scrivania/subjects/ENP30S001A/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.1187 (-4.5593) -vertex loglikelihood: -6.1454 (-3.0727) -normal dot loglikelihood: -3.6411 (-3.6411) -quad curv loglikelihood: -6.5283 (-3.2641) Total Loglikelihood : -25.4335 CORRECTING DEFECT 0 (vertices=16, convex hull=54) After retessellation of defect 0, euler #=-16 (147015,440266,293235) : difference with theory (-15) = 1 CORRECTING DEFECT 1 (vertices=311, convex hull=227) After retessellation of defect 1, euler #=-15 (147025,440411,293371) : difference with theory (-14) = 1 CORRECTING DEFECT 2 (vertices=13, convex hull=28) After retessellation of defect 2, euler #=-14 (147028,440428,293386) : difference with theory (-13) = 1 CORRECTING DEFECT 3 (vertices=254, convex hull=151) After retessellation of defect 3, euler #=-13 (147114,440766,293639) : difference with theory (-12) = 1 CORRECTING DEFECT 4 (vertices=338, convex hull=99) After retessellation of defect 4, euler #=-12 (147139,440878,293727) : difference with theory (-11) = 1 CORRECTING DEFECT 5 (vertices=5, convex hull=27) After retessellation of defect 5, euler #=-11 (147141,440892,293740) : difference with theory (-10) = 1 CORRECTING DEFECT 6 (vertices=725, convex hull=456) After retessellation of defect 6, euler #=-9 (147313,441641,294319) : difference with theory (-9) = 0 CORRECTING DEFECT 7 (vertices=64, convex hull=113) After retessellation of defect 7, euler #=-8 (147330,441741,294403) : difference with theory (-8) = 0 CORRECTING DEFECT 8 (vertices=40, convex hull=63) After retessellation of defect 8, euler #=-7 (147347,441815,294461) : difference with theory (-7) = 0 CORRECTING DEFECT 9 (vertices=30, convex hull=57) After retessellation of defect 9, euler #=-6 (147365,441893,294522) : difference with theory (-6) = 0 CORRECTING DEFECT 10 (vertices=161, convex hull=74) After retessellation of defect 10, euler #=-5 (147385,441979,294589) : difference with theory (-5) = 0 CORRECTING DEFECT 11 (vertices=88, convex hull=33) After retessellation of defect 11, euler #=-4 (147395,442019,294620) : difference with theory (-4) = 0 CORRECTING DEFECT 12 (vertices=19, convex hull=44) After retessellation of defect 12, euler #=-3 (147404,442063,294656) : difference with theory (-3) = 0 CORRECTING DEFECT 13 (vertices=855, convex hull=139) After retessellation of defect 13, euler #=-2 (147444,442250,294804) : difference with theory (-2) = 0 CORRECTING DEFECT 14 (vertices=13, convex hull=33) After retessellation of defect 14, euler #=-1 (147447,442267,294819) : difference with theory (-1) = 0 CORRECTING DEFECT 15 (vertices=66, convex hull=32) After retessellation of defect 15, euler #=0 (147452,442294,294842) : difference with theory (0) = 0 CORRECTING DEFECT 16 (vertices=75, convex hull=128) After retessellation of defect 16, euler #=1 (147499,442486,294988) : difference with theory (1) = 0 CORRECTING DEFECT 17 (vertices=17, convex hull=20) After retessellation of defect 17, euler #=2 (147504,442506,295004) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.22 (0.11-->9.97) (max @ vno 54443 --> 60501) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.22 (0.11-->9.97) (max @ vno 54443 --> 60501) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 65 mutations (34.4%), 124 crossovers (65.6%), 320 vertices were eliminated building final representation... 2594 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=147504, nf=295004, ne=442506, g=0) writing corrected surface to /root/Scrivania/subjects/ENP30S001A/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 16.4 minutes 0 defective edges removing intersecting faces 000: 266 intersecting 001: 13 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 147504 - 442506 + 295004 = 2 --> 0 holes F =2V-4: 295004 = 295008-4 (0) 2E=3F: 885012 = 885012 (0) total defect index = 0 /root/Scrivania/subjects/ENP30S001A/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 51 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Wed Sep 6 12:12:55 CEST 2017 /root/Scrivania/subjects/ENP30S001A/scripts mris_make_surfaces -noaparc -mgz -T1 brain.finalsurfs ENP30S001A lh not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /root/Scrivania/subjects/ENP30S001A/mri/filled.mgz... reading volume /root/Scrivania/subjects/ENP30S001A/mri/brain.finalsurfs.mgz... reading volume /root/Scrivania/subjects/ENP30S001A/mri/wm.mgz... 15082 bright wm thresholded. 257 bright non-wm voxels segmented. reading original surface position from /root/Scrivania/subjects/ENP30S001A/surf/lh.orig... computing class statistics... border white: 279213 voxels (1.66%) border gray 305834 voxels (1.82%) WM (95.0): 96.2 +- 8.0 [70.0 --> 110.0] GM (82.0) : 80.5 +- 11.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 58.3 (was 70) setting MAX_BORDER_WHITE to 113.0 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 46.5 (was 40) setting MAX_GRAY to 97.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.1 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 34.8 (was 40) repositioning cortical surface to gray/white boundary reading volume /root/Scrivania/subjects/ENP30S001A/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.03-->5.11) (max @ vno 147215 --> 147225) face area 0.28 +- 0.12 (0.00-->4.41) mean absolute distance = 0.72 +- 0.92 3158 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=70 mean inside = 95.4, mean outside = 76.9 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group mean border=81.6, 63 (63) missing vertices, mean dist 0.2 [0.6 (%38.5)->0.8 (%61.5))] %67 local maxima, %28 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=Brain, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.25 (0.11-->5.56) (max @ vno 61866 --> 70213) face area 0.28 +- 0.13 (0.00-->6.01) mean absolute distance = 0.36 +- 0.60 2966 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5657202.0, rms=10.37 001: dt: 0.5000, sse=6295746.5, rms=7.264 (0.000%) 002: dt: 0.5000, sse=6680853.5, rms=5.396 (0.000%) 003: dt: 0.5000, sse=7001209.0, rms=4.303 (0.000%) 004: dt: 0.5000, sse=7266023.0, rms=3.652 (0.000%) 005: dt: 0.5000, sse=7439146.5, rms=3.382 (0.000%) 006: dt: 0.5000, sse=7540030.0, rms=3.209 (0.000%) rms = 3.18, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=7586327.5, rms=3.183 (0.000%) 008: dt: 0.2500, sse=4553411.0, rms=2.071 (0.000%) 009: dt: 0.2500, sse=4131929.8, rms=1.782 (0.000%) 010: dt: 0.2500, sse=3965712.2, rms=1.710 (0.000%) rms = 1.68, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=3908679.0, rms=1.676 (0.000%) rms = 1.64, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=3844914.5, rms=1.641 (0.000%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=84.6, 66 (36) missing vertices, mean dist -0.2 [0.4 (%71.6)->0.2 (%28.4))] %77 local maxima, %18 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=Brain, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.24 (0.06-->5.69) (max @ vno 61866 --> 70213) face area 0.35 +- 0.16 (0.00-->8.23) mean absolute distance = 0.25 +- 0.36 3616 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4533491.0, rms=4.76 013: dt: 0.5000, sse=4869790.0, rms=3.016 (0.000%) 014: dt: 0.5000, sse=5351834.0, rms=2.934 (0.000%) 015: dt: 0.5000, sse=5945726.0, rms=2.811 (0.000%) rms = 3.09, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=4769637.5, rms=1.935 (0.000%) 017: dt: 0.2500, sse=4371681.0, rms=1.530 (0.000%) 018: dt: 0.2500, sse=4226138.5, rms=1.406 (0.000%) rms = 1.39, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=4156737.2, rms=1.388 (0.000%) rms = 1.35, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=4108307.5, rms=1.354 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group mean border=87.2, 49 (16) missing vertices, mean dist -0.1 [0.3 (%73.9)->0.2 (%26.1))] %87 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=Brain, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.24 (0.08-->5.74) (max @ vno 61866 --> 70213) face area 0.33 +- 0.16 (0.00-->8.32) mean absolute distance = 0.20 +- 0.29 3258 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4361166.0, rms=3.43 021: dt: 0.5000, sse=4636350.0, rms=2.533 (0.000%) rms = 2.78, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=4330722.5, rms=1.774 (0.000%) 023: dt: 0.2500, sse=4220126.5, rms=1.366 (0.000%) 024: dt: 0.2500, sse=4199025.0, rms=1.247 (0.000%) rms = 1.24, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=4164955.8, rms=1.245 (0.000%) rms = 1.22, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=4127032.5, rms=1.218 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group mean border=88.1, 36 (6) missing vertices, mean dist -0.0 [0.2 (%58.9)->0.2 (%41.1))] %89 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=Brain, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /root/Scrivania/subjects/ENP30S001A/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=4143982.5, rms=1.63 rms = 1.68, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=4199977.5, rms=1.167 (0.000%) 028: dt: 0.2500, sse=4331419.5, rms=0.922 (0.000%) rms = 0.95, time step reduction 2 of 3 to 0.125... rms = 0.92, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=4329852.5, rms=0.922 (0.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 10 non-cortical segments detected only using segment with 1859 vertices erasing segment 1 (vno[0] = 92979) erasing segment 2 (vno[0] = 105518) erasing segment 3 (vno[0] = 108730) erasing segment 4 (vno[0] = 108850) erasing segment 5 (vno[0] = 111033) erasing segment 6 (vno[0] = 112129) erasing segment 7 (vno[0] = 116319) erasing segment 8 (vno[0] = 117171) erasing segment 9 (vno[0] = 147408) writing cortex label to /root/Scrivania/subjects/ENP30S001A/label/lh.cortex.label... writing curvature file /root/Scrivania/subjects/ENP30S001A/surf/lh.curv writing smoothed area to lh.area writing curvature file /root/Scrivania/subjects/ENP30S001A/surf/lh.area vertex spacing 0.88 +- 0.24 (0.08-->5.76) (max @ vno 61866 --> 70213) face area 0.33 +- 0.16 (0.00-->8.18) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... smoothing surface for 5 iterations... mean border=59.8, 57 (57) missing vertices, mean dist 1.7 [0.2 (%0.0)->2.4 (%100.0))] %20 local maxima, %45 large gradients and %30 min vals, 1962 gradients ignored tol=1.0e-04, sigma=2.0, host=Brain, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=25543636.0, rms=28.38 001: dt: 0.5000, sse=19441656.0, rms=24.277 (0.000%) 002: dt: 0.5000, sse=14907747.0, rms=20.745 (0.000%) 003: dt: 0.5000, sse=11703384.0, rms=17.777 (0.000%) 004: dt: 0.5000, sse=9613071.0, rms=15.318 (0.000%) 005: dt: 0.5000, sse=8222695.5, rms=13.315 (0.000%) 006: dt: 0.5000, sse=7359229.5, rms=11.672 (0.000%) 007: dt: 0.5000, sse=6819032.5, rms=10.212 (0.000%) 008: dt: 0.5000, sse=6524053.0, rms=8.846 (0.000%) 009: dt: 0.5000, sse=6316680.5, rms=7.540 (0.000%) 010: dt: 0.5000, sse=6258585.5, rms=6.337 (0.000%) 011: dt: 0.5000, sse=6311766.0, rms=5.357 (0.000%) 012: dt: 0.5000, sse=6463550.0, rms=4.687 (0.000%) 013: dt: 0.5000, sse=6660345.5, rms=4.288 (0.000%) 014: dt: 0.5000, sse=6717485.5, rms=4.037 (0.000%) 015: dt: 0.5000, sse=6826577.5, rms=3.904 (0.000%) 016: dt: 0.5000, sse=6821763.0, rms=3.798 (0.000%) rms = 3.76, time step reduction 1 of 3 to 0.250... 017: dt: 0.5000, sse=6889647.0, rms=3.757 (0.000%) 018: dt: 0.2500, sse=4698488.0, rms=2.954 (0.000%) 019: dt: 0.2500, sse=4505496.0, rms=2.726 (0.000%) rms = 2.69, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=4381880.5, rms=2.686 (0.000%) 021: dt: 0.1250, sse=4165291.0, rms=2.545 (0.000%) rms = 2.52, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=4134977.8, rms=2.525 (0.000%) positioning took 1.5 minutes mean border=57.4, 1035 (15) missing vertices, mean dist 0.1 [0.2 (%45.1)->0.5 (%54.9))] %38 local maxima, %34 large gradients and %24 min vals, 679 gradients ignored tol=1.0e-04, sigma=1.0, host=Brain, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4821551.0, rms=4.87 023: dt: 0.5000, sse=4970073.5, rms=3.754 (0.000%) 024: dt: 0.5000, sse=6358176.0, rms=3.693 (0.000%) rms = 3.75, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=5224813.0, rms=2.911 (0.000%) 026: dt: 0.2500, sse=4772492.5, rms=2.586 (0.000%) 027: dt: 0.2500, sse=4732135.0, rms=2.515 (0.000%) rms = 2.49, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=4692478.5, rms=2.490 (0.000%) 029: dt: 0.1250, sse=4516331.0, rms=2.335 (0.000%) rms = 2.31, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=4499261.5, rms=2.313 (0.000%) positioning took 0.6 minutes mean border=55.7, 1397 (13) missing vertices, mean dist 0.1 [0.2 (%39.9)->0.3 (%60.1))] %51 local maxima, %21 large gradients and %23 min vals, 736 gradients ignored tol=1.0e-04, sigma=0.5, host=Brain, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4683497.0, rms=3.35 rms = 3.49, time step reduction 1 of 3 to 0.250... 031: dt: 0.2500, sse=4496808.5, rms=2.792 (0.000%) 032: dt: 0.2500, sse=4486482.0, rms=2.455 (0.000%) 033: dt: 0.2500, sse=4679203.5, rms=2.367 (0.000%) rms = 2.35, time step reduction 2 of 3 to 0.125... 034: dt: 0.2500, sse=4710668.0, rms=2.354 (0.000%) 035: dt: 0.1250, sse=4578261.0, rms=2.235 (0.000%) rms = 2.22, time step reduction 3 of 3 to 0.062... 036: dt: 0.1250, sse=4588261.5, rms=2.216 (0.000%) positioning took 0.5 minutes mean border=54.8, 2958 (13) missing vertices, mean dist 0.0 [0.2 (%45.4)->0.3 (%54.6))] %55 local maxima, %16 large gradients and %22 min vals, 625 gradients ignored tol=1.0e-04, sigma=0.2, host=Brain, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /root/Scrivania/subjects/ENP30S001A/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=4627021.0, rms=2.52 rms = 3.06, time step reduction 1 of 3 to 0.250... 037: dt: 0.2500, sse=4527738.0, rms=2.305 (0.000%) 038: dt: 0.2500, sse=4683505.5, rms=2.241 (0.000%) rms = 2.23, time step reduction 2 of 3 to 0.125... 039: dt: 0.2500, sse=4742968.0, rms=2.227 (0.000%) 040: dt: 0.1250, sse=4663334.5, rms=2.142 (0.000%) rms = 2.13, time step reduction 3 of 3 to 0.062... 041: dt: 0.1250, sse=4669977.0, rms=2.128 (0.000%) positioning took 0.4 minutes writing curvature file /root/Scrivania/subjects/ENP30S001A/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /root/Scrivania/subjects/ENP30S001A/surf/lh.area.pial vertex spacing 0.97 +- 0.39 (0.08-->8.02) (max @ vno 54443 --> 54444) face area 0.38 +- 0.27 (0.00-->9.50) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 147504 vertices processed 25000 of 147504 vertices processed 50000 of 147504 vertices processed 75000 of 147504 vertices processed 100000 of 147504 vertices processed 125000 of 147504 vertices processed 0 of 147504 vertices processed 25000 of 147504 vertices processed 50000 of 147504 vertices processed 75000 of 147504 vertices processed 100000 of 147504 vertices processed 125000 of 147504 vertices processed thickness calculation complete, 540:705 truncations. 34277 vertices at 0 distance 105816 vertices at 1 distance 90224 vertices at 2 distance 35317 vertices at 3 distance 11366 vertices at 4 distance 3668 vertices at 5 distance 1200 vertices at 6 distance 403 vertices at 7 distance 104 vertices at 8 distance 47 vertices at 9 distance 51 vertices at 10 distance 25 vertices at 11 distance 15 vertices at 12 distance 19 vertices at 13 distance 13 vertices at 14 distance 3 vertices at 15 distance 12 vertices at 16 distance 4 vertices at 17 distance 4 vertices at 18 distance 6 vertices at 19 distance 6 vertices at 20 distance writing curvature file /root/Scrivania/subjects/ENP30S001A/surf/lh.thickness positioning took 7.5 minutes #-------------------------------------------- #@# Smooth2 lh Wed Sep 6 12:20:28 CEST 2017 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /root/Scrivania/subjects/ENP30S001A/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 lh Wed Sep 6 12:20:30 CEST 2017 /root/Scrivania/subjects/ENP30S001A/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 48.3 mm, total surface area = 88495 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.114 (target=0.015) step 005: RMS=0.078 (target=0.015) step 010: RMS=0.056 (target=0.015) step 015: RMS=0.046 (target=0.015) step 020: RMS=0.038 (target=0.015) step 025: RMS=0.031 (target=0.015) step 030: RMS=0.027 (target=0.015) step 035: RMS=0.023 (target=0.015) step 040: RMS=0.020 (target=0.015) step 045: RMS=0.018 (target=0.015) step 050: RMS=0.016 (target=0.015) inflation complete. inflation took 0.3 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 184 vertices thresholded to be in k1 ~ [-0.20 1.99], k2 ~ [-0.09 0.06] total integrated curvature = 0.593*4pi (7.452) --> 0 handles ICI = 1.8, FI = 11.5, variation=195.170 111 vertices thresholded to be in [-0.01 0.01] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 110 vertices thresholded to be in [-0.11 0.49] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.015, std = 0.025 done. #----------------------------------------- #@# Curvature Stats lh Wed Sep 6 12:21:46 CEST 2017 /root/Scrivania/subjects/ENP30S001A/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm ENP30S001A lh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/lh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ ENP30S001A/lh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 274 ] Gb_filter = 0 WARN: S lookup min: -0.235098 WARN: S explicit min: 0.000000 vertex = 910 #-------------------------------------------- #@# Tessellate rh Wed Sep 6 12:21:49 CEST 2017 /root/Scrivania/subjects/ENP30S001A/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 2 found - 2 modified | TOTAL: 3 pass 2 (xy-): 0 found - 2 modified | TOTAL: 3 pass 1 (yz+): 1 found - 1 modified | TOTAL: 4 pass 2 (yz+): 0 found - 1 modified | TOTAL: 4 pass 1 (yz-): 1 found - 1 modified | TOTAL: 5 pass 2 (yz-): 0 found - 1 modified | TOTAL: 5 pass 1 (xz+): 1 found - 1 modified | TOTAL: 6 pass 2 (xz+): 0 found - 1 modified | TOTAL: 6 pass 1 (xz-): 4 found - 4 modified | TOTAL: 10 pass 2 (xz-): 0 found - 4 modified | TOTAL: 10 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 2 found - 2 modified | TOTAL: 3 pass 2 (--): 0 found - 2 modified | TOTAL: 3 pass 1 (-+): 3 found - 3 modified | TOTAL: 6 pass 2 (-+): 0 found - 3 modified | TOTAL: 6 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 16 (out of 306836: 0.005215) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 50: 1741 vertices, 1865 faces slice 60: 8006 vertices, 8296 faces slice 70: 17928 vertices, 18288 faces slice 80: 29254 vertices, 29637 faces slice 90: 40592 vertices, 40993 faces slice 100: 52403 vertices, 52788 faces slice 110: 64349 vertices, 64762 faces slice 120: 76555 vertices, 76977 faces slice 130: 88923 vertices, 89377 faces slice 140: 100892 vertices, 101335 faces slice 150: 111863 vertices, 112236 faces slice 160: 121972 vertices, 122349 faces slice 170: 130708 vertices, 131005 faces slice 180: 138064 vertices, 138334 faces slice 190: 144573 vertices, 144824 faces slice 200: 148115 vertices, 148184 faces slice 210: 148266 vertices, 148304 faces slice 220: 148266 vertices, 148304 faces slice 230: 148266 vertices, 148304 faces slice 240: 148266 vertices, 148304 faces slice 250: 148266 vertices, 148304 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 148266 voxel in cpt #1: X=-38 [v=148266,e=444912,f=296608] located at (29.803556, -10.062510, 0.052271) For the whole surface: X=-38 [v=148266,e=444912,f=296608] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Wed Sep 6 12:21:53 CEST 2017 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /root/Scrivania/subjects/ENP30S001A/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 rh Wed Sep 6 12:21:56 CEST 2017 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /root/Scrivania/subjects/ENP30S001A/scripts avg radius = 47.3 mm, total surface area = 77888 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.4 minutes Not saving sulc step 000: RMS=0.099 (target=0.015) step 005: RMS=0.072 (target=0.015) step 010: RMS=0.052 (target=0.015) step 015: RMS=0.044 (target=0.015) step 020: RMS=0.037 (target=0.015) step 025: RMS=0.033 (target=0.015) step 030: RMS=0.030 (target=0.015) step 035: RMS=0.027 (target=0.015) step 040: RMS=0.026 (target=0.015) step 045: RMS=0.025 (target=0.015) step 050: RMS=0.024 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.022 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere rh Wed Sep 6 12:22:18 CEST 2017 /root/Scrivania/subjects/ENP30S001A/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.97 +- 0.53 (0.00-->6.32) (max @ vno 58132 --> 59359) face area 0.03 +- 0.03 (-0.19-->0.51) scaling brain by 0.318... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.914, avgs=0 005/300: dt: 0.9000, rms radial error=175.655, avgs=0 010/300: dt: 0.9000, rms radial error=175.098, avgs=0 015/300: dt: 0.9000, rms radial error=174.368, avgs=0 020/300: dt: 0.9000, rms radial error=173.537, avgs=0 025/300: dt: 0.9000, rms radial error=172.647, avgs=0 030/300: dt: 0.9000, rms radial error=171.725, avgs=0 035/300: dt: 0.9000, rms radial error=170.791, avgs=0 040/300: dt: 0.9000, rms radial error=169.850, avgs=0 045/300: dt: 0.9000, rms radial error=168.906, avgs=0 050/300: dt: 0.9000, rms radial error=167.962, avgs=0 055/300: dt: 0.9000, rms radial error=167.021, avgs=0 060/300: dt: 0.9000, rms radial error=166.084, avgs=0 065/300: dt: 0.9000, rms radial error=165.151, avgs=0 070/300: dt: 0.9000, rms radial error=164.223, avgs=0 075/300: dt: 0.9000, rms radial error=163.299, avgs=0 080/300: dt: 0.9000, rms radial error=162.380, avgs=0 085/300: dt: 0.9000, rms radial error=161.467, avgs=0 090/300: dt: 0.9000, rms radial error=160.558, avgs=0 095/300: dt: 0.9000, rms radial error=159.654, avgs=0 100/300: dt: 0.9000, rms radial error=158.755, avgs=0 105/300: dt: 0.9000, rms radial error=157.861, avgs=0 110/300: dt: 0.9000, rms radial error=156.972, avgs=0 115/300: dt: 0.9000, rms radial error=156.088, avgs=0 120/300: dt: 0.9000, rms radial error=155.208, avgs=0 125/300: dt: 0.9000, rms radial error=154.334, avgs=0 130/300: dt: 0.9000, rms radial error=153.465, avgs=0 135/300: dt: 0.9000, rms radial error=152.600, avgs=0 140/300: dt: 0.9000, rms radial error=151.740, avgs=0 145/300: dt: 0.9000, rms radial error=150.885, avgs=0 150/300: dt: 0.9000, rms radial error=150.035, avgs=0 155/300: dt: 0.9000, rms radial error=149.189, avgs=0 160/300: dt: 0.9000, rms radial error=148.348, avgs=0 165/300: dt: 0.9000, rms radial error=147.513, avgs=0 170/300: dt: 0.9000, rms radial error=146.681, avgs=0 175/300: dt: 0.9000, rms radial error=145.855, avgs=0 180/300: dt: 0.9000, rms radial error=145.033, avgs=0 185/300: dt: 0.9000, rms radial error=144.215, avgs=0 190/300: dt: 0.9000, rms radial error=143.402, avgs=0 195/300: dt: 0.9000, rms radial error=142.594, avgs=0 200/300: dt: 0.9000, rms radial error=141.790, avgs=0 205/300: dt: 0.9000, rms radial error=140.991, avgs=0 210/300: dt: 0.9000, rms radial error=140.196, avgs=0 215/300: dt: 0.9000, rms radial error=139.406, avgs=0 220/300: dt: 0.9000, rms radial error=138.620, avgs=0 225/300: dt: 0.9000, rms radial error=137.839, avgs=0 230/300: dt: 0.9000, rms radial error=137.062, avgs=0 235/300: dt: 0.9000, rms radial error=136.289, avgs=0 240/300: dt: 0.9000, rms radial error=135.521, avgs=0 245/300: dt: 0.9000, rms radial error=134.757, avgs=0 250/300: dt: 0.9000, rms radial error=133.998, avgs=0 255/300: dt: 0.9000, rms radial error=133.242, avgs=0 260/300: dt: 0.9000, rms radial error=132.491, avgs=0 265/300: dt: 0.9000, rms radial error=131.745, avgs=0 270/300: dt: 0.9000, rms radial error=131.002, avgs=0 275/300: dt: 0.9000, rms radial error=130.263, avgs=0 280/300: dt: 0.9000, rms radial error=129.529, avgs=0 285/300: dt: 0.9000, rms radial error=128.799, avgs=0 290/300: dt: 0.9000, rms radial error=128.073, avgs=0 295/300: dt: 0.9000, rms radial error=127.351, avgs=0 300/300: dt: 0.9000, rms radial error=126.633, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 17188.96 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00014 epoch 2 (K=40.0), pass 1, starting sse = 2770.32 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00003 epoch 3 (K=160.0), pass 1, starting sse = 255.64 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.08/11 = 0.00712 epoch 4 (K=640.0), pass 1, starting sse = 14.72 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.13/16 = 0.00796 final writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.05 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology rh Wed Sep 6 12:25:20 CEST 2017 cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated /root/Scrivania/subjects/ENP30S001A/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 ENP30S001A rh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ before topology correction, eno=-38 (nv=148266, nf=296608, ne=444912, g=20) 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 6 iterations marking ambiguous vertices... 4017 ambiguous faces found in tessellation segmenting defects... 17 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 10 into 9 16 defects to be corrected 0 vertices coincident reading input surface /root/Scrivania/subjects/ENP30S001A/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.1666 (-4.5833) -vertex loglikelihood: -6.1626 (-3.0813) -normal dot loglikelihood: -3.6725 (-3.6725) -quad curv loglikelihood: -6.5927 (-3.2963) Total Loglikelihood : -25.5943 CORRECTING DEFECT 0 (vertices=65, convex hull=108) After retessellation of defect 0, euler #=-14 (145942,437112,291156) : difference with theory (-13) = 1 CORRECTING DEFECT 1 (vertices=38, convex hull=84) After retessellation of defect 1, euler #=-13 (145959,437196,291224) : difference with theory (-12) = 1 CORRECTING DEFECT 2 (vertices=23, convex hull=55) After retessellation of defect 2, euler #=-12 (145970,437250,291268) : difference with theory (-11) = 1 CORRECTING DEFECT 3 (vertices=20, convex hull=33) After retessellation of defect 3, euler #=-11 (145974,437275,291290) : difference with theory (-10) = 1 CORRECTING DEFECT 4 (vertices=127, convex hull=116) After retessellation of defect 4, euler #=-10 (145992,437377,291375) : difference with theory (-9) = 1 CORRECTING DEFECT 5 (vertices=33, convex hull=49) After retessellation of defect 5, euler #=-9 (146002,437423,291412) : difference with theory (-8) = 1 CORRECTING DEFECT 6 (vertices=22, convex hull=20) After retessellation of defect 6, euler #=-8 (146006,437442,291428) : difference with theory (-7) = 1 CORRECTING DEFECT 7 (vertices=7, convex hull=27) After retessellation of defect 7, euler #=-7 (146009,437459,291443) : difference with theory (-6) = 1 CORRECTING DEFECT 8 (vertices=5, convex hull=27) After retessellation of defect 8, euler #=-6 (146011,437472,291455) : difference with theory (-5) = 1 CORRECTING DEFECT 9 (vertices=949, convex hull=468) After retessellation of defect 9, euler #=-4 (146276,438502,292222) : difference with theory (-4) = 0 CORRECTING DEFECT 10 (vertices=30, convex hull=62) After retessellation of defect 10, euler #=-3 (146293,438581,292285) : difference with theory (-3) = 0 CORRECTING DEFECT 11 (vertices=73, convex hull=29) After retessellation of defect 11, euler #=-2 (146300,438613,292311) : difference with theory (-2) = 0 CORRECTING DEFECT 12 (vertices=195, convex hull=83) After retessellation of defect 12, euler #=-1 (146318,438706,292387) : difference with theory (-1) = 0 CORRECTING DEFECT 13 (vertices=676, convex hull=329) After retessellation of defect 13, euler #=0 (146436,439229,292793) : difference with theory (0) = 0 CORRECTING DEFECT 14 (vertices=73, convex hull=128) normal vector of length zero at vertex 148223 with 3 faces After retessellation of defect 14, euler #=1 (146488,439443,292956) : difference with theory (1) = 0 CORRECTING DEFECT 15 (vertices=19, convex hull=44) After retessellation of defect 15, euler #=2 (146494,439476,292984) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.22 (0.08-->10.07) (max @ vno 57834 --> 57844) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.22 (0.08-->10.07) (max @ vno 57834 --> 57844) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 69 mutations (37.9%), 113 crossovers (62.1%), 162 vertices were eliminated building final representation... 1772 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=146494, nf=292984, ne=439476, g=0) writing corrected surface to /root/Scrivania/subjects/ENP30S001A/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 9.4 minutes 0 defective edges removing intersecting faces 000: 190 intersecting 001: 6 intersecting 002: 2 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 146494 - 439476 + 292984 = 2 --> 0 holes F =2V-4: 292984 = 292988-4 (0) 2E=3F: 878952 = 878952 (0) total defect index = 0 /root/Scrivania/subjects/ENP30S001A/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 60 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Wed Sep 6 12:34:49 CEST 2017 /root/Scrivania/subjects/ENP30S001A/scripts mris_make_surfaces -noaparc -mgz -T1 brain.finalsurfs ENP30S001A rh not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /root/Scrivania/subjects/ENP30S001A/mri/filled.mgz... reading volume /root/Scrivania/subjects/ENP30S001A/mri/brain.finalsurfs.mgz... reading volume /root/Scrivania/subjects/ENP30S001A/mri/wm.mgz... 15270 bright wm thresholded. 253 bright non-wm voxels segmented. reading original surface position from /root/Scrivania/subjects/ENP30S001A/surf/rh.orig... computing class statistics... border white: 279213 voxels (1.66%) border gray 305834 voxels (1.82%) WM (95.0): 96.2 +- 8.0 [70.0 --> 110.0] GM (82.0) : 80.5 +- 11.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 59.2 (was 70) setting MAX_BORDER_WHITE to 113.0 (was 105) setting MIN_BORDER_WHITE to 71.0 (was 85) setting MAX_CSF to 47.5 (was 40) setting MAX_GRAY to 97.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 65.1 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 35.7 (was 40) repositioning cortical surface to gray/white boundary reading volume /root/Scrivania/subjects/ENP30S001A/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.04-->4.93) (max @ vno 115644 --> 146363) face area 0.28 +- 0.12 (0.00-->3.16) mean absolute distance = 0.72 +- 0.94 3175 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=71 mean inside = 95.4, mean outside = 76.9 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group mean border=81.7, 44 (44) missing vertices, mean dist 0.2 [0.7 (%38.7)->0.8 (%61.3))] %63 local maxima, %32 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=Brain, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.25 (0.09-->7.17) (max @ vno 146363 --> 105868) face area 0.28 +- 0.13 (0.00-->3.99) mean absolute distance = 0.35 +- 0.62 2794 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5702343.0, rms=10.46 001: dt: 0.5000, sse=6405871.0, rms=7.318 (0.000%) 002: dt: 0.5000, sse=6826688.5, rms=5.434 (0.000%) 003: dt: 0.5000, sse=7166785.5, rms=4.323 (0.000%) 004: dt: 0.5000, sse=7463928.5, rms=3.664 (0.000%) 005: dt: 0.5000, sse=7598569.5, rms=3.406 (0.000%) 006: dt: 0.5000, sse=7705287.5, rms=3.236 (0.000%) rms = 3.22, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=7724298.0, rms=3.216 (0.000%) 008: dt: 0.2500, sse=4660595.5, rms=2.092 (0.000%) 009: dt: 0.2500, sse=4222490.5, rms=1.798 (0.000%) 010: dt: 0.2500, sse=4037516.8, rms=1.727 (0.000%) rms = 1.69, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=3981314.8, rms=1.690 (0.000%) rms = 1.65, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=3912573.2, rms=1.653 (0.000%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=84.7, 50 (27) missing vertices, mean dist -0.2 [0.4 (%71.8)->0.2 (%28.2))] %74 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=Brain, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.24 (0.10-->7.62) (max @ vno 146363 --> 105868) face area 0.35 +- 0.16 (0.00-->5.36) mean absolute distance = 0.25 +- 0.39 3400 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4544403.0, rms=4.50 013: dt: 0.5000, sse=4911992.5, rms=2.799 (0.000%) rms = 2.85, time step reduction 1 of 3 to 0.250... 014: dt: 0.2500, sse=4552014.5, rms=2.210 (0.000%) 015: dt: 0.2500, sse=4360258.0, rms=1.699 (0.000%) 016: dt: 0.2500, sse=4265820.5, rms=1.489 (0.000%) 017: dt: 0.2500, sse=4205783.0, rms=1.427 (0.000%) rms = 1.40, time step reduction 2 of 3 to 0.125... 018: dt: 0.2500, sse=4178903.5, rms=1.398 (0.000%) rms = 1.37, time step reduction 3 of 3 to 0.062... 019: dt: 0.1250, sse=4130657.8, rms=1.370 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=87.3, 34 (24) missing vertices, mean dist -0.2 [0.3 (%74.1)->0.2 (%25.9))] %85 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=Brain, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.24 (0.06-->7.81) (max @ vno 146363 --> 105868) face area 0.34 +- 0.16 (0.00-->5.50) mean absolute distance = 0.20 +- 0.29 2761 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4372754.0, rms=3.38 020: dt: 0.5000, sse=4658310.0, rms=2.480 (0.000%) rms = 2.77, time step reduction 1 of 3 to 0.250... 021: dt: 0.2500, sse=4366053.0, rms=1.737 (0.000%) 022: dt: 0.2500, sse=4271424.0, rms=1.355 (0.000%) 023: dt: 0.2500, sse=4252276.0, rms=1.251 (0.000%) rms = 1.25, time step reduction 2 of 3 to 0.125... rms = 1.24, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=4226660.0, rms=1.236 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=88.2, 30 (17) missing vertices, mean dist -0.0 [0.2 (%58.0)->0.2 (%42.0))] %88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=Brain, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /root/Scrivania/subjects/ENP30S001A/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=4242564.0, rms=1.61 rms = 1.75, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=4273110.5, rms=1.149 (0.000%) 026: dt: 0.2500, sse=4404211.5, rms=0.936 (0.000%) rms = 0.96, time step reduction 2 of 3 to 0.125... rms = 0.93, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=4402747.0, rms=0.935 (0.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 19 non-cortical segments detected only using segment with 2202 vertices erasing segment 1 (vno[0] = 62620) erasing segment 2 (vno[0] = 92515) erasing segment 3 (vno[0] = 94741) erasing segment 4 (vno[0] = 95898) erasing segment 5 (vno[0] = 95914) erasing segment 6 (vno[0] = 102530) erasing segment 7 (vno[0] = 103624) erasing segment 8 (vno[0] = 103688) erasing segment 9 (vno[0] = 103728) erasing segment 10 (vno[0] = 104751) erasing segment 11 (vno[0] = 104822) erasing segment 12 (vno[0] = 106808) erasing segment 13 (vno[0] = 107794) erasing segment 14 (vno[0] = 109732) erasing segment 15 (vno[0] = 111591) erasing segment 16 (vno[0] = 111600) erasing segment 17 (vno[0] = 111619) erasing segment 18 (vno[0] = 111654) writing cortex label to /root/Scrivania/subjects/ENP30S001A/label/rh.cortex.label... writing curvature file /root/Scrivania/subjects/ENP30S001A/surf/rh.curv writing smoothed area to rh.area writing curvature file /root/Scrivania/subjects/ENP30S001A/surf/rh.area vertex spacing 0.89 +- 0.25 (0.06-->7.87) (max @ vno 105868 --> 146363) face area 0.33 +- 0.16 (0.00-->5.42) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... smoothing surface for 5 iterations... mean border=60.5, 38 (38) missing vertices, mean dist 1.7 [0.1 (%0.0)->2.3 (%100.0))] %22 local maxima, %47 large gradients and %26 min vals, 2197 gradients ignored tol=1.0e-04, sigma=2.0, host=Brain, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=24539720.0, rms=27.79 001: dt: 0.5000, sse=18647480.0, rms=23.718 (0.000%) 002: dt: 0.5000, sse=14287355.0, rms=20.215 (0.000%) 003: dt: 0.5000, sse=11284376.0, rms=17.302 (0.000%) 004: dt: 0.5000, sse=9317794.0, rms=14.879 (0.000%) 005: dt: 0.5000, sse=8024025.5, rms=12.890 (0.000%) 006: dt: 0.5000, sse=7175750.5, rms=11.253 (0.000%) 007: dt: 0.5000, sse=6657254.5, rms=9.798 (0.000%) 008: dt: 0.5000, sse=6366998.0, rms=8.468 (0.000%) 009: dt: 0.5000, sse=6185964.0, rms=7.222 (0.000%) 010: dt: 0.5000, sse=6137974.0, rms=6.101 (0.000%) 011: dt: 0.5000, sse=6207756.0, rms=5.199 (0.000%) 012: dt: 0.5000, sse=6282500.0, rms=4.569 (0.000%) 013: dt: 0.5000, sse=6451894.0, rms=4.184 (0.000%) 014: dt: 0.5000, sse=6508639.5, rms=3.928 (0.000%) 015: dt: 0.5000, sse=6616787.5, rms=3.790 (0.000%) 016: dt: 0.5000, sse=6596986.0, rms=3.695 (0.000%) rms = 3.66, time step reduction 1 of 3 to 0.250... 017: dt: 0.5000, sse=6679531.0, rms=3.661 (0.000%) 018: dt: 0.2500, sse=4492114.0, rms=2.857 (0.000%) 019: dt: 0.2500, sse=4287860.5, rms=2.629 (0.000%) rms = 2.59, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=4171476.8, rms=2.591 (0.000%) 021: dt: 0.1250, sse=3977533.8, rms=2.449 (0.000%) rms = 2.43, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=3951687.8, rms=2.431 (0.000%) positioning took 1.5 minutes mean border=57.6, 740 (11) missing vertices, mean dist 0.2 [0.2 (%43.6)->0.5 (%56.4))] %41 local maxima, %35 large gradients and %20 min vals, 606 gradients ignored tol=1.0e-04, sigma=1.0, host=Brain, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4768926.0, rms=5.29 023: dt: 0.5000, sse=4797700.5, rms=3.869 (0.000%) 024: dt: 0.5000, sse=6160785.5, rms=3.720 (0.000%) rms = 3.78, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=5046288.0, rms=2.916 (0.000%) 026: dt: 0.2500, sse=4597392.5, rms=2.574 (0.000%) 027: dt: 0.2500, sse=4552962.5, rms=2.495 (0.000%) rms = 2.48, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=4524732.5, rms=2.475 (0.000%) 029: dt: 0.1250, sse=4341472.5, rms=2.296 (0.000%) rms = 2.27, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=4323674.0, rms=2.270 (0.000%) positioning took 0.6 minutes mean border=55.7, 950 (3) missing vertices, mean dist 0.1 [0.2 (%37.9)->0.3 (%62.1))] %54 local maxima, %22 large gradients and %19 min vals, 660 gradients ignored tol=1.0e-04, sigma=0.5, host=Brain, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4546630.5, rms=3.52 rms = 3.53, time step reduction 1 of 3 to 0.250... 031: dt: 0.2500, sse=4351162.0, rms=2.900 (0.000%) 032: dt: 0.2500, sse=4324523.0, rms=2.468 (0.000%) 033: dt: 0.2500, sse=4493762.0, rms=2.366 (0.000%) rms = 2.35, time step reduction 2 of 3 to 0.125... 034: dt: 0.2500, sse=4545132.5, rms=2.354 (0.000%) 035: dt: 0.1250, sse=4408806.0, rms=2.218 (0.000%) rms = 2.19, time step reduction 3 of 3 to 0.062... 036: dt: 0.1250, sse=4412772.5, rms=2.195 (0.000%) positioning took 0.5 minutes mean border=54.8, 2296 (2) missing vertices, mean dist 0.0 [0.2 (%44.0)->0.3 (%56.0))] %59 local maxima, %17 large gradients and %19 min vals, 534 gradients ignored tol=1.0e-04, sigma=0.2, host=Brain, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /root/Scrivania/subjects/ENP30S001A/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=4454894.0, rms=2.53 rms = 3.08, time step reduction 1 of 3 to 0.250... 037: dt: 0.2500, sse=4351642.0, rms=2.274 (0.000%) 038: dt: 0.2500, sse=4487932.5, rms=2.176 (0.000%) rms = 2.16, time step reduction 2 of 3 to 0.125... 039: dt: 0.2500, sse=4553325.5, rms=2.159 (0.000%) 040: dt: 0.1250, sse=4474079.5, rms=2.062 (0.000%) rms = 2.04, time step reduction 3 of 3 to 0.062... 041: dt: 0.1250, sse=4481417.0, rms=2.045 (0.000%) positioning took 0.4 minutes writing curvature file /root/Scrivania/subjects/ENP30S001A/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /root/Scrivania/subjects/ENP30S001A/surf/rh.area.pial vertex spacing 0.98 +- 0.40 (0.10-->8.78) (max @ vno 95909 --> 95896) face area 0.38 +- 0.27 (0.00-->7.96) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 146494 vertices processed 25000 of 146494 vertices processed 50000 of 146494 vertices processed 75000 of 146494 vertices processed 100000 of 146494 vertices processed 125000 of 146494 vertices processed 0 of 146494 vertices processed 25000 of 146494 vertices processed 50000 of 146494 vertices processed 75000 of 146494 vertices processed 100000 of 146494 vertices processed 125000 of 146494 vertices processed thickness calculation complete, 468:642 truncations. 35696 vertices at 0 distance 105049 vertices at 1 distance 88664 vertices at 2 distance 35183 vertices at 3 distance 11107 vertices at 4 distance 3442 vertices at 5 distance 1051 vertices at 6 distance 356 vertices at 7 distance 139 vertices at 8 distance 51 vertices at 9 distance 30 vertices at 10 distance 20 vertices at 11 distance 14 vertices at 12 distance 20 vertices at 13 distance 11 vertices at 14 distance 17 vertices at 15 distance 17 vertices at 16 distance 10 vertices at 17 distance 6 vertices at 18 distance 3 vertices at 19 distance 6 vertices at 20 distance writing curvature file /root/Scrivania/subjects/ENP30S001A/surf/rh.thickness positioning took 7.4 minutes #-------------------------------------------- #@# Smooth2 rh Wed Sep 6 12:42:12 CEST 2017 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /root/Scrivania/subjects/ENP30S001A/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 rh Wed Sep 6 12:42:14 CEST 2017 /root/Scrivania/subjects/ENP30S001A/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 47.4 mm, total surface area = 87954 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.114 (target=0.015) step 005: RMS=0.077 (target=0.015) step 010: RMS=0.055 (target=0.015) step 015: RMS=0.045 (target=0.015) step 020: RMS=0.037 (target=0.015) step 025: RMS=0.031 (target=0.015) step 030: RMS=0.025 (target=0.015) step 035: RMS=0.021 (target=0.015) step 040: RMS=0.018 (target=0.015) step 045: RMS=0.016 (target=0.015) inflation complete. inflation took 0.3 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 274 vertices thresholded to be in k1 ~ [-0.23 0.35], k2 ~ [-0.09 0.06] total integrated curvature = 0.545*4pi (6.843) --> 0 handles ICI = 1.9, FI = 14.3, variation=235.554 143 vertices thresholded to be in [-0.01 0.01] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 146 vertices thresholded to be in [-0.12 0.18] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.015, std = 0.028 done. #----------------------------------------- #@# Curvature Stats rh Wed Sep 6 12:43:29 CEST 2017 /root/Scrivania/subjects/ENP30S001A/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm ENP30S001A rh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/rh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ ENP30S001A/rh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 252 ] Gb_filter = 0 WARN: S lookup min: -0.036446 WARN: S explicit min: 0.000000 vertex = 321 #-------------------------------------------- #@# ASeg Stats Wed Sep 6 12:43:32 CEST 2017 INFO: mri_segstats will not calculate Supratentorial due to missing ribbon.mgz file /root/Scrivania/subjects/ENP30S001A mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/freesurfer/ASegStatsLUT.txt --subject ENP30S001A $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/freesurfer/ASegStatsLUT.txt --subject ENP30S001A sysname Linux hostname Braindata machine x86_64 user root UseRobust 0 atlas_icv (eTIV) = 1682783 mm^3 (det: 1.157669 ) mghRead(/root/Scrivania/subjects/ENP30S001A/mri/ribbon.mgz, -1): could not open file Computing euler number orig.nofix lheno = -34, rheno = -38 orig.nofix lhholes = 18, rhholes = 20 Loading mri/aseg.mgz Getting Brain Volume Statistics Linux Braindata 3.19.0-15-generic #15-Ubuntu SMP Thu Apr 16 23:32:37 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux recon-all -s ENP30S001A exited with ERRORS at Wed Sep 6 12:43:39 CEST 2017 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting