Thu May 7 14:24:01 UTC 2020 /output_dir/freesurfer/sub-01 /opt/freesurfer/bin/recon-all -all -no-isrunning -parallel -openmp 1 -subjid /output_dir/freesurfer/sub-01 -sd /output_dir/freesurfer subjid sub-01 setenv SUBJECTS_DIR /output_dir/freesurfer FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /opt/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a Linux cc31617c633f 4.19.76-linuxkit #1 SMP Thu Oct 17 19:31:58 UTC 2019 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 1048576 memorylocked 82000 kbytes maxproc unlimited maxlocks unlimited maxsignal 7822 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 2037620 254704 1443396 64 339520 1617036 Swap: 1048572 174604 873968 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/05/07-14:24:02-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: root Machine: cc31617c633f Platform: Linux PlatformVersion: 4.19.76-linuxkit CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/05/07-14:24:02-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: root Machine: cc31617c633f Platform: Linux PlatformVersion: 4.19.76-linuxkit CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/05/07-14:24:02-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: root Machine: cc31617c633f Platform: Linux PlatformVersion: 4.19.76-linuxkit CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/05/07-14:24:02-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: root Machine: cc31617c633f Platform: Linux PlatformVersion: 4.19.76-linuxkit CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/05/07-14:24:02-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: root Machine: cc31617c633f Platform: Linux PlatformVersion: 4.19.76-linuxkit CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/05/07-14:24:02-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: root Machine: cc31617c633f Platform: Linux PlatformVersion: 4.19.76-linuxkit CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/05/07-14:24:02-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: root Machine: cc31617c633f Platform: Linux PlatformVersion: 4.19.76-linuxkit CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/05/07-14:24:02-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: root Machine: cc31617c633f Platform: Linux PlatformVersion: 4.19.76-linuxkit CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/05/07-14:24:02-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: cc31617c633f Platform: Linux PlatformVersion: 4.19.76-linuxkit CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/05/07-14:24:02-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: root Machine: cc31617c633f Platform: Linux PlatformVersion: 4.19.76-linuxkit CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/05/07-14:24:02-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: cc31617c633f Platform: Linux PlatformVersion: 4.19.76-linuxkit CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/05/07-14:24:02-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: cc31617c633f Platform: Linux PlatformVersion: 4.19.76-linuxkit CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/05/07-14:24:02-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: root Machine: cc31617c633f Platform: Linux PlatformVersion: 4.19.76-linuxkit CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/05/07-14:24:03-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: root Machine: cc31617c633f Platform: Linux PlatformVersion: 4.19.76-linuxkit CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/05/07-14:24:03-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: root Machine: cc31617c633f Platform: Linux PlatformVersion: 4.19.76-linuxkit CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/05/07-14:24:03-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: root Machine: cc31617c633f Platform: Linux PlatformVersion: 4.19.76-linuxkit CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/05/07-14:24:03-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: root Machine: cc31617c633f Platform: Linux PlatformVersion: 4.19.76-linuxkit CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/05/07-14:24:03-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: root Machine: cc31617c633f Platform: Linux PlatformVersion: 4.19.76-linuxkit CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/05/07-14:24:03-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: root Machine: cc31617c633f Platform: Linux PlatformVersion: 4.19.76-linuxkit CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/05/07-14:24:03-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: root Machine: cc31617c633f Platform: Linux PlatformVersion: 4.19.76-linuxkit CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/05/07-14:24:03-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: root Machine: cc31617c633f Platform: Linux PlatformVersion: 4.19.76-linuxkit CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/05/07-14:24:03-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: root Machine: cc31617c633f Platform: Linux PlatformVersion: 4.19.76-linuxkit CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/05/07-14:24:03-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: root Machine: cc31617c633f Platform: Linux PlatformVersion: 4.19.76-linuxkit CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/05/07-14:24:03-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: root Machine: cc31617c633f Platform: Linux PlatformVersion: 4.19.76-linuxkit CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/05/07-14:24:03-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: root Machine: cc31617c633f Platform: Linux PlatformVersion: 4.19.76-linuxkit CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/05/07-14:24:03-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: root Machine: cc31617c633f Platform: Linux PlatformVersion: 4.19.76-linuxkit CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/05/07-14:24:03-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: root Machine: cc31617c633f Platform: Linux PlatformVersion: 4.19.76-linuxkit CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2020/05/07-14:24:03-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: root Machine: cc31617c633f Platform: Linux PlatformVersion: 4.19.76-linuxkit CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/05/07-14:24:03-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: root Machine: cc31617c633f Platform: Linux PlatformVersion: 4.19.76-linuxkit CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/05/07-14:24:03-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: root Machine: cc31617c633f Platform: Linux PlatformVersion: 4.19.76-linuxkit CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/05/07-14:24:03-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: root Machine: cc31617c633f Platform: Linux PlatformVersion: 4.19.76-linuxkit CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/05/07-14:24:03-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: root Machine: cc31617c633f Platform: Linux PlatformVersion: 4.19.76-linuxkit CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/05/07-14:24:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: root Machine: cc31617c633f Platform: Linux PlatformVersion: 4.19.76-linuxkit CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/05/07-14:24:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: root Machine: cc31617c633f Platform: Linux PlatformVersion: 4.19.76-linuxkit CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/05/07-14:24:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: root Machine: cc31617c633f Platform: Linux PlatformVersion: 4.19.76-linuxkit CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/05/07-14:24:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: root Machine: cc31617c633f Platform: Linux PlatformVersion: 4.19.76-linuxkit CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/05/07-14:24:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: root Machine: cc31617c633f Platform: Linux PlatformVersion: 4.19.76-linuxkit CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/05/07-14:24:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: root Machine: cc31617c633f Platform: Linux PlatformVersion: 4.19.76-linuxkit CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/05/07-14:24:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: root Machine: cc31617c633f Platform: Linux PlatformVersion: 4.19.76-linuxkit CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /opt/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /opt/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #-------------------------------------------- #@# MotionCor Thu May 7 14:24:04 UTC 2020 Found 1 runs /output_dir/freesurfer/sub-01/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 /output_dir/freesurfer/sub-01/mri/orig/001.mgz /output_dir/freesurfer/sub-01/mri/rawavg.mgz /output_dir/freesurfer/sub-01 mri_convert /output_dir/freesurfer/sub-01/mri/rawavg.mgz /output_dir/freesurfer/sub-01/mri/orig.mgz --conform mri_convert.bin /output_dir/freesurfer/sub-01/mri/rawavg.mgz /output_dir/freesurfer/sub-01/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /output_dir/freesurfer/sub-01/mri/rawavg.mgz... TR=2400.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /output_dir/freesurfer/sub-01/mri/orig.mgz... mri_add_xform_to_header -c /output_dir/freesurfer/sub-01/mri/transforms/talairach.xfm /output_dir/freesurfer/sub-01/mri/orig.mgz /output_dir/freesurfer/sub-01/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu May 7 14:24:18 UTC 2020 /output_dir/freesurfer/sub-01/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /output_dir/freesurfer/sub-01/mri /opt/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux cc31617c633f 4.19.76-linuxkit #1 SMP Thu Oct 17 19:31:58 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux Thu May 7 14:24:18 UTC 2020 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.235 /output_dir/freesurfer/sub-01/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.235/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.235/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=2400.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.235/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu May 7 14:24:23 UTC 2020 nu_correct -clobber ./tmp.mri_nu_correct.mni.235/nu0.mnc ./tmp.mri_nu_correct.mni.235/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.235/0/ -iterations 1000 -distance 50 [root@cc31617c633f:/output_dir/freesurfer/sub-01/mri/] [2020-05-07 14:24:23] running: /opt/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.235/0/ ./tmp.mri_nu_correct.mni.235/nu0.mnc ./tmp.mri_nu_correct.mni.235/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 60 CV of field change: 0.000986827 mri_convert ./tmp.mri_nu_correct.mni.235/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.235/nu1.mnc orig_nu.mgz --like orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.235/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz... Thu May 7 14:27:12 UTC 2020 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at Thu May 7 14:27:12 UTC 2020 Ended at Thu May 7 14:28:06 UTC 2020 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Thu May 7 14:28:08 UTC 2020 /output_dir/freesurfer/sub-01/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.5289, pval=0.2115 >= threshold=0.0050) awk -f /opt/freesurfer/bin/extract_talairach_avi_QA.awk /output_dir/freesurfer/sub-01/mri/transforms/talairach_avi.log tal_QC_AZS /output_dir/freesurfer/sub-01/mri/transforms/talairach_avi.log TalAviQA: 0.97660 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Thu May 7 14:28:08 UTC 2020 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /output_dir/freesurfer/sub-01/mri /opt/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 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux cc31617c633f 4.19.76-linuxkit #1 SMP Thu Oct 17 19:31:58 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux Thu May 7 14:28:09 UTC 2020 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.1186 /output_dir/freesurfer/sub-01/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1186/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.1186/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=2400.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.1186/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu May 7 14:28:15 UTC 2020 nu_correct -clobber ./tmp.mri_nu_correct.mni.1186/nu0.mnc ./tmp.mri_nu_correct.mni.1186/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1186/0/ [root@cc31617c633f:/output_dir/freesurfer/sub-01/mri/] [2020-05-07 14:28:15] running: /opt/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.1186/0/ ./tmp.mri_nu_correct.mni.1186/nu0.mnc ./tmp.mri_nu_correct.mni.1186/nu1.imp Processing:.................................................................Done 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Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 40 CV of field change: 0.000988175 -------------------------------------------------------- Iteration 2 Thu May 7 14:30:14 UTC 2020 nu_correct -clobber ./tmp.mri_nu_correct.mni.1186/nu1.mnc ./tmp.mri_nu_correct.mni.1186/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.1186/1/ [root@cc31617c633f:/output_dir/freesurfer/sub-01/mri/] [2020-05-07 14:30:15] running: /opt/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.1186/1/ ./tmp.mri_nu_correct.mni.1186/nu1.mnc ./tmp.mri_nu_correct.mni.1186/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 13 CV of field change: 0.000989478 mri_binarize --i ./tmp.mri_nu_correct.mni.1186/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.1186/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /output_dir/freesurfer/sub-01/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.1186/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.1186/ones.mgz sysname Linux hostname cc31617c633f machine x86_64 user root input ./tmp.mri_nu_correct.mni.1186/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.1186/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 16777216 values in range Counting number of voxels in first frame Found 16777216 voxels in final mask Count: 16777216 16777216.000000 16777216 100.000000 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.1186/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.1186/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1186/input.mean.dat $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.1186/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.1186/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1186/input.mean.dat sysname Linux hostname cc31617c633f machine x86_64 user root UseRobust 0 Loading ./tmp.mri_nu_correct.mni.1186/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.1186/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.1186/ones.mgz --i ./tmp.mri_nu_correct.mni.1186/nu2.mnc --sum ./tmp.mri_nu_correct.mni.1186/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1186/output.mean.dat $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.1186/ones.mgz --i ./tmp.mri_nu_correct.mni.1186/nu2.mnc --sum ./tmp.mri_nu_correct.mni.1186/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1186/output.mean.dat sysname Linux hostname cc31617c633f machine x86_64 user root UseRobust 0 Loading ./tmp.mri_nu_correct.mni.1186/ones.mgz Loading ./tmp.mri_nu_correct.mni.1186/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.1186/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.1186/nu2.mnc ./tmp.mri_nu_correct.mni.1186/nu2.mnc mul .93057704235076591810 Saving result to './tmp.mri_nu_correct.mni.1186/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.1186/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.1186/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.1186/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 11 seconds. mapping ( 7, 192) to ( 3, 110) Thu May 7 14:32:38 UTC 2020 mri_nu_correct.mni done mri_add_xform_to_header -c /output_dir/freesurfer/sub-01/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Thu May 7 14:32:40 UTC 2020 /output_dir/freesurfer/sub-01/mri mri_normalize -g 1 -mprage nu.mgz T1.mgz using max gradient = 1.000 assuming input volume is MGH (Van der Kouwe) MP-RAGE reading from nu.mgz... normalizing image... talairach transform 0.97874 0.00365 -0.02891 -1.72799; 0.00952 0.93676 0.39509 -27.79348; 0.03352 -0.36412 0.97134 -10.22691; 0.00000 0.00000 0.00000 1.00000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 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 110 white matter peak found at 110 gm peak at 83 (83), valley at 49 (49) csf peak at 42, setting threshold to 69 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 81 (81), valley at 40 (40) csf peak at 41, setting threshold to 67 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 55 seconds. #-------------------------------------------- #@# Skull Stripping Thu May 7 14:35:38 UTC 2020 /output_dir/freesurfer/sub-01/mri mri_em_register -rusage /output_dir/freesurfer/sub-01/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /opt/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach_with_skull.log reading '/opt/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca'... average std = 22.9 using min determinant for regularization = 52.6 0 singular and 9002 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 8.7 or > 569.1 total sample mean = 77.6 (1399 zeros) ************************************************ spacing=8, using 3243 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3243, passno 0, spacing 8 resetting wm mean[0]: 100 --> 108 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=7.0 skull bounding box = (42, 27, 18) --> (211, 255, 192) using (98, 103, 105) as brain centroid... mean wm in atlas = 108, using box (77,75,84) --> (118, 131,126) to find MRI wm before smoothing, mri peak at 108 robust fit to distribution - 107 +- 4.2 after smoothing, mri peak at 107, scaling input intensities by 1.009 scaling channel 0 by 1.00935 initial log_p = -4.422 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.403026 @ (-9.091, 9.091, -9.091) max log p = -4.290405 @ (4.545, -4.545, 4.545) max log p = -4.255305 @ (2.273, 2.273, -6.818) max log p = -4.239756 @ (3.409, -1.136, 1.136) max log p = -4.238553 @ (-2.841, -1.705, 0.568) max log p = -4.238553 @ (0.000, 0.000, 0.000) Found translation: (-1.7, 4.0, -9.7): log p = -4.239 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.078, old_max_log_p =-4.239 (thresh=-4.2) 1.00000 0.00000 0.00000 -1.70455; 0.00000 0.98278 0.40708 -36.47281; 0.00000 -0.40708 0.98278 42.98589; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.063, old_max_log_p =-4.078 (thresh=-4.1) 1.00000 0.00000 0.00000 -1.70455; 0.00000 0.98278 0.40708 -36.47281; 0.00000 -0.37655 0.90907 48.08119; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.063, old_max_log_p =-4.063 (thresh=-4.1) 1.00000 0.00000 0.00000 -1.70455; 0.00000 0.98278 0.40708 -36.47281; 0.00000 -0.37655 0.90907 48.08119; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.999, old_max_log_p =-4.063 (thresh=-4.1) 0.98072 0.03349 0.01155 -4.94527; -0.03333 1.06199 0.36630 -33.76284; 0.00000 -0.31731 0.95125 38.95714; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.991, old_max_log_p =-3.999 (thresh=-4.0) 0.98072 0.03349 0.01155 -4.94527; -0.03396 1.08190 0.37317 -37.06165; 0.00000 -0.31731 0.95125 38.95714; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.986, old_max_log_p =-3.991 (thresh=-4.0) 0.98131 -0.00193 -0.00067 0.98867; -0.00189 1.10271 0.38035 -44.65178; 0.00000 -0.31136 0.93342 40.30651; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.986, old_max_log_p =-3.986 (thresh=-4.0) 0.96291 -0.00189 -0.00065 3.31155; -0.00189 1.10271 0.38035 -44.65178; 0.00000 -0.31719 0.95092 38.98245; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.971, old_max_log_p =-3.986 (thresh=-4.0) 0.96617 0.00360 -0.01616 4.03104; -0.00188 1.09352 0.39447 -45.14351; 0.01584 -0.33636 0.94775 39.81982; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 8 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.967, old_max_log_p =-3.971 (thresh=-4.0) 0.96730 0.00361 -0.01618 3.88976; -0.00201 1.09623 0.38670 -45.02428; 0.01584 -0.32779 0.95206 38.67336; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3243 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.96730 0.00361 -0.01618 3.88976; -0.00201 1.09623 0.38670 -45.02428; 0.01584 -0.32779 0.95206 38.67336; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 0.96730 0.00361 -0.01618 3.88976; -0.00201 1.09623 0.38670 -45.02428; 0.01584 -0.32779 0.95206 38.67336; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.96730 0.00361 -0.01618 3.88976; -0.00201 1.09623 0.38670 -45.02428; 0.01584 -0.32779 0.95206 38.67336; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.967 (old=-4.422) transform before final EM align: 0.96730 0.00361 -0.01618 3.88976; -0.00201 1.09623 0.38670 -45.02428; 0.01584 -0.32779 0.95206 38.67336; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 364799 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.96730 0.00361 -0.01618 3.88976; -0.00201 1.09623 0.38670 -45.02428; 0.01584 -0.32779 0.95206 38.67336; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 0.96730 0.00361 -0.01618 3.88976; -0.00201 1.09623 0.38670 -45.02428; 0.01584 -0.32779 0.95206 38.67336; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 013: -log(p) = 4.3 tol 0.000000 final transform: 0.96730 0.00361 -0.01618 3.88976; -0.00201 1.09623 0.38670 -45.02428; 0.01584 -0.32779 0.95206 38.67336; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 1686.641713 mri_em_register stimesec 10.184470 mri_em_register ru_maxrss 612084 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 157207 mri_em_register ru_majflt 6 mri_em_register ru_nswap 0 mri_em_register ru_inblock 158576 mri_em_register ru_oublock 0 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 94 mri_em_register ru_nivcsw 211780 registration took 28 minutes and 50 seconds. mri_watershed -rusage /output_dir/freesurfer/sub-01/touch/rusage.mri_watershed.dat -T1 -brain_atlas /opt/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=127 y=107 z=112 r=85 first estimation of the main basin volume: 2638115 voxels Looking for seedpoints 2 found in the cerebellum 18 found in the rest of the brain global maximum in x=149, y=103, z=72, 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=533410275 voxels, voxel volume =1.000 = 533410275 mmm3 = 533410.272 cm3 done. PostAnalyze...Basin Prior 6 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=126,y=115, z=109, r=9953 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=5, CSF_MAX=57 , nb = 41502 RIGHT_CER CSF_MIN=0, CSF_intensity=4, CSF_MAX=24 , nb = -1031461199 LEFT_CER CSF_MIN=0, CSF_intensity=4, CSF_MAX=26 , nb = 1064635789 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=5, CSF_MAX=59 , nb = 1079974927 LEFT_BRAIN CSF_MIN=0, CSF_intensity=6, CSF_MAX=66 , nb = 1068638864 OTHER CSF_MIN=0, CSF_intensity=4, CSF_MAX=11 , nb = 1083848228 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 57, 57, 58, 78 after analyzing : 35, 57, 58, 62 RIGHT_CER before analyzing : 24, 39, 58, 81 after analyzing : 24, 51, 58, 58 LEFT_CER before analyzing : 26, 42, 58, 79 after analyzing : 26, 52, 58, 58 RIGHT_BRAIN before analyzing : 59, 57, 57, 77 after analyzing : 35, 57, 57, 62 LEFT_BRAIN before analyzing : 66, 60, 58, 78 after analyzing : 46, 60, 60, 64 OTHER before analyzing : 11, 28, 72, 90 after analyzing : 11, 57, 72, 65 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...75 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.012 curvature mean = 71.668, std = 6.879 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 4.52, sigma = 7.25 after rotation: sse = 4.52, sigma = 7.25 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 5.30, its var is 9.49 before Erosion-Dilatation 3.13% 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...52 iterations mri_strip_skull: done peeling brain Brain Size = 1898341 voxels, voxel volume = 1.000 mm3 = 1898341 mmm3 = 1898.341 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 26.966177 mri_watershed stimesec 0.658077 mri_watershed ru_maxrss 838812 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 213142 mri_watershed ru_majflt 10 mri_watershed ru_nswap 0 mri_watershed ru_inblock 26272 mri_watershed ru_oublock 0 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 365 mri_watershed ru_nivcsw 6364 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Thu May 7 15:04:58 UTC 2020 /output_dir/freesurfer/sub-01/mri mri_em_register -rusage /output_dir/freesurfer/sub-01/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading '/opt/freesurfer/average/RB_all_2016-05-10.vc700.gca'... average std = 7.3 using min determinant for regularization = 5.3 0 singular and 841 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 6.3 or > 503.7 total sample mean = 78.8 (1011 zeros) ************************************************ spacing=8, using 2830 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2830, passno 0, spacing 8 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=24.1 skull bounding box = (54, 45, 33) --> (198, 199, 199) using (102, 96, 116) as brain centroid... mean wm in atlas = 107, using box (84,77,96) --> (119, 114,136) to find MRI wm before smoothing, mri peak at 108 robust fit to distribution - 108 +- 3.8 after smoothing, mri peak at 108, scaling input intensities by 0.991 scaling channel 0 by 0.990741 initial log_p = -4.147 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.021534 @ (-9.091, 9.091, -9.091) max log p = -3.960050 @ (4.545, -4.545, 4.545) max log p = -3.837039 @ (2.273, 6.818, -2.273) max log p = -3.802392 @ (1.136, -1.136, -1.136) max log p = -3.802392 @ (0.000, 0.000, 0.000) max log p = -3.796303 @ (-0.852, -0.284, -0.284) Found translation: (-2.0, 9.9, -8.2): log p = -3.796 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.565, old_max_log_p =-3.796 (thresh=-3.8) 1.00000 0.00000 0.00000 -1.98864; 0.00000 0.92388 0.38268 -25.23789; 0.00000 -0.38268 0.92388 49.76019; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.565, old_max_log_p =-3.565 (thresh=-3.6) 1.00000 0.00000 0.00000 -1.98864; 0.00000 0.92388 0.38268 -25.23789; 0.00000 -0.38268 0.92388 49.76019; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.477, old_max_log_p =-3.565 (thresh=-3.6) 0.94410 -0.02633 -0.01091 11.07999; 0.03708 0.97582 0.40420 -41.95483; 0.00000 -0.38268 0.92388 49.76019; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.477, old_max_log_p =-3.477 (thresh=-3.5) 0.94410 -0.02633 -0.01091 11.07999; 0.03708 0.97582 0.40420 -41.95483; 0.00000 -0.38268 0.92388 49.76019; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.440, old_max_log_p =-3.477 (thresh=-3.5) 0.94033 -0.02778 -0.02927 13.24473; 0.04464 0.96904 0.41009 -43.24454; 0.01509 -0.39055 0.91917 48.77933; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.440, old_max_log_p =-3.440 (thresh=-3.4) 0.94033 -0.02778 -0.02927 13.24473; 0.04464 0.96904 0.41009 -43.24454; 0.01509 -0.39055 0.91917 48.77933; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2830 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.94033 -0.02778 -0.02927 13.24473; 0.04464 0.96904 0.41009 -43.24454; 0.01509 -0.39055 0.91917 48.77933; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 0.94033 -0.02778 -0.02927 13.24473; 0.04464 0.96904 0.41009 -43.24454; 0.01509 -0.39055 0.91917 48.77933; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.94033 -0.02778 -0.02927 13.24473; 0.04464 0.96904 0.41009 -43.24454; 0.01509 -0.39055 0.91917 48.77933; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.440 (old=-4.147) transform before final EM align: 0.94033 -0.02778 -0.02927 13.24473; 0.04464 0.96904 0.41009 -43.24454; 0.01509 -0.39055 0.91917 48.77933; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 315557 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.94033 -0.02778 -0.02927 13.24473; 0.04464 0.96904 0.41009 -43.24454; 0.01509 -0.39055 0.91917 48.77933; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 0.94033 -0.02778 -0.02927 13.24473; 0.04464 0.96904 0.41009 -43.24454; 0.01509 -0.39055 0.91917 48.77933; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = 3.9 tol 0.000000 final transform: 0.94033 -0.02778 -0.02927 13.24473; 0.04464 0.96904 0.41009 -43.24454; 0.01509 -0.39055 0.91917 48.77933; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 1068.525808 mri_em_register stimesec 8.868303 mri_em_register ru_maxrss 601568 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 157947 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 151376 mri_em_register ru_oublock 0 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 120 mri_em_register ru_nivcsw 149483 registration took 18 minutes and 25 seconds. #-------------------------------------- #@# CA Normalize Thu May 7 15:23:24 UTC 2020 /output_dir/freesurfer/sub-01/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/opt/freesurfer/average/RB_all_2016-05-10.vc700.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=24.1 skull bounding box = (54, 45, 33) --> (198, 199, 199) using (102, 96, 116) as brain centroid... mean wm in atlas = 107, using box (84,77,96) --> (119, 114,136) to find MRI wm before smoothing, mri peak at 108 robust fit to distribution - 108 +- 3.8 after smoothing, mri peak at 108, scaling input intensities by 0.991 scaling channel 0 by 0.990741 using 246344 sample points... INFO: compute sample coordinates transform 0.94033 -0.02778 -0.02927 13.24473; 0.04464 0.96904 0.41009 -43.24454; 0.01509 -0.39055 0.91917 48.77933; 0.00000 0.00000 0.00000 1.00000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (125, 51, 35) --> (198, 172, 197) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0 0 of 5770 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (58, 52, 36) --> (129, 165, 197) Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0 3 of 6192 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (129, 144, 70) --> (181, 185, 124) Left_Cerebellum_White_Matter: limiting intensities to 103.0 --> 132.0 0 of 10 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (81, 144, 68) --> (128, 185, 124) Right_Cerebellum_White_Matter: limiting intensities to 108.0 --> 132.0 8 of 22 (36.4%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (110, 126, 101) --> (148, 192, 134) Brain_Stem: limiting intensities to 94.0 --> 132.0 0 of 123 (0.0%) samples deleted using 12117 total control points for intensity normalization... bias field = 0.985 +- 0.040 131 of 12106 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (125, 51, 35) --> (198, 172, 197) Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 3 of 6064 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (58, 52, 36) --> (129, 165, 197) Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 7 of 6583 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (129, 144, 70) --> (181, 185, 124) Left_Cerebellum_White_Matter: limiting intensities to 90.0 --> 132.0 0 of 74 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (81, 144, 68) --> (128, 185, 124) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 3 of 53 (5.7%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (110, 126, 101) --> (148, 192, 134) Brain_Stem: limiting intensities to 88.0 --> 132.0 0 of 211 (0.0%) samples deleted using 12985 total control points for intensity normalization... bias field = 1.036 +- 0.046 188 of 12904 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (125, 51, 35) --> (198, 172, 197) Left_Cerebral_White_Matter: limiting intensities to 90.0 --> 131.0 4 of 6079 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (58, 52, 36) --> (129, 165, 197) Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 131.0 8 of 6443 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (129, 144, 70) --> (181, 185, 124) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 131.0 14 of 117 (12.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (81, 144, 68) --> (128, 185, 124) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 131.0 8 of 82 (9.8%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (110, 126, 101) --> (148, 192, 134) Brain_Stem: limiting intensities to 88.0 --> 131.0 7 of 259 (2.7%) samples deleted using 12980 total control points for intensity normalization... bias field = 1.034 +- 0.042 138 of 12649 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 40 seconds. #-------------------------------------- #@# CA Reg Thu May 7 15:25:04 UTC 2020 /output_dir/freesurfer/sub-01/mri mri_ca_register -rusage /output_dir/freesurfer/sub-01/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_ca_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/opt/freesurfer/average/RB_all_2016-05-10.vc700.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 0.99 (predicted orig area = 8.1) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.843, neg=0, invalid=762 0001: dt=221.952000, rms=0.749 (11.140%), neg=0, invalid=762 0002: dt=224.979592, rms=0.733 (2.208%), neg=0, invalid=762 0003: dt=165.362162, rms=0.722 (1.416%), neg=0, invalid=762 0004: dt=221.952000, rms=0.717 (0.701%), neg=0, invalid=762 0005: dt=295.936000, rms=0.713 (0.602%), neg=0, invalid=762 0006: dt=129.472000, rms=0.710 (0.399%), neg=0, invalid=762 0007: dt=517.888000, rms=0.706 (0.588%), neg=0, invalid=762 0008: dt=129.472000, rms=0.705 (0.222%), neg=0, invalid=762 0009: dt=129.472000, rms=0.704 (0.136%), neg=0, invalid=762 0010: dt=129.472000, rms=0.702 (0.214%), neg=0, invalid=762 0011: dt=129.472000, rms=0.700 (0.269%), neg=0, invalid=762 0012: dt=129.472000, rms=0.698 (0.274%), neg=0, invalid=762 0013: dt=129.472000, rms=0.696 (0.254%), neg=0, invalid=762 0014: dt=129.472000, rms=0.695 (0.268%), neg=0, invalid=762 0015: dt=129.472000, rms=0.693 (0.250%), neg=0, invalid=762 0016: dt=129.472000, rms=0.691 (0.227%), neg=0, invalid=762 0017: dt=129.472000, rms=0.690 (0.182%), neg=0, invalid=762 0018: dt=129.472000, rms=0.689 (0.130%), neg=0, invalid=762 0019: dt=129.472000, rms=0.688 (0.136%), neg=0, invalid=762 0020: dt=129.472000, rms=0.687 (0.145%), neg=0, invalid=762 0021: dt=129.472000, rms=0.686 (0.137%), neg=0, invalid=762 0022: dt=129.472000, rms=0.685 (0.149%), neg=0, invalid=762 0023: dt=129.472000, rms=0.684 (0.113%), neg=0, invalid=762 0024: dt=129.472000, rms=0.684 (0.097%), neg=0, invalid=762 0025: dt=517.888000, rms=0.683 (0.101%), neg=0, invalid=762 0026: dt=129.472000, rms=0.683 (0.029%), neg=0, invalid=762 0027: dt=129.472000, rms=0.683 (0.037%), neg=0, invalid=762 0028: dt=129.472000, rms=0.682 (0.041%), neg=0, invalid=762 0029: dt=129.472000, rms=0.682 (0.041%), neg=0, invalid=762 0030: dt=129.472000, rms=0.682 (0.053%), neg=0, invalid=762 0031: dt=129.472000, rms=0.681 (0.063%), neg=0, invalid=762 0032: dt=129.472000, rms=0.681 (0.086%), neg=0, invalid=762 0033: dt=129.472000, rms=0.680 (0.085%), neg=0, invalid=762 0034: dt=129.472000, rms=0.680 (0.068%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.680, neg=0, invalid=762 0035: dt=295.936000, rms=0.677 (0.525%), neg=0, invalid=762 0036: dt=129.472000, rms=0.676 (0.106%), neg=0, invalid=762 0037: dt=129.472000, rms=0.676 (0.032%), neg=0, invalid=762 0038: dt=129.472000, rms=0.675 (0.070%), neg=0, invalid=762 0039: dt=129.472000, rms=0.674 (0.100%), neg=0, invalid=762 0040: dt=129.472000, rms=0.674 (0.112%), neg=0, invalid=762 0041: dt=129.472000, rms=0.673 (0.093%), neg=0, invalid=762 0042: dt=129.472000, rms=0.673 (0.085%), neg=0, invalid=762 0043: dt=0.000000, rms=0.673 (-0.003%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.680, neg=0, invalid=762 0044: dt=36.288000, rms=0.678 (0.254%), neg=0, invalid=762 0045: dt=196.266667, rms=0.673 (0.718%), neg=0, invalid=762 0046: dt=182.320542, rms=0.660 (1.974%), neg=0, invalid=762 0047: dt=25.920000, rms=0.658 (0.308%), neg=0, invalid=762 0048: dt=15.552000, rms=0.658 (0.041%), neg=0, invalid=762 0049: dt=15.552000, rms=0.658 (0.008%), neg=0, invalid=762 0050: dt=15.552000, rms=0.658 (0.001%), neg=0, invalid=762 0051: dt=15.552000, rms=0.658 (-0.017%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.658, neg=0, invalid=762 0052: dt=143.567568, rms=0.652 (0.960%), neg=0, invalid=762 0053: dt=36.288000, rms=0.650 (0.242%), neg=0, invalid=762 0054: dt=36.288000, rms=0.650 (0.105%), neg=0, invalid=762 0055: dt=36.288000, rms=0.649 (0.133%), neg=0, invalid=762 0056: dt=36.288000, rms=0.647 (0.208%), neg=0, invalid=762 0057: dt=36.288000, rms=0.645 (0.312%), neg=0, invalid=762 0058: dt=36.288000, rms=0.643 (0.362%), neg=0, invalid=762 0059: dt=36.288000, rms=0.641 (0.349%), neg=0, invalid=762 0060: dt=36.288000, rms=0.639 (0.331%), neg=0, invalid=762 0061: dt=36.288000, rms=0.637 (0.300%), neg=0, invalid=762 0062: dt=36.288000, rms=0.635 (0.271%), neg=0, invalid=762 0063: dt=36.288000, rms=0.633 (0.263%), neg=0, invalid=762 0064: dt=36.288000, rms=0.632 (0.269%), neg=0, invalid=762 0065: dt=36.288000, rms=0.630 (0.269%), neg=0, invalid=762 0066: dt=36.288000, rms=0.628 (0.232%), neg=0, invalid=762 0067: dt=36.288000, rms=0.627 (0.208%), neg=0, invalid=762 0068: dt=36.288000, rms=0.626 (0.185%), neg=0, invalid=762 0069: dt=36.288000, rms=0.625 (0.165%), neg=0, invalid=762 0070: dt=36.288000, rms=0.624 (0.167%), neg=0, invalid=762 0071: dt=36.288000, rms=0.623 (0.171%), neg=0, invalid=762 0072: dt=36.288000, rms=0.622 (0.151%), neg=0, invalid=762 0073: dt=36.288000, rms=0.621 (0.142%), neg=0, invalid=762 0074: dt=36.288000, rms=0.620 (0.130%), neg=0, invalid=762 0075: dt=36.288000, rms=0.620 (0.106%), neg=0, invalid=762 0076: dt=36.288000, rms=0.619 (0.105%), neg=0, invalid=762 0077: dt=103.680000, rms=0.619 (0.063%), neg=0, invalid=762 0078: dt=103.680000, rms=0.619 (-0.040%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.642, neg=0, invalid=762 0079: dt=6.400000, rms=0.641 (0.132%), neg=0, invalid=762 0080: dt=2.400000, rms=0.641 (0.005%), neg=0, invalid=762 0081: dt=2.400000, rms=0.641 (0.002%), neg=0, invalid=762 0082: dt=2.400000, rms=0.641 (-0.023%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.641, neg=0, invalid=762 0083: dt=1.600000, rms=0.641 (0.090%), neg=0, invalid=762 0084: dt=0.600000, rms=0.641 (0.001%), neg=0, invalid=762 0085: dt=0.600000, rms=0.641 (0.001%), neg=0, invalid=762 0086: dt=0.600000, rms=0.641 (-0.005%), neg=0, invalid=762 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.700, neg=0, invalid=762 0087: dt=6.363636, rms=0.682 (2.489%), neg=0, invalid=762 0088: dt=4.620690, rms=0.681 (0.162%), neg=0, invalid=762 0089: dt=4.620690, rms=0.681 (-0.022%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.681, neg=0, invalid=762 0090: dt=0.216000, rms=0.681 (0.072%), neg=0, invalid=762 0091: dt=0.063000, rms=0.681 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.732, neg=0, invalid=762 0092: dt=0.448000, rms=0.731 (0.179%), neg=0, invalid=762 0093: dt=1.024000, rms=0.730 (0.149%), neg=0, invalid=762 0094: dt=1.024000, rms=0.728 (0.318%), neg=0, invalid=762 0095: dt=1.024000, rms=0.726 (0.232%), neg=0, invalid=762 0096: dt=1.024000, rms=0.726 (-0.148%), neg=0, invalid=762 0097: dt=1.792000, rms=0.725 (0.101%), neg=0, invalid=762 0098: dt=4.096000, rms=0.723 (0.326%), neg=0, invalid=762 0099: dt=0.000000, rms=0.723 (0.002%), neg=0, invalid=762 0100: dt=0.100000, rms=0.723 (-0.007%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.723, neg=0, invalid=762 0101: dt=0.112000, rms=0.723 (0.070%), neg=0, invalid=762 0102: dt=0.112000, rms=0.723 (0.003%), neg=0, invalid=762 0103: dt=0.112000, rms=0.723 (-0.002%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.690, neg=0, invalid=762 0104: dt=0.729899, rms=0.675 (2.136%), neg=0, invalid=762 0105: dt=0.064000, rms=0.674 (0.078%), neg=0, invalid=762 0106: dt=0.064000, rms=0.674 (-0.057%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.675, neg=0, invalid=762 0107: dt=0.028000, rms=0.674 (0.080%), neg=0, invalid=762 0108: dt=-0.000053, rms=0.674 (0.001%), neg=0, invalid=762 0109: dt=-0.000053, rms=0.674 (0.000%), neg=0, invalid=762 0110: dt=-0.000053, rms=0.674 (0.000%), neg=0, invalid=762 0111: dt=-0.000053, rms=0.674 (0.000%), neg=0, invalid=762 0112: dt=-0.000053, rms=0.674 (0.000%), neg=0, invalid=762 0113: dt=-0.000053, rms=0.674 (-0.000%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.17982 (31) Left_Lateral_Ventricle (4): linear fit = 1.78 x + 0.0 (1261 voxels, overlap=0.204) Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (1261 voxels, peak = 36), gca=30.0 gca peak = 0.15565 (16) mri peak = 0.20398 (31) Right_Lateral_Ventricle (43): linear fit = 1.97 x + 0.0 (1360 voxels, overlap=0.054) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (1360 voxels, peak = 31), gca=24.0 gca peak = 0.26829 (96) mri peak = 0.09929 (102) Right_Pallidum (52): linear fit = 1.05 x + 0.0 (1130 voxels, overlap=0.999) Right_Pallidum (52): linear fit = 1.05 x + 0.0 (1130 voxels, peak = 101), gca=101.3 gca peak = 0.20183 (93) mri peak = 0.06714 (100) Left_Pallidum (13): linear fit = 1.03 x + 0.0 (984 voxels, overlap=1.009) Left_Pallidum (13): linear fit = 1.03 x + 0.0 (984 voxels, peak = 96), gca=96.3 gca peak = 0.21683 (55) mri peak = 0.09771 (74) Right_Hippocampus (53): linear fit = 1.29 x + 0.0 (1261 voxels, overlap=0.011) Right_Hippocampus (53): linear fit = 1.29 x + 0.0 (1261 voxels, peak = 71), gca=71.2 gca peak = 0.30730 (58) mri peak = 0.07157 (69) Left_Hippocampus (17): linear fit = 1.22 x + 0.0 (1079 voxels, overlap=0.021) Left_Hippocampus (17): linear fit = 1.22 x + 0.0 (1079 voxels, peak = 70), gca=70.5 gca peak = 0.11430 (101) mri peak = 0.13851 (104) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (85660 voxels, overlap=0.687) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (85660 voxels, peak = 104), gca=103.5 gca peak = 0.12076 (102) mri peak = 0.15327 (105) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (88124 voxels, overlap=0.656) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (88124 voxels, peak = 104), gca=103.5 gca peak = 0.14995 (59) mri peak = 0.04236 (79) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (34277 voxels, overlap=0.000) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (34277 voxels, peak = 79), gca=79.4 gca peak = 0.15082 (58) mri peak = 0.04216 (78) Right_Cerebral_Cortex (42): linear fit = 1.33 x + 0.0 (37501 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.33 x + 0.0 (37501 voxels, peak = 77), gca=76.9 gca peak = 0.14161 (67) mri peak = 0.08534 (83) Right_Caudate (50): linear fit = 1.25 x + 0.0 (1065 voxels, overlap=0.013) Right_Caudate (50): linear fit = 1.25 x + 0.0 (1065 voxels, peak = 84), gca=84.1 gca peak = 0.15243 (71) mri peak = 0.09569 (90) Left_Caudate (11): linear fit = 1.21 x + 0.0 (1336 voxels, overlap=0.018) Left_Caudate (11): linear fit = 1.21 x + 0.0 (1336 voxels, peak = 86), gca=85.6 gca peak = 0.13336 (57) mri peak = 0.04491 (79) Left_Cerebellum_Cortex (8): linear fit = 1.38 x + 0.0 (22424 voxels, overlap=0.001) Left_Cerebellum_Cortex (8): linear fit = 1.38 x + 0.0 (22424 voxels, peak = 79), gca=78.9 gca peak = 0.13252 (56) mri peak = 0.04190 (79) Right_Cerebellum_Cortex (47): linear fit = 1.41 x + 0.0 (25274 voxels, overlap=0.001) Right_Cerebellum_Cortex (47): linear fit = 1.41 x + 0.0 (25274 voxels, peak = 79), gca=79.2 gca peak = 0.18181 (84) mri peak = 0.07649 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.12 x + 0.0 (10665 voxels, overlap=0.002) Left_Cerebellum_White_Matter (7): linear fit = 1.12 x + 0.0 (10665 voxels, peak = 94), gca=94.5 gca peak = 0.20573 (83) mri peak = 0.06448 (92) Right_Cerebellum_White_Matter (46): linear fit = 1.15 x + 0.0 (8126 voxels, overlap=0.443) Right_Cerebellum_White_Matter (46): linear fit = 1.15 x + 0.0 (8126 voxels, peak = 96), gca=95.9 gca peak = 0.21969 (57) mri peak = 0.09585 (72) Left_Amygdala (18): linear fit = 1.23 x + 0.0 (471 voxels, overlap=0.049) Left_Amygdala (18): linear fit = 1.23 x + 0.0 (471 voxels, peak = 70), gca=69.8 gca peak = 0.39313 (56) mri peak = 0.09568 (74) Right_Amygdala (54): linear fit = 1.29 x + 0.0 (649 voxels, overlap=0.025) Right_Amygdala (54): linear fit = 1.29 x + 0.0 (649 voxels, peak = 73), gca=72.5 gca peak = 0.14181 (85) mri peak = 0.07971 (102) Left_Thalamus_Proper (10): linear fit = 1.13 x + 0.0 (6800 voxels, overlap=0.172) Left_Thalamus_Proper (10): linear fit = 1.13 x + 0.0 (6800 voxels, peak = 96), gca=96.5 gca peak = 0.11978 (83) mri peak = 0.07054 (97) Right_Thalamus_Proper (49): linear fit = 1.15 x + 0.0 (5481 voxels, overlap=0.250) Right_Thalamus_Proper (49): linear fit = 1.15 x + 0.0 (5481 voxels, peak = 96), gca=95.9 gca peak = 0.13399 (79) mri peak = 0.06202 (90) Left_Putamen (12): linear fit = 1.15 x + 0.0 (3100 voxels, overlap=0.259) Left_Putamen (12): linear fit = 1.15 x + 0.0 (3100 voxels, peak = 91), gca=91.2 gca peak = 0.14159 (79) mri peak = 0.07377 (90) Right_Putamen (51): linear fit = 1.14 x + 0.0 (3038 voxels, overlap=0.122) Right_Putamen (51): linear fit = 1.14 x + 0.0 (3038 voxels, peak = 90), gca=90.5 gca peak = 0.10025 (80) mri peak = 0.11358 (92) Brain_Stem (16): linear fit = 1.15 x + 0.0 (14379 voxels, overlap=0.029) Brain_Stem (16): linear fit = 1.15 x + 0.0 (14379 voxels, peak = 92), gca=92.4 gca peak = 0.13281 (86) mri peak = 0.20380 (99) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1347 voxels, overlap=0.070) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1347 voxels, peak = 96), gca=95.9 gca peak = 0.12801 (89) mri peak = 0.13944 (99) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1571 voxels, overlap=0.389) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1571 voxels, peak = 97), gca=97.5 gca peak = 0.20494 (23) mri peak = 0.11115 (27) Third_Ventricle (14): linear fit = 1.27 x + 0.0 (51 voxels, overlap=0.300) Third_Ventricle (14): linear fit = 1.27 x + 0.0 (51 voxels, peak = 29), gca=29.3 gca peak = 0.15061 (21) mri peak = 0.20354 (29) Fourth_Ventricle (15): linear fit = 1.63 x + 0.0 (634 voxels, overlap=0.083) Fourth_Ventricle (15): linear fit = 1.63 x + 0.0 (634 voxels, peak = 34), gca=34.3 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18056 (32) gca peak Left_Thalamus = 0.64095 (94) gca peak Fourth_Ventricle = 0.15061 (21) gca peak CSF = 0.20999 (34) gca peak Left_Accumbens_area = 0.39030 (62) gca peak Left_undetermined = 0.95280 (25) gca peak Left_vessel = 0.67734 (53) gca peak Left_choroid_plexus = 0.09433 (44) gca peak Right_Inf_Lat_Vent = 0.23544 (26) gca peak Right_Accumbens_area = 0.30312 (64) gca peak Right_vessel = 0.46315 (51) gca peak Right_choroid_plexus = 0.14086 (44) gca peak Fifth_Ventricle = 0.51669 (36) gca peak WM_hypointensities = 0.09722 (76) gca peak non_WM_hypointensities = 0.11899 (47) gca peak Optic_Chiasm = 0.39033 (72) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 1.28 x + 0.0 estimating mean wm scale to be 1.02 x + 0.0 estimating mean csf scale to be 1.43 x + 0.0 Right_Pallidum too bright - rescaling by 0.992 (from 1.055) to 100.4 (was 101.3) saving intensity scales to talairach.label_intensities.txt **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.682, neg=0, invalid=762 0114: dt=129.472000, rms=0.651 (4.549%), neg=0, invalid=762 0115: dt=369.920000, rms=0.641 (1.474%), neg=0, invalid=762 0116: dt=295.936000, rms=0.635 (0.940%), neg=0, invalid=762 0117: dt=129.472000, rms=0.633 (0.364%), neg=0, invalid=762 0118: dt=369.920000, rms=0.630 (0.411%), neg=0, invalid=762 0119: dt=129.472000, rms=0.628 (0.277%), neg=0, invalid=762 0120: dt=295.936000, rms=0.627 (0.265%), neg=0, invalid=762 0121: dt=129.472000, rms=0.626 (0.188%), neg=0, invalid=762 0122: dt=443.904000, rms=0.624 (0.242%), neg=0, invalid=762 0123: dt=129.472000, rms=0.623 (0.220%), neg=0, invalid=762 0124: dt=295.936000, rms=0.622 (0.129%), neg=0, invalid=762 0125: dt=129.472000, rms=0.621 (0.155%), neg=0, invalid=762 0126: dt=369.920000, rms=0.620 (0.138%), neg=0, invalid=762 0127: dt=129.472000, rms=0.619 (0.136%), neg=0, invalid=762 0128: dt=369.920000, rms=0.619 (0.119%), neg=0, invalid=762 0129: dt=129.472000, rms=0.618 (0.121%), neg=0, invalid=762 0130: dt=295.936000, rms=0.617 (0.105%), neg=0, invalid=762 0131: dt=129.472000, rms=0.617 (0.086%), neg=0, invalid=762 0132: dt=517.888000, rms=0.616 (0.121%), neg=0, invalid=762 0133: dt=110.976000, rms=0.615 (0.124%), neg=0, invalid=762 0134: dt=517.888000, rms=0.614 (0.149%), neg=0, invalid=762 0135: dt=129.472000, rms=0.614 (0.062%), neg=0, invalid=762 0136: dt=369.920000, rms=0.613 (0.094%), neg=0, invalid=762 0137: dt=110.976000, rms=0.613 (0.052%), neg=0, invalid=762 0138: dt=1183.744000, rms=0.612 (0.211%), neg=0, invalid=762 0139: dt=92.480000, rms=0.611 (0.122%), neg=0, invalid=762 0140: dt=2071.552000, rms=0.609 (0.377%), neg=0, invalid=762 0141: dt=92.480000, rms=0.608 (0.094%), neg=0, invalid=762 0142: dt=517.888000, rms=0.608 (0.025%), neg=0, invalid=762 0143: dt=517.888000, rms=0.608 (0.035%), neg=0, invalid=762 0144: dt=517.888000, rms=0.608 (-0.665%), neg=0, invalid=762 0145: dt=92.480000, rms=0.607 (0.113%), neg=0, invalid=762 0146: dt=129.472000, rms=0.607 (0.014%), neg=0, invalid=762 0147: dt=129.472000, rms=0.607 (0.016%), neg=0, invalid=762 0148: dt=129.472000, rms=0.607 (0.036%), neg=0, invalid=762 0149: dt=129.472000, rms=0.606 (0.047%), neg=0, invalid=762 0150: dt=129.472000, rms=0.606 (0.063%), neg=0, invalid=762 0151: dt=129.472000, rms=0.605 (0.074%), neg=0, invalid=762 0152: dt=129.472000, rms=0.605 (0.085%), neg=0, invalid=762 0153: dt=129.472000, rms=0.604 (0.086%), neg=0, invalid=762 0154: dt=129.472000, rms=0.604 (0.087%), neg=0, invalid=762 0155: dt=129.472000, rms=0.603 (0.087%), neg=0, invalid=762 0156: dt=129.472000, rms=0.603 (0.095%), neg=0, invalid=762 0157: dt=129.472000, rms=0.602 (0.097%), neg=0, invalid=762 0158: dt=129.472000, rms=0.602 (0.091%), neg=0, invalid=762 0159: dt=129.472000, rms=0.601 (0.094%), neg=0, invalid=762 0160: dt=129.472000, rms=0.600 (0.094%), neg=0, invalid=762 0161: dt=129.472000, rms=0.600 (0.084%), neg=0, invalid=762 0162: dt=129.472000, rms=0.600 (0.076%), neg=0, invalid=762 0163: dt=129.472000, rms=0.599 (0.076%), neg=0, invalid=762 0164: dt=129.472000, rms=0.599 (0.074%), neg=0, invalid=762 0165: dt=129.472000, rms=0.598 (0.068%), neg=0, invalid=762 0166: dt=129.472000, rms=0.598 (0.064%), neg=0, invalid=762 0167: dt=129.472000, rms=0.597 (0.062%), neg=0, invalid=762 0168: dt=129.472000, rms=0.597 (0.063%), neg=0, invalid=762 0169: dt=129.472000, rms=0.597 (0.059%), neg=0, invalid=762 0170: dt=129.472000, rms=0.596 (0.051%), neg=0, invalid=762 0171: dt=129.472000, rms=0.596 (0.046%), neg=0, invalid=762 0172: dt=129.472000, rms=0.596 (0.054%), neg=0, invalid=762 0173: dt=129.472000, rms=0.596 (0.047%), neg=0, invalid=762 0174: dt=129.472000, rms=0.595 (0.048%), neg=0, invalid=762 0175: dt=129.472000, rms=0.595 (0.044%), neg=0, invalid=762 0176: dt=129.472000, rms=0.595 (0.045%), neg=0, invalid=762 0177: dt=129.472000, rms=0.594 (0.044%), neg=0, invalid=762 0178: dt=129.472000, rms=0.594 (0.043%), neg=0, invalid=762 0179: dt=129.472000, rms=0.594 (0.039%), neg=0, invalid=762 0180: dt=129.472000, rms=0.594 (0.039%), neg=0, invalid=762 0181: dt=129.472000, rms=0.594 (0.037%), neg=0, invalid=762 0182: dt=129.472000, rms=0.593 (0.032%), neg=0, invalid=762 0183: dt=129.472000, rms=0.593 (0.034%), neg=0, invalid=762 0184: dt=129.472000, rms=0.593 (0.033%), neg=0, invalid=762 0185: dt=129.472000, rms=0.593 (0.030%), neg=0, invalid=762 0186: dt=129.472000, rms=0.593 (0.027%), neg=0, invalid=762 0187: dt=129.472000, rms=0.592 (0.033%), neg=0, invalid=762 0188: dt=129.472000, rms=0.592 (0.032%), neg=0, invalid=762 0189: dt=129.472000, rms=0.592 (0.029%), neg=0, invalid=762 0190: dt=129.472000, rms=0.592 (0.027%), neg=0, invalid=762 0191: dt=129.472000, rms=0.592 (0.033%), neg=0, invalid=762 0192: dt=129.472000, rms=0.592 (0.032%), neg=0, invalid=762 0193: dt=129.472000, rms=0.591 (0.032%), neg=0, invalid=762 0194: dt=129.472000, rms=0.591 (0.024%), neg=0, invalid=762 0195: dt=129.472000, rms=0.591 (0.034%), neg=0, invalid=762 0196: dt=129.472000, rms=0.591 (0.033%), neg=0, invalid=762 0197: dt=129.472000, rms=0.591 (0.029%), neg=0, invalid=762 0198: dt=129.472000, rms=0.590 (0.023%), neg=0, invalid=762 0199: dt=129.472000, rms=0.590 (0.020%), neg=0, invalid=762 0200: dt=2071.552000, rms=0.590 (0.042%), neg=0, invalid=762 0201: dt=8.092000, rms=0.590 (-0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.590, neg=0, invalid=762 0202: dt=129.472000, rms=0.590 (0.089%), neg=0, invalid=762 0203: dt=887.808000, rms=0.588 (0.262%), neg=0, invalid=762 0204: dt=73.984000, rms=0.588 (0.007%), neg=0, invalid=762 0205: dt=73.984000, rms=0.588 (0.007%), neg=0, invalid=762 0206: dt=73.984000, rms=0.588 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.590, neg=0, invalid=762 0207: dt=145.152000, rms=0.587 (0.525%), neg=0, invalid=762 0208: dt=145.152000, rms=0.582 (0.876%), neg=0, invalid=762 0209: dt=90.229508, rms=0.580 (0.291%), neg=0, invalid=762 0210: dt=145.152000, rms=0.577 (0.524%), neg=0, invalid=762 0211: dt=68.768627, rms=0.576 (0.271%), neg=0, invalid=762 0212: dt=331.776000, rms=0.572 (0.687%), neg=0, invalid=762 0213: dt=36.288000, rms=0.570 (0.316%), neg=0, invalid=762 0214: dt=82.944000, rms=0.569 (0.163%), neg=0, invalid=762 0215: dt=145.152000, rms=0.567 (0.287%), neg=0, invalid=762 0216: dt=36.288000, rms=0.566 (0.125%), neg=0, invalid=762 0217: dt=145.152000, rms=0.565 (0.176%), neg=0, invalid=762 0218: dt=88.470588, rms=0.564 (0.216%), neg=0, invalid=762 0219: dt=62.208000, rms=0.564 (0.102%), neg=0, invalid=762 0220: dt=331.776000, rms=0.562 (0.331%), neg=0, invalid=762 0221: dt=36.288000, rms=0.561 (0.182%), neg=0, invalid=762 0222: dt=82.944000, rms=0.560 (0.105%), neg=0, invalid=762 0223: dt=124.416000, rms=0.559 (0.164%), neg=0, invalid=762 0224: dt=36.288000, rms=0.559 (0.070%), neg=0, invalid=762 0225: dt=331.776000, rms=0.558 (0.150%), neg=0, invalid=762 0226: dt=68.659004, rms=0.557 (0.256%), neg=0, invalid=762 0227: dt=103.680000, rms=0.556 (0.075%), neg=0, invalid=762 0228: dt=124.416000, rms=0.556 (0.122%), neg=0, invalid=762 0229: dt=36.288000, rms=0.555 (0.055%), neg=0, invalid=762 0230: dt=145.152000, rms=0.555 (0.087%), neg=0, invalid=762 0231: dt=103.680000, rms=0.554 (0.111%), neg=0, invalid=762 0232: dt=36.288000, rms=0.554 (0.039%), neg=0, invalid=762 0233: dt=36.288000, rms=0.554 (0.031%), neg=0, invalid=762 0234: dt=36.288000, rms=0.553 (0.047%), neg=0, invalid=762 0235: dt=36.288000, rms=0.553 (0.072%), neg=0, invalid=762 0236: dt=36.288000, rms=0.553 (0.095%), neg=0, invalid=762 0237: dt=36.288000, rms=0.552 (0.110%), neg=0, invalid=762 0238: dt=36.288000, rms=0.551 (0.117%), neg=0, invalid=762 0239: dt=36.288000, rms=0.551 (0.125%), neg=0, invalid=762 0240: dt=36.288000, rms=0.550 (0.128%), neg=0, invalid=762 0241: dt=36.288000, rms=0.549 (0.128%), neg=0, invalid=762 0242: dt=36.288000, rms=0.548 (0.135%), neg=0, invalid=762 0243: dt=36.288000, rms=0.548 (0.131%), neg=0, invalid=762 0244: dt=36.288000, rms=0.547 (0.126%), neg=0, invalid=762 0245: dt=36.288000, rms=0.546 (0.121%), neg=0, invalid=762 0246: dt=36.288000, rms=0.546 (0.115%), neg=0, invalid=762 0247: dt=36.288000, rms=0.545 (0.119%), neg=0, invalid=762 0248: dt=36.288000, rms=0.544 (0.122%), neg=0, invalid=762 0249: dt=36.288000, rms=0.544 (0.122%), neg=0, invalid=762 0250: dt=36.288000, rms=0.543 (0.119%), neg=0, invalid=762 0251: dt=36.288000, rms=0.543 (0.113%), neg=0, invalid=762 0252: dt=36.288000, rms=0.542 (0.107%), neg=0, invalid=762 0253: dt=36.288000, rms=0.541 (0.110%), neg=0, invalid=762 0254: dt=36.288000, rms=0.541 (0.110%), neg=0, invalid=762 0255: dt=36.288000, rms=0.540 (0.102%), neg=0, invalid=762 0256: dt=36.288000, rms=0.540 (0.095%), neg=0, invalid=762 0257: dt=36.288000, rms=0.539 (0.082%), neg=0, invalid=762 0258: dt=36.288000, rms=0.539 (0.071%), neg=0, invalid=762 0259: dt=36.288000, rms=0.538 (0.084%), neg=0, invalid=762 0260: dt=36.288000, rms=0.538 (0.087%), neg=0, invalid=762 0261: dt=36.288000, rms=0.537 (0.086%), neg=0, invalid=762 0262: dt=36.288000, rms=0.537 (0.083%), neg=0, invalid=762 0263: dt=36.288000, rms=0.537 (0.074%), neg=0, invalid=762 0264: dt=36.288000, rms=0.536 (0.068%), neg=0, invalid=762 0265: dt=36.288000, rms=0.536 (0.066%), neg=0, invalid=762 0266: dt=36.288000, rms=0.536 (0.070%), neg=0, invalid=762 0267: dt=36.288000, rms=0.535 (0.068%), neg=0, invalid=762 0268: dt=36.288000, rms=0.535 (0.060%), neg=0, invalid=762 0269: dt=36.288000, rms=0.535 (0.056%), neg=0, invalid=762 0270: dt=36.288000, rms=0.534 (0.056%), neg=0, invalid=762 0271: dt=36.288000, rms=0.534 (0.060%), neg=0, invalid=762 0272: dt=36.288000, rms=0.534 (0.060%), neg=0, invalid=762 0273: dt=36.288000, rms=0.533 (0.060%), neg=0, invalid=762 0274: dt=36.288000, rms=0.533 (0.050%), neg=0, invalid=762 0275: dt=36.288000, rms=0.533 (0.045%), neg=0, invalid=762 0276: dt=36.288000, rms=0.533 (0.043%), neg=0, invalid=762 0277: dt=36.288000, rms=0.532 (0.048%), neg=0, invalid=762 0278: dt=36.288000, rms=0.532 (0.048%), neg=0, invalid=762 0279: dt=36.288000, rms=0.532 (0.045%), neg=0, invalid=762 0280: dt=36.288000, rms=0.532 (0.042%), neg=0, invalid=762 0281: dt=36.288000, rms=0.531 (0.041%), neg=0, invalid=762 0282: dt=36.288000, rms=0.531 (0.037%), neg=0, invalid=762 0283: dt=36.288000, rms=0.531 (0.045%), neg=0, invalid=762 0284: dt=36.288000, rms=0.531 (0.037%), neg=0, invalid=762 0285: dt=36.288000, rms=0.531 (0.037%), neg=0, invalid=762 0286: dt=36.288000, rms=0.530 (0.035%), neg=0, invalid=762 0287: dt=36.288000, rms=0.530 (0.035%), neg=0, invalid=762 0288: dt=36.288000, rms=0.530 (0.032%), neg=0, invalid=762 0289: dt=36.288000, rms=0.530 (0.035%), neg=0, invalid=762 0290: dt=36.288000, rms=0.530 (0.032%), neg=0, invalid=762 0291: dt=36.288000, rms=0.529 (0.029%), neg=0, invalid=762 0292: dt=36.288000, rms=0.529 (0.028%), neg=0, invalid=762 0293: dt=36.288000, rms=0.529 (0.027%), neg=0, invalid=762 0294: dt=36.288000, rms=0.529 (0.031%), neg=0, invalid=762 0295: dt=36.288000, rms=0.529 (0.028%), neg=0, invalid=762 0296: dt=36.288000, rms=0.529 (0.028%), neg=0, invalid=762 0297: dt=36.288000, rms=0.529 (0.029%), neg=0, invalid=762 0298: dt=36.288000, rms=0.528 (0.028%), neg=0, invalid=762 0299: dt=36.288000, rms=0.528 (0.022%), neg=0, invalid=762 0300: dt=36.288000, rms=0.528 (0.021%), neg=0, invalid=762 0301: dt=580.608000, rms=0.528 (0.047%), neg=0, invalid=762 0302: dt=20.736000, rms=0.528 (0.001%), neg=0, invalid=762 0303: dt=20.736000, rms=0.528 (0.002%), neg=0, invalid=762 0304: dt=20.736000, rms=0.528 (-0.009%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.528, neg=0, invalid=762 0305: dt=145.152000, rms=0.526 (0.428%), neg=0, invalid=762 0306: dt=103.680000, rms=0.525 (0.094%), neg=0, invalid=762 0307: dt=103.680000, rms=0.525 (0.067%), neg=0, invalid=762 0308: dt=82.944000, rms=0.525 (0.031%), neg=0, invalid=762 0309: dt=82.944000, rms=0.525 (0.044%), neg=0, invalid=762 0310: dt=82.944000, rms=0.524 (0.048%), neg=0, invalid=762 0311: dt=82.944000, rms=0.524 (0.052%), neg=0, invalid=762 0312: dt=82.944000, rms=0.524 (0.050%), neg=0, invalid=762 0313: dt=82.944000, rms=0.524 (0.066%), neg=0, invalid=762 0314: dt=82.944000, rms=0.523 (0.045%), neg=0, invalid=762 0315: dt=82.944000, rms=0.523 (0.033%), neg=0, invalid=762 0316: dt=82.944000, rms=0.523 (0.054%), neg=0, invalid=762 0317: dt=82.944000, rms=0.523 (0.049%), neg=0, invalid=762 0318: dt=82.944000, rms=0.522 (0.055%), neg=0, invalid=762 0319: dt=82.944000, rms=0.522 (0.067%), neg=0, invalid=762 0320: dt=82.944000, rms=0.522 (0.055%), neg=0, invalid=762 0321: dt=82.944000, rms=0.521 (0.056%), neg=0, invalid=762 0322: dt=82.944000, rms=0.521 (0.052%), neg=0, invalid=762 0323: dt=82.944000, rms=0.521 (0.061%), neg=0, invalid=762 0324: dt=82.944000, rms=0.521 (0.055%), neg=0, invalid=762 0325: dt=82.944000, rms=0.520 (0.046%), neg=0, invalid=762 0326: dt=82.944000, rms=0.520 (0.052%), neg=0, invalid=762 0327: dt=82.944000, rms=0.520 (0.055%), neg=0, invalid=762 0328: dt=82.944000, rms=0.519 (0.048%), neg=0, invalid=762 0329: dt=82.944000, rms=0.519 (0.044%), neg=0, invalid=762 0330: dt=82.944000, rms=0.519 (0.045%), neg=0, invalid=762 0331: dt=82.944000, rms=0.519 (0.048%), neg=0, invalid=762 0332: dt=82.944000, rms=0.519 (0.044%), neg=0, invalid=762 0333: dt=82.944000, rms=0.518 (0.048%), neg=0, invalid=762 0334: dt=82.944000, rms=0.518 (0.033%), neg=0, invalid=762 0335: dt=82.944000, rms=0.518 (0.038%), neg=0, invalid=762 0336: dt=82.944000, rms=0.518 (0.049%), neg=0, invalid=762 0337: dt=82.944000, rms=0.517 (0.041%), neg=0, invalid=762 0338: dt=82.944000, rms=0.517 (0.034%), neg=0, invalid=762 0339: dt=82.944000, rms=0.517 (0.026%), neg=0, invalid=762 0340: dt=82.944000, rms=0.517 (0.042%), neg=0, invalid=762 0341: dt=82.944000, rms=0.517 (0.031%), neg=0, invalid=762 0342: dt=82.944000, rms=0.517 (0.035%), neg=0, invalid=762 0343: dt=82.944000, rms=0.516 (0.031%), neg=0, invalid=762 0344: dt=82.944000, rms=0.516 (0.046%), neg=0, invalid=762 0345: dt=82.944000, rms=0.516 (0.032%), neg=0, invalid=762 0346: dt=82.944000, rms=0.516 (0.031%), neg=0, invalid=762 0347: dt=82.944000, rms=0.516 (0.022%), neg=0, invalid=762 0348: dt=82.944000, rms=0.516 (0.046%), neg=0, invalid=762 0349: dt=82.944000, rms=0.515 (0.033%), neg=0, invalid=762 0350: dt=82.944000, rms=0.515 (0.031%), neg=0, invalid=762 0351: dt=82.944000, rms=0.515 (0.024%), neg=0, invalid=762 0352: dt=82.944000, rms=0.515 (0.033%), neg=0, invalid=762 0353: dt=82.944000, rms=0.515 (0.024%), neg=0, invalid=762 0354: dt=82.944000, rms=0.515 (0.026%), neg=0, invalid=762 0355: dt=82.944000, rms=0.514 (0.026%), neg=0, invalid=762 0356: dt=82.944000, rms=0.514 (0.030%), neg=0, invalid=762 0357: dt=82.944000, rms=0.514 (0.021%), neg=0, invalid=762 0358: dt=82.944000, rms=0.514 (0.021%), neg=0, invalid=762 0359: dt=145.152000, rms=0.514 (0.005%), neg=0, invalid=762 0360: dt=145.152000, rms=0.514 (-0.008%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.524, neg=0, invalid=762 0361: dt=11.200000, rms=0.524 (0.082%), neg=0, invalid=762 0362: dt=9.600000, rms=0.524 (0.014%), neg=0, invalid=762 0363: dt=9.600000, rms=0.524 (0.013%), neg=0, invalid=762 0364: dt=9.600000, rms=0.524 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.524, neg=0, invalid=762 0365: dt=44.800000, rms=0.522 (0.427%), neg=0, invalid=762 0366: dt=101.670886, rms=0.520 (0.307%), neg=0, invalid=762 0367: dt=38.400000, rms=0.518 (0.344%), neg=0, invalid=762 0368: dt=32.000000, rms=0.518 (0.148%), neg=0, invalid=762 0369: dt=44.800000, rms=0.516 (0.254%), neg=0, invalid=762 0370: dt=11.200000, rms=0.516 (0.089%), neg=0, invalid=762 0371: dt=11.200000, rms=0.515 (0.077%), neg=0, invalid=762 0372: dt=0.175000, rms=0.515 (0.005%), neg=0, invalid=762 0373: dt=0.175000, rms=0.515 (0.001%), neg=0, invalid=762 0374: dt=0.043750, rms=0.515 (0.000%), neg=0, invalid=762 0375: dt=0.010937, rms=0.515 (0.000%), neg=0, invalid=762 0376: dt=0.009375, rms=0.515 (0.000%), neg=0, invalid=762 0377: dt=0.000000, rms=0.515 (0.000%), neg=0, invalid=762 0378: dt=0.000000, rms=0.515 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.534, neg=0, invalid=762 0379: dt=8.082902, rms=0.533 (0.331%), neg=0, invalid=762 0380: dt=12.773109, rms=0.532 (0.226%), neg=0, invalid=762 0381: dt=37.062409, rms=0.529 (0.523%), neg=0, invalid=762 0382: dt=25.142857, rms=0.528 (0.186%), neg=0, invalid=762 0383: dt=23.757576, rms=0.527 (0.193%), neg=0, invalid=762 0384: dt=11.789474, rms=0.526 (0.072%), neg=0, invalid=762 0385: dt=46.080000, rms=0.525 (0.175%), neg=0, invalid=762 0386: dt=12.936170, rms=0.525 (0.054%), neg=0, invalid=762 0387: dt=16.128000, rms=0.525 (0.071%), neg=0, invalid=762 0388: dt=13.600000, rms=0.525 (0.029%), neg=0, invalid=762 0389: dt=13.600000, rms=0.524 (0.043%), neg=0, invalid=762 0390: dt=13.600000, rms=0.524 (0.069%), neg=0, invalid=762 0391: dt=13.600000, rms=0.524 (0.085%), neg=0, invalid=762 0392: dt=13.600000, rms=0.523 (0.091%), neg=0, invalid=762 0393: dt=13.600000, rms=0.523 (0.108%), neg=0, invalid=762 0394: dt=13.600000, rms=0.522 (0.112%), neg=0, invalid=762 0395: dt=13.600000, rms=0.521 (0.106%), neg=0, invalid=762 0396: dt=13.600000, rms=0.521 (0.072%), neg=0, invalid=762 0397: dt=13.600000, rms=0.521 (0.061%), neg=0, invalid=762 0398: dt=13.600000, rms=0.520 (0.083%), neg=0, invalid=762 0399: dt=13.600000, rms=0.520 (0.073%), neg=0, invalid=762 0400: dt=13.600000, rms=0.520 (0.043%), neg=0, invalid=762 0401: dt=13.600000, rms=0.519 (0.055%), neg=0, invalid=762 0402: dt=13.600000, rms=0.519 (0.055%), neg=0, invalid=762 0403: dt=13.600000, rms=0.519 (0.048%), neg=0, invalid=762 0404: dt=13.600000, rms=0.519 (0.036%), neg=0, invalid=762 0405: dt=13.600000, rms=0.519 (0.022%), neg=0, invalid=762 0406: dt=13.600000, rms=0.518 (0.028%), neg=0, invalid=762 0407: dt=13.600000, rms=0.518 (0.034%), neg=0, invalid=762 0408: dt=13.600000, rms=0.518 (0.007%), neg=0, invalid=762 0409: dt=13.600000, rms=0.518 (0.024%), neg=0, invalid=762 0410: dt=13.600000, rms=0.518 (0.020%), neg=0, invalid=762 0411: dt=5.333333, rms=0.518 (0.008%), neg=0, invalid=762 0412: dt=5.333333, rms=0.518 (0.009%), neg=0, invalid=762 0413: dt=5.333333, rms=0.518 (0.002%), neg=0, invalid=762 0414: dt=5.333333, rms=0.518 (-0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.518, neg=0, invalid=762 0415: dt=8.000000, rms=0.518 (0.100%), neg=0, invalid=762 0416: dt=0.011250, rms=0.518 (0.001%), neg=0, invalid=762 0417: dt=0.011250, rms=0.518 (0.000%), neg=0, invalid=762 0418: dt=0.011250, rms=0.518 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.538, neg=0, invalid=762 0419: dt=0.000000, rms=0.538 (0.048%), neg=0, invalid=762 0420: dt=0.000000, rms=0.538 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.538, neg=0, invalid=762 0421: dt=0.000000, rms=0.538 (0.048%), neg=0, invalid=762 0422: dt=0.000000, rms=0.538 (0.000%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.504, neg=0, invalid=762 0423: dt=0.448000, rms=0.491 (2.651%), neg=0, invalid=762 0424: dt=0.448000, rms=0.488 (0.577%), neg=0, invalid=762 0425: dt=0.448000, rms=0.486 (0.353%), neg=0, invalid=762 0426: dt=0.448000, rms=0.485 (0.221%), neg=0, invalid=762 0427: dt=0.571429, rms=0.484 (0.216%), neg=0, invalid=762 0428: dt=0.448000, rms=0.483 (0.111%), neg=0, invalid=762 0429: dt=0.448000, rms=0.483 (0.099%), neg=0, invalid=762 0430: dt=0.448000, rms=0.483 (0.074%), neg=0, invalid=762 0431: dt=0.448000, rms=0.482 (0.067%), neg=0, invalid=762 0432: dt=0.448000, rms=0.482 (0.052%), neg=0, invalid=762 0433: dt=0.448000, rms=0.482 (0.051%), neg=0, invalid=762 0434: dt=0.448000, rms=0.482 (0.037%), neg=0, invalid=762 0435: dt=0.448000, rms=0.481 (0.039%), neg=0, invalid=762 0436: dt=0.448000, rms=0.481 (0.064%), neg=0, invalid=762 0437: dt=0.448000, rms=0.481 (0.075%), neg=0, invalid=762 0438: dt=0.448000, rms=0.480 (0.085%), neg=0, invalid=762 0439: dt=0.448000, rms=0.480 (0.084%), neg=0, invalid=762 0440: dt=0.448000, rms=0.480 (0.067%), neg=0, invalid=762 0441: dt=0.448000, rms=0.479 (0.046%), neg=0, invalid=762 0442: dt=0.448000, rms=0.479 (0.036%), neg=0, invalid=762 0443: dt=0.448000, rms=0.479 (-0.004%), neg=0, invalid=762 0444: dt=0.028000, rms=0.479 (0.000%), neg=0, invalid=762 0445: dt=0.000250, rms=0.479 (0.000%), neg=0, invalid=762 0446: dt=0.000020, rms=0.479 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.480, neg=0, invalid=762 0447: dt=0.448000, rms=0.476 (0.813%), neg=0, invalid=762 0448: dt=0.448000, rms=0.475 (0.075%), neg=0, invalid=762 0449: dt=0.448000, rms=0.475 (0.018%), neg=0, invalid=762 0450: dt=0.448000, rms=0.475 (0.000%), neg=0, invalid=762 0451: dt=0.448000, rms=0.475 (-0.009%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) ********************* ALLOWING NEGATIVE NODES IN DEFORMATION******************************** **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.473, neg=0, invalid=762 0452: dt=0.000000, rms=0.473 (0.064%), neg=0, invalid=762 0453: dt=0.000000, rms=0.473 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.473, neg=0, invalid=762 0454: dt=221.952000, rms=0.472 (0.156%), neg=0, invalid=762 0455: dt=110.976000, rms=0.472 (0.045%), neg=0, invalid=762 0456: dt=110.976000, rms=0.472 (0.025%), neg=0, invalid=762 0457: dt=110.976000, rms=0.472 (0.037%), neg=0, invalid=762 0458: dt=110.976000, rms=0.472 (0.035%), neg=0, invalid=762 0459: dt=110.976000, rms=0.471 (0.045%), neg=0, invalid=762 0460: dt=110.976000, rms=0.471 (0.035%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.472, neg=0, invalid=762 0461: dt=31.104000, rms=0.471 (0.100%), neg=0, invalid=762 0462: dt=36.288000, rms=0.471 (0.023%), neg=0, invalid=762 0463: dt=36.288000, rms=0.471 (0.025%), neg=0, invalid=762 0464: dt=36.288000, rms=0.471 (0.014%), neg=0, invalid=762 0465: dt=36.288000, rms=0.471 (-0.005%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.471, neg=0, invalid=762 0466: dt=143.258278, rms=0.468 (0.675%), neg=0, invalid=762 0467: dt=36.288000, rms=0.467 (0.137%), neg=0, invalid=762 0468: dt=36.288000, rms=0.467 (0.061%), neg=0, invalid=762 0469: dt=36.288000, rms=0.467 (0.070%), neg=0, invalid=762 0470: dt=36.288000, rms=0.466 (0.081%), neg=0, invalid=762 0471: dt=36.288000, rms=0.466 (0.107%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0472: dt=36.288000, rms=0.465 (0.142%), neg=0, invalid=762 0473: dt=36.288000, rms=0.465 (0.139%), neg=0, invalid=762 0474: dt=36.288000, rms=0.464 (0.120%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0475: dt=36.288000, rms=0.463 (0.106%), neg=0, invalid=762 0476: dt=103.680000, rms=0.463 (0.023%), neg=0, invalid=762 0477: dt=103.680000, rms=0.463 (0.026%), neg=0, invalid=762 0478: dt=103.680000, rms=0.463 (0.074%), neg=0, invalid=762 0479: dt=103.680000, rms=0.463 (0.067%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0480: dt=103.680000, rms=0.462 (0.104%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0481: dt=103.680000, rms=0.462 (0.099%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.463, neg=0, invalid=762 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0482: dt=32.000000, rms=0.461 (0.318%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 9 iterations, nbhd size=1, neg = 0 0483: dt=95.238095, rms=0.459 (0.539%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0484: dt=32.000000, rms=0.457 (0.284%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0485: dt=38.400000, rms=0.456 (0.255%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0486: dt=25.600000, rms=0.456 (0.140%), neg=0, invalid=762 0487: dt=25.600000, rms=0.455 (0.156%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0488: dt=25.600000, rms=0.454 (0.183%), neg=0, invalid=762 0489: dt=25.600000, rms=0.453 (0.199%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 3 iterations, nbhd size=0, neg = 0 0490: dt=25.600000, rms=0.452 (0.228%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 3 iterations, nbhd size=0, neg = 0 0491: dt=25.600000, rms=0.451 (0.231%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 10 iterations, nbhd size=1, neg = 0 0492: dt=25.600000, rms=0.450 (0.197%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 2 iterations, nbhd size=0, neg = 0 0493: dt=25.600000, rms=0.449 (0.166%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 1 iterations, nbhd size=0, neg = 0 0494: dt=25.600000, rms=0.449 (0.175%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 10 iterations, nbhd size=1, neg = 0 0495: dt=25.600000, rms=0.448 (0.158%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 11 iterations, nbhd size=1, neg = 0 0496: dt=25.600000, rms=0.447 (0.119%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 0497: dt=25.600000, rms=0.447 (0.130%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0498: dt=25.600000, rms=0.446 (0.126%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 7 iterations, nbhd size=1, neg = 0 0499: dt=25.600000, rms=0.446 (0.102%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0500: dt=25.600000, rms=0.445 (0.077%), neg=0, invalid=762 0501: dt=32.000000, rms=0.445 (0.054%), neg=0, invalid=762 0502: dt=32.000000, rms=0.445 (-0.050%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.445, neg=0, invalid=762 0503: dt=66.226087, rms=0.442 (0.792%), neg=0, invalid=762 0504: dt=25.600000, rms=0.441 (0.254%), neg=0, invalid=762 0505: dt=25.600000, rms=0.440 (0.103%), neg=0, invalid=762 0506: dt=25.600000, rms=0.440 (0.058%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0507: dt=25.600000, rms=0.440 (0.095%), neg=0, invalid=762 0508: dt=25.600000, rms=0.439 (0.075%), neg=0, invalid=762 0509: dt=25.600000, rms=0.439 (0.064%), neg=0, invalid=762 0510: dt=19.200000, rms=0.439 (0.049%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.447, neg=0, invalid=762 0511: dt=0.432000, rms=0.447 (0.056%), neg=0, invalid=762 0512: dt=0.063000, rms=0.447 (0.002%), neg=0, invalid=762 0513: dt=0.063000, rms=0.447 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.447, neg=0, invalid=762 0514: dt=4.032000, rms=0.446 (0.122%), neg=0, invalid=762 0515: dt=1.008000, rms=0.446 (0.012%), neg=0, invalid=762 0516: dt=1.008000, rms=0.446 (0.004%), neg=0, invalid=762 0517: dt=1.008000, rms=0.446 (-0.006%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.459, neg=0, invalid=762 0518: dt=1.280000, rms=0.458 (0.242%), neg=0, invalid=762 0519: dt=0.256000, rms=0.458 (0.007%), neg=0, invalid=762 0520: dt=0.256000, rms=0.458 (-0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.458, neg=0, invalid=762 0521: dt=1.792000, rms=0.457 (0.283%), neg=0, invalid=762 0522: dt=1.024000, rms=0.456 (0.028%), neg=0, invalid=762 0523: dt=1.024000, rms=0.456 (0.000%), neg=0, invalid=762 0524: dt=1.024000, rms=0.456 (-0.073%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.448, neg=0, invalid=762 iter 0, gcam->neg = 484 after 14 iterations, nbhd size=1, neg = 0 0525: dt=2.269133, rms=0.422 (5.830%), neg=0, invalid=762 0526: dt=0.112000, rms=0.422 (0.113%), neg=0, invalid=762 0527: dt=0.112000, rms=0.422 (-0.070%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.422, neg=0, invalid=762 0528: dt=0.080000, rms=0.422 (0.125%), neg=0, invalid=762 0529: dt=0.005000, rms=0.422 (0.003%), neg=0, invalid=762 0530: dt=0.005000, rms=0.422 (-0.000%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.408, neg=0, invalid=762 0531: dt=0.000000, rms=0.408 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.408, neg=0, invalid=762 0532: dt=73.984000, rms=0.408 (0.009%), neg=0, invalid=762 0533: dt=129.472000, rms=0.407 (0.007%), neg=0, invalid=762 0534: dt=129.472000, rms=0.407 (0.001%), neg=0, invalid=762 0535: dt=129.472000, rms=0.407 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.408, neg=0, invalid=762 0536: dt=0.000000, rms=0.408 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.408, neg=0, invalid=762 0537: dt=145.152000, rms=0.407 (0.099%), neg=0, invalid=762 0538: dt=145.152000, rms=0.407 (0.097%), neg=0, invalid=762 0539: dt=145.152000, rms=0.407 (-0.141%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.407, neg=0, invalid=762 0540: dt=11.200000, rms=0.407 (0.109%), neg=0, invalid=762 0541: dt=11.200000, rms=0.407 (0.056%), neg=0, invalid=762 0542: dt=11.200000, rms=0.407 (0.037%), neg=0, invalid=762 0543: dt=11.200000, rms=0.407 (0.007%), neg=0, invalid=762 0544: dt=11.200000, rms=0.407 (-0.068%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.407, neg=0, invalid=762 0545: dt=69.109244, rms=0.403 (0.914%), neg=0, invalid=762 0546: dt=25.600000, rms=0.402 (0.253%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0547: dt=102.400000, rms=0.401 (0.241%), neg=0, invalid=762 0548: dt=102.400000, rms=0.401 (-0.488%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.404, neg=0, invalid=762 0549: dt=4.909091, rms=0.404 (0.053%), neg=0, invalid=762 0550: dt=1.500000, rms=0.404 (0.002%), neg=0, invalid=762 0551: dt=1.500000, rms=0.404 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.404, neg=0, invalid=762 0552: dt=22.422535, rms=0.402 (0.517%), neg=0, invalid=762 0553: dt=16.833333, rms=0.401 (0.189%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0554: dt=16.833333, rms=0.401 (0.070%), neg=0, invalid=762 0555: dt=16.833333, rms=0.400 (0.154%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 3 iterations, nbhd size=0, neg = 0 0556: dt=16.833333, rms=0.399 (0.173%), neg=0, invalid=762 0557: dt=16.833333, rms=0.399 (0.117%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0558: dt=16.833333, rms=0.398 (0.080%), neg=0, invalid=762 0559: dt=10.782609, rms=0.398 (0.036%), neg=0, invalid=762 0560: dt=10.782609, rms=0.398 (-0.009%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.404, neg=0, invalid=762 0561: dt=0.000000, rms=0.404 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.404, neg=0, invalid=762 0562: dt=0.000000, rms=0.404 (0.000%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.394, neg=0, invalid=762 iter 0, gcam->neg = 332 after 14 iterations, nbhd size=1, neg = 0 0563: dt=1.642302, rms=0.384 (2.596%), neg=0, invalid=762 0564: dt=0.007000, rms=0.384 (0.000%), neg=0, invalid=762 0565: dt=0.007000, rms=0.384 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.384, neg=0, invalid=762 0566: dt=0.096000, rms=0.384 (0.051%), neg=0, invalid=762 0567: dt=0.016000, rms=0.384 (0.001%), neg=0, invalid=762 0568: dt=0.016000, rms=0.384 (-0.000%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 3 hours, 3 minutes and 51 seconds. mri_ca_register utimesec 10794.879251 mri_ca_register stimesec 34.939934 mri_ca_register ru_maxrss 1337680 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 5289762 mri_ca_register ru_majflt 19 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 9304 mri_ca_register ru_oublock 0 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 4143 mri_ca_register ru_nivcsw 1927574 FSRUNTIME@ mri_ca_register 3.0641 hours 1 threads #-------------------------------------- #@# SubCort Seg Thu May 7 18:28:56 UTC 2020 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz sysname Linux hostname cc31617c633f machine x86_64 setenv SUBJECTS_DIR /output_dir/freesurfer cd /output_dir/freesurfer/sub-01/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz == Number of threads available to mri_ca_label for OpenMP = 1 == relabeling unlikely voxels with window_size = 9 and prior threshold 0.30 using Gibbs prior factor = 0.500 renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes reading classifier array from /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca reading input volume from norm.mgz average std[0] = 7.3 reading transform from transforms/talairach.m3z setting orig areas to linear transform determinant scaled 8.08 Atlas used for the 3D morph was /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca average std = 7.3 using min determinant for regularization = 5.3 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.16259 (20) mri peak = 0.15752 (30) Left_Lateral_Ventricle (4): linear fit = 1.53 x + 0.0 (2627 voxels, overlap=0.083) Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (2627 voxels, peak = 31), gca=30.0 gca peak = 0.17677 (13) mri peak = 0.19959 (32) Right_Lateral_Ventricle (43): linear fit = 2.22 x + 0.0 (2206 voxels, overlap=0.080) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (2206 voxels, peak = 29), gca=19.5 gca peak = 0.28129 (95) mri peak = 0.14675 (102) Right_Pallidum (52): linear fit = 1.07 x + 0.0 (952 voxels, overlap=0.741) Right_Pallidum (52): linear fit = 1.07 x + 0.0 (952 voxels, peak = 101), gca=101.2 gca peak = 0.16930 (96) mri peak = 0.11497 (102) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (922 voxels, overlap=0.745) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (922 voxels, peak = 100), gca=100.3 gca peak = 0.24553 (55) mri peak = 0.09167 (77) Right_Hippocampus (53): linear fit = 1.29 x + 0.0 (1434 voxels, overlap=0.020) Right_Hippocampus (53): linear fit = 1.29 x + 0.0 (1434 voxels, peak = 71), gca=71.2 gca peak = 0.30264 (59) mri peak = 0.07787 (73) Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (1089 voxels, overlap=0.025) Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (1089 voxels, peak = 72), gca=72.3 gca peak = 0.07580 (103) mri peak = 0.16140 (104) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (54820 voxels, overlap=0.588) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (54820 voxels, peak = 103), gca=103.0 gca peak = 0.07714 (104) mri peak = 0.18111 (105) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (55061 voxels, overlap=0.611) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (55061 voxels, peak = 104), gca=104.0 gca peak = 0.09712 (58) mri peak = 0.04781 (77) Left_Cerebral_Cortex (3): linear fit = 1.29 x + 0.0 (44635 voxels, overlap=0.008) Left_Cerebral_Cortex (3): linear fit = 1.29 x + 0.0 (44635 voxels, peak = 75), gca=75.1 gca peak = 0.11620 (58) mri peak = 0.04973 (77) Right_Cerebral_Cortex (42): linear fit = 1.29 x + 0.0 (40704 voxels, overlap=0.001) Right_Cerebral_Cortex (42): linear fit = 1.29 x + 0.0 (40704 voxels, peak = 75), gca=75.1 gca peak = 0.30970 (66) mri peak = 0.12070 (87) Right_Caudate (50): linear fit = 1.26 x + 0.0 (1193 voxels, overlap=0.020) Right_Caudate (50): linear fit = 1.26 x + 0.0 (1193 voxels, peak = 83), gca=83.5 gca peak = 0.15280 (69) mri peak = 0.13153 (87) Left_Caudate (11): linear fit = 1.17 x + 0.0 (1180 voxels, overlap=0.019) Left_Caudate (11): linear fit = 1.17 x + 0.0 (1180 voxels, peak = 81), gca=81.1 gca peak = 0.13902 (56) mri peak = 0.06094 (77) Left_Cerebellum_Cortex (8): linear fit = 1.38 x + 0.0 (26101 voxels, overlap=0.001) Left_Cerebellum_Cortex (8): linear fit = 1.38 x + 0.0 (26101 voxels, peak = 77), gca=77.0 gca peak = 0.14777 (55) mri peak = 0.06118 (79) Right_Cerebellum_Cortex (47): linear fit = 1.42 x + 0.0 (27065 voxels, overlap=0.001) Right_Cerebellum_Cortex (47): linear fit = 1.42 x + 0.0 (27065 voxels, peak = 78), gca=78.4 gca peak = 0.16765 (84) mri peak = 0.12360 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.12 x + 0.0 (7167 voxels, overlap=0.003) Left_Cerebellum_White_Matter (7): linear fit = 1.12 x + 0.0 (7167 voxels, peak = 94), gca=94.5 gca peak = 0.18739 (84) mri peak = 0.13817 (95) Right_Cerebellum_White_Matter (46): linear fit = 1.13 x + 0.0 (6257 voxels, overlap=0.003) Right_Cerebellum_White_Matter (46): linear fit = 1.13 x + 0.0 (6257 voxels, peak = 95), gca=95.3 gca peak = 0.29869 (57) mri peak = 0.10452 (74) Left_Amygdala (18): linear fit = 1.26 x + 0.0 (773 voxels, overlap=0.061) Left_Amygdala (18): linear fit = 1.26 x + 0.0 (773 voxels, peak = 72), gca=72.1 gca peak = 0.33601 (57) mri peak = 0.08636 (74) Right_Amygdala (54): linear fit = 1.30 x + 0.0 (716 voxels, overlap=0.049) Right_Amygdala (54): linear fit = 1.30 x + 0.0 (716 voxels, peak = 74), gca=74.4 gca peak = 0.11131 (90) mri peak = 0.08394 (96) Left_Thalamus_Proper (10): linear fit = 1.09 x + 0.0 (5732 voxels, overlap=0.529) Left_Thalamus_Proper (10): linear fit = 1.09 x + 0.0 (5732 voxels, peak = 98), gca=97.7 gca peak = 0.11793 (83) mri peak = 0.08553 (95) Right_Thalamus_Proper (49): linear fit = 1.14 x + 0.0 (5442 voxels, overlap=0.261) Right_Thalamus_Proper (49): linear fit = 1.14 x + 0.0 (5442 voxels, peak = 95), gca=95.0 gca peak = 0.08324 (81) mri peak = 0.09339 (92) Left_Putamen (12): linear fit = 1.15 x + 0.0 (2503 voxels, overlap=0.157) Left_Putamen (12): linear fit = 1.15 x + 0.0 (2503 voxels, peak = 94), gca=93.6 gca peak = 0.10360 (77) mri peak = 0.07816 (90) Right_Putamen (51): linear fit = 1.16 x + 0.0 (2673 voxels, overlap=0.241) Right_Putamen (51): linear fit = 1.16 x + 0.0 (2673 voxels, peak = 90), gca=89.7 gca peak = 0.08424 (78) mri peak = 0.10644 (92) Brain_Stem (16): linear fit = 1.13 x + 0.0 (16924 voxels, overlap=0.160) Brain_Stem (16): linear fit = 1.13 x + 0.0 (16924 voxels, peak = 89), gca=88.5 gca peak = 0.12631 (89) mri peak = 0.14469 (99) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1897 voxels, overlap=0.082) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1897 voxels, peak = 99), gca=99.2 gca peak = 0.14500 (87) mri peak = 0.13017 (99) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (1968 voxels, overlap=0.243) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (1968 voxels, peak = 96), gca=96.1 gca peak = 0.14975 (24) mri peak = 0.17073 (34) gca peak = 0.19357 (14) mri peak = 0.14532 (29) Fourth_Ventricle (15): linear fit = 1.97 x + 0.0 (523 voxels, overlap=0.121) Fourth_Ventricle (15): linear fit = 1.97 x + 0.0 (523 voxels, peak = 28), gca=27.5 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 1.00000 (94) gca peak Third_Ventricle = 0.14975 (24) gca peak Fourth_Ventricle = 0.19357 (14) gca peak CSF = 0.23379 (36) gca peak Left_Accumbens_area = 0.70037 (62) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.24655 (23) gca peak Right_Accumbens_area = 0.45042 (65) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.65475 (32) gca peak WM_hypointensities = 0.07854 (76) gca peak non_WM_hypointensities = 0.08491 (43) gca peak Optic_Chiasm = 0.71127 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.28 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.50 x + 0.0 Left_Putamen too bright - rescaling by 0.996 (from 1.155) to 93.2 (was 93.6) Left_Pallidum too bright - rescaling by 1.001 (from 1.045) to 100.4 (was 100.3) Right_Pallidum too bright - rescaling by 0.992 (from 1.065) to 100.4 (was 101.2) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.12544 (31) mri peak = 0.15752 (30) Left_Lateral_Ventricle (4): linear fit = 1.04 x + 0.0 (2627 voxels, overlap=0.612) Left_Lateral_Ventricle (4): linear fit = 1.04 x + 0.0 (2627 voxels, peak = 32), gca=32.4 gca peak = 0.13981 (19) mri peak = 0.19959 (32) Right_Lateral_Ventricle (43): linear fit = 1.57 x + 0.0 (2206 voxels, overlap=0.254) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (2206 voxels, peak = 30), gca=28.5 gca peak = 0.27281 (101) mri peak = 0.14675 (102) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (952 voxels, overlap=1.006) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (952 voxels, peak = 101), gca=101.0 gca peak = 0.16136 (101) mri peak = 0.11497 (102) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (922 voxels, overlap=1.000) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (922 voxels, peak = 102), gca=101.5 gca peak = 0.26672 (72) mri peak = 0.09167 (77) Right_Hippocampus (53): linear fit = 1.03 x + 0.0 (1434 voxels, overlap=1.001) Right_Hippocampus (53): linear fit = 1.03 x + 0.0 (1434 voxels, peak = 75), gca=74.5 gca peak = 0.28531 (69) mri peak = 0.07787 (73) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (1089 voxels, overlap=1.007) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (1089 voxels, peak = 69), gca=69.0 gca peak = 0.07591 (103) mri peak = 0.16140 (104) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (54820 voxels, overlap=0.588) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (54820 voxels, peak = 103), gca=103.0 gca peak = 0.07714 (104) mri peak = 0.18111 (105) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (55061 voxels, overlap=0.611) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (55061 voxels, peak = 104), gca=104.0 gca peak = 0.07484 (75) mri peak = 0.04781 (77) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (44635 voxels, overlap=0.945) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (44635 voxels, peak = 75), gca=75.0 gca peak = 0.09082 (75) mri peak = 0.04973 (77) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (40704 voxels, overlap=0.943) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (40704 voxels, peak = 75), gca=75.0 gca peak = 0.21449 (83) mri peak = 0.12070 (87) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1193 voxels, overlap=1.001) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1193 voxels, peak = 83), gca=83.0 gca peak = 0.14945 (91) mri peak = 0.13153 (87) Left_Caudate (11): linear fit = 0.99 x + 0.0 (1180 voxels, overlap=0.997) Left_Caudate (11): linear fit = 0.99 x + 0.0 (1180 voxels, peak = 90), gca=89.6 gca peak = 0.10472 (76) mri peak = 0.06094 (77) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (26101 voxels, overlap=0.953) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (26101 voxels, peak = 76), gca=75.6 gca peak = 0.10604 (78) mri peak = 0.06118 (79) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (27065 voxels, overlap=0.919) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (27065 voxels, peak = 77), gca=76.8 gca peak = 0.15219 (95) mri peak = 0.12360 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (7167 voxels, overlap=0.897) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (7167 voxels, peak = 95), gca=94.5 gca peak = 0.14366 (95) mri peak = 0.13817 (95) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6257 voxels, overlap=0.846) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6257 voxels, peak = 95), gca=94.5 gca peak = 0.27888 (72) mri peak = 0.10452 (74) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (773 voxels, overlap=1.016) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (773 voxels, peak = 73), gca=73.1 gca peak = 0.32954 (74) mri peak = 0.08636 (74) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (716 voxels, overlap=1.004) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (716 voxels, peak = 74), gca=74.0 gca peak = 0.10169 (97) mri peak = 0.08394 (96) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (5732 voxels, overlap=0.896) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (5732 voxels, peak = 98), gca=98.5 gca peak = 0.09624 (95) mri peak = 0.08553 (95) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (5442 voxels, overlap=0.934) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (5442 voxels, peak = 95), gca=95.0 gca peak = 0.08464 (93) mri peak = 0.09339 (92) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2503 voxels, overlap=0.817) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2503 voxels, peak = 93), gca=92.5 gca peak = 0.07854 (88) mri peak = 0.07816 (90) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2673 voxels, overlap=0.930) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2673 voxels, peak = 88), gca=87.6 gca peak = 0.07797 (89) mri peak = 0.10644 (92) Brain_Stem (16): linear fit = 1.00 x + 0.0 (16924 voxels, overlap=0.710) Brain_Stem (16): linear fit = 1.00 x + 0.0 (16924 voxels, peak = 89), gca=89.0 gca peak = 0.10823 (98) mri peak = 0.14469 (99) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1897 voxels, overlap=0.788) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1897 voxels, peak = 98), gca=98.0 gca peak = 0.15044 (96) mri peak = 0.13017 (99) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1968 voxels, overlap=0.812) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1968 voxels, peak = 96), gca=95.5 gca peak = 0.12656 (38) mri peak = 0.17073 (34) gca peak = 0.16542 (24) mri peak = 0.14532 (29) Fourth_Ventricle (15): linear fit = 1.32 x + 0.0 (523 voxels, overlap=0.304) Fourth_Ventricle (15): linear fit = 1.32 x + 0.0 (523 voxels, peak = 32), gca=31.6 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16283 (33) gca peak Left_Thalamus = 0.36646 (102) gca peak Third_Ventricle = 0.12656 (38) gca peak CSF = 0.15446 (55) gca peak Left_Accumbens_area = 0.67775 (73) gca peak Left_undetermined = 0.95280 (34) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.12303 (35) gca peak Right_Inf_Lat_Vent = 0.20762 (30) gca peak Right_Accumbens_area = 0.29938 (82) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14504 (37) gca peak Fifth_Ventricle = 0.51780 (46) gca peak WM_hypointensities = 0.07992 (76) gca peak non_WM_hypointensities = 0.08491 (43) gca peak Optic_Chiasm = 0.70565 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.01 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.29 x + 0.0 Left_Pallidum too bright - rescaling by 0.989 (from 1.005) to 100.4 (was 101.5) Right_Pallidum too bright - rescaling by 0.994 (from 1.000) to 100.4 (was 101.0) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 80648 voxels changed in iteration 0 of unlikely voxel relabeling 285 voxels changed in iteration 1 of unlikely voxel relabeling 17 voxels changed in iteration 2 of unlikely voxel relabeling 1 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 83440 gm and wm labels changed (%32 to gray, %68 to white out of all changed labels) 583 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 78946 changed. image ll: -2.147, PF=0.500 pass 2: 20703 changed. image ll: -2.146, PF=0.500 pass 3: 5979 changed. pass 4: 2292 changed. 73651 voxels changed in iteration 0 of unlikely voxel relabeling 513 voxels changed in iteration 1 of unlikely voxel relabeling 62 voxels changed in iteration 2 of unlikely voxel relabeling 3 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 8067 voxels changed in iteration 0 of unlikely voxel relabeling 131 voxels changed in iteration 1 of unlikely voxel relabeling 5 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 7378 voxels changed in iteration 0 of unlikely voxel relabeling 77 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 6254 voxels changed in iteration 0 of unlikely voxel relabeling 35 voxels changed in iteration 1 of unlikely voxel relabeling 1 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling MRItoUCHAR: min=0, max=85 MRItoUCHAR: converting to UCHAR writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 4693.596445 mri_ca_label stimesec 10.161383 mri_ca_label ru_maxrss 1823012 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 821665 mri_ca_label ru_majflt 296 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 110648 mri_ca_label ru_oublock 0 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 458 mri_ca_label ru_nivcsw 670637 auto-labeling took 79 minutes and 29 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /output_dir/freesurfer/sub-01/mri/transforms/cc_up.lta sub-01 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /output_dir/freesurfer/sub-01/mri/transforms/cc_up.lta reading aseg from /output_dir/freesurfer/sub-01/mri/aseg.auto_noCCseg.mgz reading norm from /output_dir/freesurfer/sub-01/mri/norm.mgz 18712 voxels in left wm, 27747 in right wm, xrange [123, 129] searching rotation angles z=[-7 7], y=[-7 7] searching scale 1 Z rot -7.1 searching scale 1 Z rot -6.9 searching scale 1 Z rot -6.6 searching scale 1 Z rot -6.4 searching scale 1 Z rot -6.1 searching scale 1 Z rot -5.9 searching scale 1 Z rot -5.6 searching scale 1 Z rot -5.4 searching scale 1 Z rot -5.1 searching scale 1 Z rot -4.9 searching scale 1 Z rot -4.6 searching scale 1 Z rot -4.4 searching scale 1 Z rot -4.1 searching scale 1 Z rot -3.9 searching scale 1 Z rot -3.6 searching scale 1 Z rot -3.4 searching scale 1 Z rot -3.1 searching scale 1 Z rot -2.9 searching scale 1 Z rot -2.6 searching scale 1 Z rot -2.4 searching scale 1 Z rot -2.1 searching scale 1 Z rot -1.9 searching scale 1 Z rot -1.6 searching scale 1 Z rot -1.4 searching scale 1 Z rot -1.1 searching scale 1 Z rot -0.9 searching scale 1 Z rot -0.6 searching scale 1 Z rot -0.4 searching scale 1 Z rot -0.1 searching scale 1 Z rot 0.1 searching scale 1 Z rot 0.4 searching scale 1 Z rot 0.6 searching scale 1 Z rot 0.9 searching scale 1 Z rot 1.1 searching scale 1 Z rot 1.4 searching scale 1 Z rot 1.6 searching scale 1 Z rot 1.9 searching scale 1 Z rot 2.1 searching scale 1 Z rot 2.4 searching scale 1 Z rot 2.6 searching scale 1 Z rot 2.9 searching scale 1 Z rot 3.1 searching scale 1 Z rot 3.4 searching scale 1 Z rot 3.6 searching scale 1 Z rot 3.9 searching scale 1 Z rot 4.1 searching scale 1 Z rot 4.4 searching scale 1 Z rot 4.6 searching scale 1 Z rot 4.9 searching scale 1 Z rot 5.1 searching scale 1 Z rot 5.4 searching scale 1 Z rot 5.6 searching scale 1 Z rot 5.9 searching scale 1 Z rot 6.1 searching scale 1 Z rot 6.4 global minimum found at slice 126.0, rotations (-0.33, -0.37) final transformation (x=126.0, yr=-0.329, zr=-0.371): 0.99996 0.00647 -0.00575 1.94720; -0.00647 0.99998 0.00004 25.81394; 0.00575 0.00000 0.99998 21.27746; 0.00000 0.00000 0.00000 1.00000; updating x range to be [127, 130] in xformed coordinates best xformed slice 128 cc center is found at 128 103 106 eigenvectors: -0.00031 0.00016 1.00000; -0.16532 -0.98624 0.00011; 0.98624 -0.16532 0.00033; writing aseg with callosum to /output_dir/freesurfer/sub-01/mri/aseg.auto.mgz... corpus callosum segmentation took 0.5 minutes #-------------------------------------- #@# Merge ASeg Thu May 7 19:48:58 UTC 2020 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Thu May 7 19:48:59 UTC 2020 /output_dir/freesurfer/sub-01/mri mri_normalize -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz assuming input volume is MGH (Van der Kouwe) MP-RAGE using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.presurf.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 945 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 110 white matter peak found at 110 gm peak at 83 (83), valley at 56 (56) csf peak at 30, setting threshold to 65 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 81 (81), valley at 48 (48) csf peak at 30, setting threshold to 64 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 3 minutes and 40 seconds. #-------------------------------------------- #@# Mask BFS Thu May 7 19:52:42 UTC 2020 /output_dir/freesurfer/sub-01/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1869632 voxels in mask (pct= 11.14) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Thu May 7 19:52:45 UTC 2020 mri_segment -mprage brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (104.0): 103.9 +- 5.6 [79.0 --> 125.0] GM (79.0) : 77.7 +- 11.3 [30.0 --> 95.0] setting bottom of white matter range to 88.9 setting top of gray matter range to 100.2 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... 7113 sparsely connected voxels removed... thickening thin strands.... 20 segments, 5655 filled 47 bright non-wm voxels segmented. 4282 diagonally connected voxels added... white matter segmentation took 1.7 minutes writing output to wm.seg.mgz... assuming input volume is MGH (Van der Kouwe) MP-RAGE mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.54 minutes reading wm segmentation from wm.seg.mgz... 276 voxels added to wm to prevent paths from MTL structures to cortex 4865 additional wm voxels added 0 additional wm voxels added SEG EDIT: 54872 voxels turned on, 57927 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 114 new 114 115,126,128 old 114 new 114 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 27 found - 27 modified | TOTAL: 27 pass 2 (xy+): 0 found - 27 modified | TOTAL: 27 pass 1 (xy-): 30 found - 30 modified | TOTAL: 57 pass 2 (xy-): 0 found - 30 modified | TOTAL: 57 pass 1 (yz+): 33 found - 33 modified | TOTAL: 90 pass 2 (yz+): 0 found - 33 modified | TOTAL: 90 pass 1 (yz-): 25 found - 25 modified | TOTAL: 115 pass 2 (yz-): 0 found - 25 modified | TOTAL: 115 pass 1 (xz+): 13 found - 13 modified | TOTAL: 128 pass 2 (xz+): 0 found - 13 modified | TOTAL: 128 pass 1 (xz-): 30 found - 30 modified | TOTAL: 158 pass 2 (xz-): 0 found - 30 modified | TOTAL: 158 Iteration Number : 1 pass 1 (+++): 12 found - 12 modified | TOTAL: 12 pass 2 (+++): 0 found - 12 modified | TOTAL: 12 pass 1 (+++): 4 found - 4 modified | TOTAL: 16 pass 2 (+++): 0 found - 4 modified | TOTAL: 16 pass 1 (+++): 8 found - 8 modified | TOTAL: 24 pass 2 (+++): 0 found - 8 modified | TOTAL: 24 pass 1 (+++): 7 found - 7 modified | TOTAL: 31 pass 2 (+++): 0 found - 7 modified | TOTAL: 31 Iteration Number : 1 pass 1 (++): 154 found - 154 modified | TOTAL: 154 pass 2 (++): 0 found - 154 modified | TOTAL: 154 pass 1 (+-): 137 found - 137 modified | TOTAL: 291 pass 2 (+-): 0 found - 137 modified | TOTAL: 291 pass 1 (--): 122 found - 122 modified | TOTAL: 413 pass 2 (--): 0 found - 122 modified | TOTAL: 413 pass 1 (-+): 133 found - 133 modified | TOTAL: 546 pass 2 (-+): 0 found - 133 modified | TOTAL: 546 Iteration Number : 2 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 2 found - 2 modified | TOTAL: 5 pass 2 (xy-): 0 found - 2 modified | TOTAL: 5 pass 1 (yz+): 7 found - 7 modified | TOTAL: 12 pass 2 (yz+): 0 found - 7 modified | TOTAL: 12 pass 1 (yz-): 8 found - 8 modified | TOTAL: 20 pass 2 (yz-): 0 found - 8 modified | TOTAL: 20 pass 1 (xz+): 9 found - 9 modified | TOTAL: 29 pass 2 (xz+): 0 found - 9 modified | TOTAL: 29 pass 1 (xz-): 3 found - 3 modified | TOTAL: 32 pass 2 (xz-): 0 found - 3 modified | TOTAL: 32 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 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 3 found - 3 modified | TOTAL: 4 pass 2 (+-): 0 found - 3 modified | TOTAL: 4 pass 1 (--): 3 found - 3 modified | TOTAL: 7 pass 2 (--): 0 found - 3 modified | TOTAL: 7 pass 1 (-+): 3 found - 3 modified | TOTAL: 10 pass 2 (-+): 0 found - 3 modified | TOTAL: 10 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 777 (out of 633907: 0.122573) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Thu May 7 19:55:08 UTC 2020 /output_dir/freesurfer/sub-01/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 0.94033 -0.02778 -0.02927 13.24473; 0.04464 0.96904 0.41009 -43.24454; 0.01509 -0.39055 0.91917 48.77933; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 0.94033 -0.02778 -0.02927 13.24473; 0.04464 0.96904 0.41009 -43.24454; 0.01509 -0.39055 0.91917 48.77933; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 2323 (min = 350, max = 1400), aspect = 1.24 (min = 0.10, max = 0.75) need search nearby using seed (126, 101, 96), TAL = (2.0, -32.0, 27.0) talairach voxel to voxel transform 1.06141 0.03733 0.01714 -13.27957; -0.03519 0.87343 -0.39080 57.30048; -0.03238 0.37051 0.92160 -28.50395; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (126, 101, 96) --> (2.0, -32.0, 27.0) done. writing output to filled.mgz... filling took 0.7 minutes talairach cc position changed to (2.00, -32.00, 27.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, -32.00, 27.00) SRC: (106.77, 104.20, 93.89) search lh wm seed point around talairach space (-16.00, -32.00, 27.00), SRC: (144.98, 102.93, 92.73) 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 Thu May 7 19:55:51 UTC 2020 /output_dir/freesurfer/sub-01/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-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 1 found - 1 modified | TOTAL: 2 pass 2 (xz+): 0 found - 1 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 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 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 3 (out of 306611: 0.000978) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 40: 1363 vertices, 1530 faces slice 50: 9629 vertices, 9989 faces slice 60: 22610 vertices, 23079 faces slice 70: 36595 vertices, 37073 faces slice 80: 49762 vertices, 50216 faces slice 90: 62164 vertices, 62560 faces slice 100: 75034 vertices, 75487 faces slice 110: 87519 vertices, 87969 faces slice 120: 99109 vertices, 99570 faces slice 130: 110773 vertices, 111250 faces slice 140: 122469 vertices, 122921 faces slice 150: 132361 vertices, 132752 faces slice 160: 141503 vertices, 141857 faces slice 170: 148204 vertices, 148523 faces slice 180: 154099 vertices, 154368 faces slice 190: 158115 vertices, 158320 faces slice 200: 159364 vertices, 159446 faces slice 210: 159364 vertices, 159446 faces slice 220: 159364 vertices, 159446 faces slice 230: 159364 vertices, 159446 faces slice 240: 159364 vertices, 159446 faces slice 250: 159364 vertices, 159446 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 159364 voxel in cpt #1: X=-82 [v=159364,e=478338,f=318892] located at (-28.387075, -22.592154, 21.311306) For the whole surface: X=-82 [v=159364,e=478338,f=318892] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Thu May 7 19:55:59 UTC 2020 /output_dir/freesurfer/sub-01/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 0 (out of 303866: 0.000000) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 40: 637 vertices, 737 faces slice 50: 8097 vertices, 8427 faces slice 60: 19370 vertices, 19829 faces slice 70: 33413 vertices, 33854 faces slice 80: 46608 vertices, 47100 faces slice 90: 59544 vertices, 59951 faces slice 100: 71952 vertices, 72400 faces slice 110: 83922 vertices, 84353 faces slice 120: 95330 vertices, 95788 faces slice 130: 107264 vertices, 107690 faces slice 140: 118678 vertices, 119124 faces slice 150: 129141 vertices, 129494 faces slice 160: 138006 vertices, 138365 faces slice 170: 145133 vertices, 145380 faces slice 180: 151153 vertices, 151390 faces slice 190: 155415 vertices, 155575 faces slice 200: 156724 vertices, 156772 faces slice 210: 156724 vertices, 156772 faces slice 220: 156724 vertices, 156772 faces slice 230: 156724 vertices, 156772 faces slice 240: 156724 vertices, 156772 faces slice 250: 156724 vertices, 156772 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 156724 voxel in cpt #1: X=-48 [v=156724,e=470316,f=313544] located at (31.880573, -21.002253, 20.117449) For the whole surface: X=-48 [v=156724,e=470316,f=313544] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Thu May 7 19:56:07 UTC 2020 /output_dir/freesurfer/sub-01/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix #-------------------------------------------- #@# Smooth1 rh Thu May 7 19:56:07 UTC 2020 /output_dir/freesurfer/sub-01/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix Waiting for PID 2343 of (2343 2346) to complete... Waiting for PID 2346 of (2343 2346) to complete... mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... PIDs (2343 2346) completed and logs appended. #-------------------------------------------- #@# Inflation1 lh Thu May 7 19:56:18 UTC 2020 /output_dir/freesurfer/sub-01/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix #-------------------------------------------- #@# Inflation1 rh Thu May 7 19:56:18 UTC 2020 /output_dir/freesurfer/sub-01/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Waiting for PID 2385 of (2385 2388) to complete... Waiting for PID 2388 of (2385 2388) to complete... mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 49.2 mm, total surface area = 84345 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 1.2 minutes step 000: RMS=0.155 (target=0.015) step 005: RMS=0.117 (target=0.015) step 010: RMS=0.087 (target=0.015) step 015: RMS=0.073 (target=0.015) step 020: RMS=0.063 (target=0.015) step 025: RMS=0.056 (target=0.015) step 030: RMS=0.050 (target=0.015) step 035: RMS=0.046 (target=0.015) step 040: RMS=0.043 (target=0.015) step 045: RMS=0.042 (target=0.015) step 050: RMS=0.040 (target=0.015) step 055: RMS=0.039 (target=0.015) step 060: RMS=0.039 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 47.037886 mris_inflate stimesec 0.252854 mris_inflate ru_maxrss 208076 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 50489 mris_inflate ru_majflt 34 mris_inflate ru_nswap 0 mris_inflate ru_inblock 19704 mris_inflate ru_oublock 0 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 172 mris_inflate ru_nivcsw 9902 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 48.8 mm, total surface area = 83063 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 1.2 minutes step 000: RMS=0.153 (target=0.015) step 005: RMS=0.116 (target=0.015) step 010: RMS=0.085 (target=0.015) step 015: RMS=0.071 (target=0.015) step 020: RMS=0.061 (target=0.015) step 025: RMS=0.053 (target=0.015) step 030: RMS=0.048 (target=0.015) step 035: RMS=0.043 (target=0.015) step 040: RMS=0.041 (target=0.015) step 045: RMS=0.039 (target=0.015) step 050: RMS=0.038 (target=0.015) step 055: RMS=0.037 (target=0.015) step 060: RMS=0.037 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 46.237682 mris_inflate stimesec 0.218561 mris_inflate ru_maxrss 204772 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 49701 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 11808 mris_inflate ru_oublock 0 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 134 mris_inflate ru_nivcsw 9624 PIDs (2385 2388) completed and logs appended. #-------------------------------------------- #@# QSphere lh Thu May 7 19:57:30 UTC 2020 /output_dir/freesurfer/sub-01/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix #-------------------------------------------- #@# QSphere rh Thu May 7 19:57:30 UTC 2020 /output_dir/freesurfer/sub-01/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix Waiting for PID 2427 of (2427 2430) to complete... Waiting for PID 2430 of (2427 2430) to complete... mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.93 +- 0.54 (0.00-->7.14) (max @ vno 119908 --> 121034) face area 0.02 +- 0.03 (-0.14-->0.58) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.307... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.489, avgs=0 005/300: dt: 0.9000, rms radial error=175.231, avgs=0 010/300: dt: 0.9000, rms radial error=174.677, avgs=0 015/300: dt: 0.9000, rms radial error=173.949, avgs=0 020/300: dt: 0.9000, rms radial error=173.120, avgs=0 025/300: dt: 0.9000, rms radial error=172.232, avgs=0 030/300: dt: 0.9000, rms radial error=171.312, avgs=0 035/300: dt: 0.9000, rms radial error=170.373, avgs=0 040/300: dt: 0.9000, rms radial error=169.426, avgs=0 045/300: dt: 0.9000, rms radial error=168.476, avgs=0 050/300: dt: 0.9000, rms radial error=167.525, avgs=0 055/300: dt: 0.9000, rms radial error=166.577, avgs=0 060/300: dt: 0.9000, rms radial error=165.632, avgs=0 065/300: dt: 0.9000, rms radial error=164.690, avgs=0 070/300: dt: 0.9000, rms radial error=163.752, avgs=0 075/300: dt: 0.9000, rms radial error=162.819, avgs=0 080/300: dt: 0.9000, rms radial error=161.890, avgs=0 085/300: dt: 0.9000, rms radial error=160.970, avgs=0 090/300: dt: 0.9000, rms radial error=160.060, avgs=0 095/300: dt: 0.9000, rms radial error=159.154, avgs=0 100/300: dt: 0.9000, rms radial error=158.253, avgs=0 105/300: dt: 0.9000, rms radial error=157.360, avgs=0 110/300: dt: 0.9000, rms radial error=156.472, avgs=0 115/300: dt: 0.9000, rms radial error=155.591, avgs=0 120/300: dt: 0.9000, rms radial error=154.719, avgs=0 125/300: dt: 0.9000, rms radial error=153.851, avgs=0 130/300: dt: 0.9000, rms radial error=152.989, avgs=0 135/300: dt: 0.9000, rms radial error=152.131, avgs=0 140/300: dt: 0.9000, rms radial error=151.278, avgs=0 145/300: dt: 0.9000, rms radial error=150.429, avgs=0 150/300: dt: 0.9000, rms radial error=149.585, avgs=0 155/300: dt: 0.9000, rms radial error=148.746, avgs=0 160/300: dt: 0.9000, rms radial error=147.912, avgs=0 165/300: dt: 0.9000, rms radial error=147.082, avgs=0 170/300: dt: 0.9000, rms radial error=146.257, avgs=0 175/300: dt: 0.9000, rms radial error=145.436, avgs=0 180/300: dt: 0.9000, rms radial error=144.619, avgs=0 185/300: dt: 0.9000, rms radial error=143.807, avgs=0 190/300: dt: 0.9000, rms radial error=142.999, avgs=0 195/300: dt: 0.9000, rms radial error=142.196, avgs=0 200/300: dt: 0.9000, rms radial error=141.397, avgs=0 205/300: dt: 0.9000, rms radial error=140.602, avgs=0 210/300: dt: 0.9000, rms radial error=139.812, avgs=0 215/300: dt: 0.9000, rms radial error=139.025, avgs=0 220/300: dt: 0.9000, rms radial error=138.243, avgs=0 225/300: dt: 0.9000, rms radial error=137.466, avgs=0 230/300: dt: 0.9000, rms radial error=136.692, avgs=0 235/300: dt: 0.9000, rms radial error=135.923, avgs=0 240/300: dt: 0.9000, rms radial error=135.158, avgs=0 245/300: dt: 0.9000, rms radial error=134.397, avgs=0 250/300: dt: 0.9000, rms radial error=133.641, avgs=0 255/300: dt: 0.9000, rms radial error=132.888, avgs=0 260/300: dt: 0.9000, rms radial error=132.140, avgs=0 265/300: dt: 0.9000, rms radial error=131.396, avgs=0 270/300: dt: 0.9000, rms radial error=130.655, avgs=0 275/300: dt: 0.9000, rms radial error=129.919, avgs=0 280/300: dt: 0.9000, rms radial error=129.188, avgs=0 285/300: dt: 0.9000, rms radial error=128.460, avgs=0 290/300: dt: 0.9000, rms radial error=127.736, avgs=0 295/300: dt: 0.9000, rms radial error=127.016, avgs=0 300/300: dt: 0.9000, rms radial error=126.300, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 18714.21 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 = 3164.54 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00010 epoch 3 (K=160.0), pass 1, starting sse = 336.62 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.09/11 = 0.00804 epoch 4 (K=640.0), pass 1, starting sse = 21.46 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.13/14 = 0.00903 final distance error %27.33 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.11 hours mris_sphere utimesec 256.937393 mris_sphere stimesec 0.564263 mris_sphere ru_maxrss 208720 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 50500 mris_sphere ru_majflt 37 mris_sphere ru_nswap 0 mris_sphere ru_inblock 20368 mris_sphere ru_oublock 0 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 179 mris_sphere ru_nivcsw 50550 FSRUNTIME@ mris_sphere 0.1093 hours 1 threads 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 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.94 +- 0.54 (0.00-->6.12) (max @ vno 74209 --> 74230) face area 0.03 +- 0.03 (-0.21-->0.65) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.310... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.350, avgs=0 005/300: dt: 0.9000, rms radial error=175.090, avgs=0 010/300: dt: 0.9000, rms radial error=174.532, avgs=0 015/300: dt: 0.9000, rms radial error=173.799, avgs=0 020/300: dt: 0.9000, rms radial error=172.964, avgs=0 025/300: dt: 0.9000, rms radial error=172.073, avgs=0 030/300: dt: 0.9000, rms radial error=171.158, avgs=0 035/300: dt: 0.9000, rms radial error=170.226, avgs=0 040/300: dt: 0.9000, rms radial error=169.286, avgs=0 045/300: dt: 0.9000, rms radial error=168.344, avgs=0 050/300: dt: 0.9000, rms radial error=167.403, avgs=0 055/300: dt: 0.9000, rms radial error=166.464, avgs=0 060/300: dt: 0.9000, rms radial error=165.528, avgs=0 065/300: dt: 0.9000, rms radial error=164.596, avgs=0 070/300: dt: 0.9000, rms radial error=163.670, avgs=0 075/300: dt: 0.9000, rms radial error=162.752, avgs=0 080/300: dt: 0.9000, rms radial error=161.839, avgs=0 085/300: dt: 0.9000, rms radial error=160.931, avgs=0 090/300: dt: 0.9000, rms radial error=160.030, avgs=0 095/300: dt: 0.9000, rms radial error=159.133, avgs=0 100/300: dt: 0.9000, rms radial error=158.241, avgs=0 105/300: dt: 0.9000, rms radial error=157.355, avgs=0 110/300: dt: 0.9000, rms radial error=156.473, avgs=0 115/300: dt: 0.9000, rms radial error=155.596, avgs=0 120/300: dt: 0.9000, rms radial error=154.723, avgs=0 125/300: dt: 0.9000, rms radial error=153.855, avgs=0 130/300: dt: 0.9000, rms radial error=152.992, avgs=0 135/300: dt: 0.9000, rms radial error=152.134, avgs=0 140/300: dt: 0.9000, rms radial error=151.281, avgs=0 145/300: dt: 0.9000, rms radial error=150.433, avgs=0 150/300: dt: 0.9000, rms radial error=149.589, avgs=0 155/300: dt: 0.9000, rms radial error=148.750, avgs=0 160/300: dt: 0.9000, rms radial error=147.915, avgs=0 165/300: dt: 0.9000, rms radial error=147.085, avgs=0 170/300: dt: 0.9000, rms radial error=146.259, avgs=0 175/300: dt: 0.9000, rms radial error=145.438, avgs=0 180/300: dt: 0.9000, rms radial error=144.621, avgs=0 185/300: dt: 0.9000, rms radial error=143.809, avgs=0 190/300: dt: 0.9000, rms radial error=143.002, avgs=0 195/300: dt: 0.9000, rms radial error=142.199, avgs=0 200/300: dt: 0.9000, rms radial error=141.401, avgs=0 205/300: dt: 0.9000, rms radial error=140.607, avgs=0 210/300: dt: 0.9000, rms radial error=139.817, avgs=0 215/300: dt: 0.9000, rms radial error=139.032, avgs=0 220/300: dt: 0.9000, rms radial error=138.251, avgs=0 225/300: dt: 0.9000, rms radial error=137.474, avgs=0 230/300: dt: 0.9000, rms radial error=136.702, avgs=0 235/300: dt: 0.9000, rms radial error=135.934, avgs=0 240/300: dt: 0.9000, rms radial error=135.170, avgs=0 245/300: dt: 0.9000, rms radial error=134.410, avgs=0 250/300: dt: 0.9000, rms radial error=133.654, avgs=0 255/300: dt: 0.9000, rms radial error=132.902, avgs=0 260/300: dt: 0.9000, rms radial error=132.155, avgs=0 265/300: dt: 0.9000, rms radial error=131.412, avgs=0 270/300: dt: 0.9000, rms radial error=130.672, avgs=0 275/300: dt: 0.9000, rms radial error=129.937, avgs=0 280/300: dt: 0.9000, rms radial error=129.206, avgs=0 285/300: dt: 0.9000, rms radial error=128.479, avgs=0 290/300: dt: 0.9000, rms radial error=127.756, avgs=0 295/300: dt: 0.9000, rms radial error=127.037, avgs=0 300/300: dt: 0.9000, rms radial error=126.322, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 18329.98 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00012 epoch 2 (K=40.0), pass 1, starting sse = 3059.81 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00005 epoch 3 (K=160.0), pass 1, starting sse = 314.50 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.08/11 = 0.00768 epoch 4 (K=640.0), pass 1, starting sse = 20.10 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.15/15 = 0.01031 final distance error %26.41 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.11 hours mris_sphere utimesec 256.091780 mris_sphere stimesec 0.564795 mris_sphere ru_maxrss 205420 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 49713 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 11872 mris_sphere ru_oublock 0 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 133 mris_sphere ru_nivcsw 52085 FSRUNTIME@ mris_sphere 0.1087 hours 1 threads PIDs (2427 2430) completed and logs appended. #-------------------------------------------- #@# Fix Topology Copy lh Thu May 7 20:04:04 UTC 2020 /output_dir/freesurfer/sub-01/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Thu May 7 20:04:05 UTC 2020 /output_dir/freesurfer/sub-01/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Thu May 7 20:04:05 UTC 2020 mris_fix_topology -rusage /output_dir/freesurfer/sub-01/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 sub-01 lh #@# Fix Topology rh Thu May 7 20:04:05 UTC 2020 mris_fix_topology -rusage /output_dir/freesurfer/sub-01/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 sub-01 rh Waiting for PID 2503 of (2503 2506) to complete... Waiting for PID 2506 of (2503 2506) to complete... mris_fix_topology -rusage /output_dir/freesurfer/sub-01/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 sub-01 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 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ before topology correction, eno=-82 (nv=159364, nf=318892, ne=478338, g=42) 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... 4638 ambiguous faces found in tessellation segmenting defects... 51 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 22 into 21 -merging segment 27 into 23 -merging segment 36 into 35 48 defects to be corrected 0 vertices coincident reading input surface /output_dir/freesurfer/sub-01/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.0040 (-4.5020) -vertex loglikelihood: -5.7166 (-2.8583) -normal dot loglikelihood: -3.6210 (-3.6210) -quad curv loglikelihood: -6.4818 (-3.2409) Total Loglikelihood : -24.8233 CORRECTING DEFECT 0 (vertices=18, convex hull=52, v0=5251) After retessellation of defect 0 (v0=5251), euler #=-48 (156416,467885,311421) : difference with theory (-45) = 3 CORRECTING DEFECT 1 (vertices=30, convex hull=50, v0=9750) After retessellation of defect 1 (v0=9750), euler #=-47 (156428,467941,311466) : difference with theory (-44) = 3 CORRECTING DEFECT 2 (vertices=48, convex hull=51, v0=12798) After retessellation of defect 2 (v0=12798), euler #=-46 (156437,467990,311507) : difference with theory (-43) = 3 CORRECTING DEFECT 3 (vertices=41, convex hull=41, v0=21963) After retessellation of defect 3 (v0=21963), euler #=-45 (156444,468027,311538) : difference with theory (-42) = 3 CORRECTING DEFECT 4 (vertices=72, convex hull=14, v0=22859) After retessellation of defect 4 (v0=22859), euler #=-44 (156446,468037,311547) : difference with theory (-41) = 3 CORRECTING DEFECT 5 (vertices=6, convex hull=13, v0=23490) After retessellation of defect 5 (v0=23490), euler #=-43 (156446,468040,311551) : difference with theory (-40) = 3 CORRECTING DEFECT 6 (vertices=69, convex hull=91, v0=25592) After retessellation of defect 6 (v0=25592), euler #=-42 (156482,468184,311660) : difference with theory (-39) = 3 CORRECTING DEFECT 7 (vertices=132, convex hull=134, v0=29345) After retessellation of defect 7 (v0=29345), euler #=-41 (156519,468351,311791) : difference with theory (-38) = 3 CORRECTING DEFECT 8 (vertices=26, convex hull=47, v0=42436) After retessellation of defect 8 (v0=42436), euler #=-40 (156534,468414,311840) : difference with theory (-37) = 3 CORRECTING DEFECT 9 (vertices=15, convex hull=24, v0=44024) After retessellation of defect 9 (v0=44024), euler #=-39 (156537,468430,311854) : difference with theory (-36) = 3 CORRECTING DEFECT 10 (vertices=15, convex hull=57, v0=61696) After retessellation of defect 10 (v0=61696), euler #=-38 (156547,468482,311897) : difference with theory (-35) = 3 CORRECTING DEFECT 11 (vertices=30, convex hull=78, v0=61858) After retessellation of defect 11 (v0=61858), euler #=-37 (156565,468570,311968) : difference with theory (-34) = 3 CORRECTING DEFECT 12 (vertices=49, convex hull=86, v0=63127) After retessellation of defect 12 (v0=63127), euler #=-36 (156599,468707,312072) : difference with theory (-33) = 3 CORRECTING DEFECT 13 (vertices=27, convex hull=26, v0=64684) After retessellation of defect 13 (v0=64684), euler #=-35 (156603,468729,312091) : difference with theory (-32) = 3 CORRECTING DEFECT 14 (vertices=53, convex hull=28, v0=69107) After retessellation of defect 14 (v0=69107), euler #=-34 (156609,468758,312115) : difference with theory (-31) = 3 CORRECTING DEFECT 15 (vertices=10, convex hull=27, v0=70761) After retessellation of defect 15 (v0=70761), euler #=-33 (156612,468775,312130) : difference with theory (-30) = 3 CORRECTING DEFECT 16 (vertices=58, convex hull=70, v0=73094) After retessellation of defect 16 (v0=73094), euler #=-32 (156621,468828,312175) : difference with theory (-29) = 3 CORRECTING DEFECT 17 (vertices=56, convex hull=109, v0=76059) After retessellation of defect 17 (v0=76059), euler #=-31 (156644,468948,312273) : difference with theory (-28) = 3 CORRECTING DEFECT 18 (vertices=11, convex hull=26, v0=81865) After retessellation of defect 18 (v0=81865), euler #=-30 (156646,468963,312287) : difference with theory (-27) = 3 CORRECTING DEFECT 19 (vertices=36, convex hull=62, v0=83650) After retessellation of defect 19 (v0=83650), euler #=-29 (156664,469043,312350) : difference with theory (-26) = 3 CORRECTING DEFECT 20 (vertices=6, convex hull=27, v0=87318) After retessellation of defect 20 (v0=87318), euler #=-28 (156665,469051,312358) : difference with theory (-25) = 3 CORRECTING DEFECT 21 (vertices=52, convex hull=77, v0=88943) After retessellation of defect 21 (v0=88943), euler #=-26 (156678,469125,312421) : difference with theory (-24) = 2 CORRECTING DEFECT 22 (vertices=726, convex hull=458, v0=94261) L defect detected... After retessellation of defect 22 (v0=94261), euler #=-24 (156749,469580,312807) : difference with theory (-23) = 1 CORRECTING DEFECT 23 (vertices=73, convex hull=77, v0=94315) After retessellation of defect 23 (v0=94315), euler #=-23 (156778,469703,312902) : difference with theory (-22) = 1 CORRECTING DEFECT 24 (vertices=53, convex hull=78, v0=96272) After retessellation of defect 24 (v0=96272), euler #=-22 (156794,469784,312968) : difference with theory (-21) = 1 CORRECTING DEFECT 25 (vertices=100, convex hull=21, v0=104976) After retessellation of defect 25 (v0=104976), euler #=-21 (156799,469803,312983) : difference with theory (-20) = 1 CORRECTING DEFECT 26 (vertices=65, convex hull=95, v0=106111) After retessellation of defect 26 (v0=106111), euler #=-20 (156836,469952,313096) : difference with theory (-19) = 1 CORRECTING DEFECT 27 (vertices=8, convex hull=20, v0=109780) After retessellation of defect 27 (v0=109780), euler #=-19 (156837,469961,313105) : difference with theory (-18) = 1 CORRECTING DEFECT 28 (vertices=53, convex hull=34, v0=110428) After retessellation of defect 28 (v0=110428), euler #=-18 (156843,469992,313131) : difference with theory (-17) = 1 CORRECTING DEFECT 29 (vertices=19, convex hull=29, v0=110862) After retessellation of defect 29 (v0=110862), euler #=-17 (156844,470006,313145) : difference with theory (-16) = 1 CORRECTING DEFECT 30 (vertices=69, convex hull=32, v0=113863) After retessellation of defect 30 (v0=113863), euler #=-16 (156851,470038,313171) : difference with theory (-15) = 1 CORRECTING DEFECT 31 (vertices=13, convex hull=11, v0=114944) After retessellation of defect 31 (v0=114944), euler #=-15 (156851,470041,313175) : difference with theory (-14) = 1 CORRECTING DEFECT 32 (vertices=172, convex hull=145, v0=115330) After retessellation of defect 32 (v0=115330), euler #=-14 (156887,470206,313305) : difference with theory (-13) = 1 CORRECTING DEFECT 33 (vertices=194, convex hull=185, v0=118761) After retessellation of defect 33 (v0=118761), euler #=-12 (156961,470528,313555) : difference with theory (-12) = 0 CORRECTING DEFECT 34 (vertices=56, convex hull=52, v0=124437) After retessellation of defect 34 (v0=124437), euler #=-11 (156978,470599,313610) : difference with theory (-11) = 0 CORRECTING DEFECT 35 (vertices=26, convex hull=34, v0=126386) After retessellation of defect 35 (v0=126386), euler #=-10 (156987,470637,313640) : difference with theory (-10) = 0 CORRECTING DEFECT 36 (vertices=19, convex hull=31, v0=129125) After retessellation of defect 36 (v0=129125), euler #=-9 (156992,470662,313661) : difference with theory (-9) = 0 CORRECTING DEFECT 37 (vertices=37, convex hull=71, v0=129391) After retessellation of defect 37 (v0=129391), euler #=-8 (157011,470751,313732) : difference with theory (-8) = 0 CORRECTING DEFECT 38 (vertices=49, convex hull=86, v0=130224) After retessellation of defect 38 (v0=130224), euler #=-7 (157039,470869,313823) : difference with theory (-7) = 0 CORRECTING DEFECT 39 (vertices=17, convex hull=24, v0=130247) After retessellation of defect 39 (v0=130247), euler #=-6 (157040,470879,313833) : difference with theory (-6) = 0 CORRECTING DEFECT 40 (vertices=64, convex hull=62, v0=132955) After retessellation of defect 40 (v0=132955), euler #=-5 (157052,470940,313883) : difference with theory (-5) = 0 CORRECTING DEFECT 41 (vertices=36, convex hull=68, v0=133006) After retessellation of defect 41 (v0=133006), euler #=-4 (157076,471037,313957) : difference with theory (-4) = 0 CORRECTING DEFECT 42 (vertices=48, convex hull=70, v0=134234) After retessellation of defect 42 (v0=134234), euler #=-3 (157100,471140,314037) : difference with theory (-3) = 0 CORRECTING DEFECT 43 (vertices=43, convex hull=97, v0=136824) After retessellation of defect 43 (v0=136824), euler #=-2 (157117,471233,314114) : difference with theory (-2) = 0 CORRECTING DEFECT 44 (vertices=26, convex hull=65, v0=137805) After retessellation of defect 44 (v0=137805), euler #=-1 (157130,471297,314166) : difference with theory (-1) = 0 CORRECTING DEFECT 45 (vertices=20, convex hull=53, v0=139509) After retessellation of defect 45 (v0=139509), euler #=0 (157144,471363,314219) : difference with theory (0) = 0 CORRECTING DEFECT 46 (vertices=60, convex hull=72, v0=156898) After retessellation of defect 46 (v0=156898), euler #=1 (157167,471462,314296) : difference with theory (1) = 0 CORRECTING DEFECT 47 (vertices=44, convex hull=86, v0=158920) After retessellation of defect 47 (v0=158920), euler #=2 (157189,471561,314374) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.23 (0.06-->11.67) (max @ vno 104454 --> 107941) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.23 (0.06-->11.67) (max @ vno 104454 --> 107941) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 174 mutations (34.7%), 327 crossovers (65.3%), 309 vertices were eliminated building final representation... 2175 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=157189, nf=314374, ne=471561, g=0) writing corrected surface to /output_dir/freesurfer/sub-01/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 40.3 minutes 0 defective edges removing intersecting faces 000: 342 intersecting mris_fix_topology utimesec 1803.424817 mris_fix_topology stimesec 3.280524 mris_fix_topology ru_maxrss 494772 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 122820 mris_fix_topology ru_majflt 37 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 31520 mris_fix_topology ru_oublock 0 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 486 mris_fix_topology ru_nivcsw 336287 FSRUNTIME@ mris_fix_topology lh 0.6709 hours 1 threads mris_fix_topology -rusage /output_dir/freesurfer/sub-01/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 sub-01 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 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ before topology correction, eno=-48 (nv=156724, nf=313544, ne=470316, g=25) 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... 2846 ambiguous faces found in tessellation segmenting defects... 40 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 11 into 10 -merging segment 18 into 17 -merging segment 28 into 26 37 defects to be corrected 0 vertices coincident reading input surface /output_dir/freesurfer/sub-01/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.0711 (-4.5356) -vertex loglikelihood: -5.7077 (-2.8538) -normal dot loglikelihood: -3.6546 (-3.6546) -quad curv loglikelihood: -6.5171 (-3.2586) Total Loglikelihood : -24.9505 CORRECTING DEFECT 0 (vertices=25, convex hull=30, v0=14078) After retessellation of defect 0 (v0=14078), euler #=-34 (154889,463800,308877) : difference with theory (-34) = 0 CORRECTING DEFECT 1 (vertices=31, convex hull=56, v0=28669) After retessellation of defect 1 (v0=28669), euler #=-33 (154898,463851,308920) : difference with theory (-33) = 0 CORRECTING DEFECT 2 (vertices=21, convex hull=43, v0=35324) After retessellation of defect 2 (v0=35324), euler #=-32 (154908,463898,308958) : difference with theory (-32) = 0 CORRECTING DEFECT 3 (vertices=38, convex hull=63, v0=36971) After retessellation of defect 3 (v0=36971), euler #=-31 (154924,463971,309016) : difference with theory (-31) = 0 CORRECTING DEFECT 4 (vertices=31, convex hull=24, v0=54844) After retessellation of defect 4 (v0=54844), euler #=-30 (154926,463985,309029) : difference with theory (-30) = 0 CORRECTING DEFECT 5 (vertices=38, convex hull=86, v0=55529) After retessellation of defect 5 (v0=55529), euler #=-29 (154945,464079,309105) : difference with theory (-29) = 0 CORRECTING DEFECT 6 (vertices=269, convex hull=202, v0=65092) After retessellation of defect 6 (v0=65092), euler #=-28 (155038,464452,309386) : difference with theory (-28) = 0 CORRECTING DEFECT 7 (vertices=5, convex hull=13, v0=68717) After retessellation of defect 7 (v0=68717), euler #=-27 (155039,464456,309390) : difference with theory (-27) = 0 CORRECTING DEFECT 8 (vertices=41, convex hull=75, v0=73908) After retessellation of defect 8 (v0=73908), euler #=-26 (155057,464540,309457) : difference with theory (-26) = 0 CORRECTING DEFECT 9 (vertices=28, convex hull=57, v0=75597) After retessellation of defect 9 (v0=75597), euler #=-25 (155066,464585,309494) : difference with theory (-25) = 0 CORRECTING DEFECT 10 (vertices=22, convex hull=39, v0=77656) After retessellation of defect 10 (v0=77656), euler #=-23 (155073,464616,309520) : difference with theory (-24) = -1 CORRECTING DEFECT 11 (vertices=20, convex hull=21, v0=86286) After retessellation of defect 11 (v0=86286), euler #=-22 (155075,464631,309534) : difference with theory (-23) = -1 CORRECTING DEFECT 12 (vertices=5, convex hull=18, v0=89179) After retessellation of defect 12 (v0=89179), euler #=-21 (155076,464638,309541) : difference with theory (-22) = -1 CORRECTING DEFECT 13 (vertices=6, convex hull=17, v0=94221) After retessellation of defect 13 (v0=94221), euler #=-20 (155076,464642,309546) : difference with theory (-21) = -1 CORRECTING DEFECT 14 (vertices=6, convex hull=28, v0=95580) After retessellation of defect 14 (v0=95580), euler #=-19 (155077,464653,309557) : difference with theory (-20) = -1 CORRECTING DEFECT 15 (vertices=34, convex hull=44, v0=96077) After retessellation of defect 15 (v0=96077), euler #=-18 (155085,464692,309589) : difference with theory (-19) = -1 CORRECTING DEFECT 16 (vertices=196, convex hull=95, v0=97453) After retessellation of defect 16 (v0=97453), euler #=-16 (155135,464888,309737) : difference with theory (-18) = -2 CORRECTING DEFECT 17 (vertices=23, convex hull=35, v0=102192) After retessellation of defect 17 (v0=102192), euler #=-15 (155141,464917,309761) : difference with theory (-17) = -2 CORRECTING DEFECT 18 (vertices=39, convex hull=78, v0=107012) After retessellation of defect 18 (v0=107012), euler #=-14 (155155,464991,309822) : difference with theory (-16) = -2 CORRECTING DEFECT 19 (vertices=31, convex hull=60, v0=108309) After retessellation of defect 19 (v0=108309), euler #=-13 (155164,465042,309865) : difference with theory (-15) = -2 CORRECTING DEFECT 20 (vertices=82, convex hull=34, v0=108926) After retessellation of defect 20 (v0=108926), euler #=-12 (155170,465071,309889) : difference with theory (-14) = -2 CORRECTING DEFECT 21 (vertices=32, convex hull=53, v0=109362) After retessellation of defect 21 (v0=109362), euler #=-11 (155188,465144,309945) : difference with theory (-13) = -2 CORRECTING DEFECT 22 (vertices=117, convex hull=47, v0=111474) After retessellation of defect 22 (v0=111474), euler #=-10 (155199,465195,309986) : difference with theory (-12) = -2 CORRECTING DEFECT 23 (vertices=143, convex hull=87, v0=117111) After retessellation of defect 23 (v0=117111), euler #=-9 (155217,465290,310064) : difference with theory (-11) = -2 CORRECTING DEFECT 24 (vertices=145, convex hull=115, v0=117223) After retessellation of defect 24 (v0=117223), euler #=-9 (155269,465510,310232) : difference with theory (-10) = -1 CORRECTING DEFECT 25 (vertices=83, convex hull=94, v0=121568) After retessellation of defect 25 (v0=121568), euler #=-9 (155295,465634,310330) : difference with theory (-9) = 0 CORRECTING DEFECT 26 (vertices=18, convex hull=24, v0=124406) After retessellation of defect 26 (v0=124406), euler #=-8 (155298,465650,310344) : difference with theory (-8) = 0 CORRECTING DEFECT 27 (vertices=17, convex hull=52, v0=130582) After retessellation of defect 27 (v0=130582), euler #=-7 (155308,465701,310386) : difference with theory (-7) = 0 CORRECTING DEFECT 28 (vertices=37, convex hull=25, v0=130752) After retessellation of defect 28 (v0=130752), euler #=-6 (155314,465729,310409) : difference with theory (-6) = 0 CORRECTING DEFECT 29 (vertices=66, convex hull=103, v0=138770) After retessellation of defect 29 (v0=138770), euler #=-5 (155347,465886,310534) : difference with theory (-5) = 0 CORRECTING DEFECT 30 (vertices=48, convex hull=61, v0=140509) After retessellation of defect 30 (v0=140509), euler #=-4 (155370,465978,310604) : difference with theory (-4) = 0 CORRECTING DEFECT 31 (vertices=37, convex hull=66, v0=145514) After retessellation of defect 31 (v0=145514), euler #=-3 (155379,466034,310652) : difference with theory (-3) = 0 CORRECTING DEFECT 32 (vertices=18, convex hull=47, v0=147878) After retessellation of defect 32 (v0=147878), euler #=-2 (155389,466085,310694) : difference with theory (-2) = 0 CORRECTING DEFECT 33 (vertices=25, convex hull=34, v0=155410) After retessellation of defect 33 (v0=155410), euler #=-1 (155392,466112,310719) : difference with theory (-1) = 0 CORRECTING DEFECT 34 (vertices=28, convex hull=68, v0=156125) After retessellation of defect 34 (v0=156125), euler #=0 (155408,466186,310778) : difference with theory (0) = 0 CORRECTING DEFECT 35 (vertices=27, convex hull=70, v0=156399) After retessellation of defect 35 (v0=156399), euler #=1 (155425,466266,310842) : difference with theory (1) = 0 CORRECTING DEFECT 36 (vertices=5, convex hull=13, v0=156696) After retessellation of defect 36 (v0=156696), euler #=2 (155426,466272,310848) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.22 (0.10-->7.28) (max @ vno 68651 --> 76012) 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 (0.10-->7.28) (max @ vno 68651 --> 76012) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 154 mutations (38.2%), 249 crossovers (61.8%), 120 vertices were eliminated building final representation... 1298 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=155426, nf=310848, ne=466272, g=0) writing corrected surface to /output_dir/freesurfer/sub-01/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 29.0 minutes 0 defective edges removing intersecting faces 000: 222 intersecting mris_fix_topology utimesec 1135.916264 mris_fix_topology stimesec 2.155086 mris_fix_topology ru_maxrss 487992 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 121092 mris_fix_topology ru_majflt 1 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 25064 mris_fix_topology ru_oublock 0 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 442 mris_fix_topology ru_nivcsw 227809 FSRUNTIME@ mris_fix_topology rh 0.4837 hours 1 threads PIDs (2503 2506) completed and logs appended. mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 157189 - 471561 + 314374 = 2 --> 0 holes F =2V-4: 314374 = 314378-4 (0) 2E=3F: 943122 = 943122 (0) total defect index = 0 mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 155426 - 466272 + 310848 = 2 --> 0 holes F =2V-4: 310848 = 310852-4 (0) 2E=3F: 932544 = 932544 (0) total defect index = 0 /output_dir/freesurfer/sub-01/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 42 intersecting 001: 4 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated /output_dir/freesurfer/sub-01/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 37 intersecting 001: 2 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf lh Thu May 7 20:44:33 UTC 2020 /output_dir/freesurfer/sub-01/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub-01 lh #-------------------------------------------- #@# Make White Surf rh Thu May 7 20:44:34 UTC 2020 /output_dir/freesurfer/sub-01/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub-01 rh Waiting for PID 2591 of (2591 2594) to complete... Waiting for PID 2594 of (2591 2594) to complete... mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub-01 lh using white.preaparc as white matter name... only generating white matter surface using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /output_dir/freesurfer/sub-01/mri/filled.mgz... reading volume /output_dir/freesurfer/sub-01/mri/brain.finalsurfs.mgz... reading volume /output_dir/freesurfer/sub-01/mri/../mri/aseg.presurf.mgz... reading volume /output_dir/freesurfer/sub-01/mri/wm.mgz... 29674 bright wm thresholded. 67 bright non-wm voxels segmented. reading original surface position from /output_dir/freesurfer/sub-01/surf/lh.orig... computing class statistics... border white: 299912 voxels (1.79%) border gray 323525 voxels (1.93%) WM (104.0): 103.2 +- 6.1 [70.0 --> 110.0] GM (84.0) : 82.9 +- 9.9 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 70.1 (was 70) setting MAX_BORDER_WHITE to 113.1 (was 105) setting MIN_BORDER_WHITE to 80.0 (was 85) setting MAX_CSF to 60.1 (was 40) setting MAX_GRAY to 100.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 70.1 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 50.2 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.02-->4.04) (max @ vno 104453 --> 156697) face area 0.28 +- 0.12 (0.00-->3.13) mean absolute distance = 0.86 +- 1.01 4336 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=107+-3.5, GM=80+-6.1 mean inside = 100.0, mean outside = 85.9 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group mean border=87.8, 101 (101) missing vertices, mean dist 0.4 [0.7 (%28.9)->0.9 (%71.1))] %55 local maxima, %40 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=cc316, 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 0.93 +- 0.26 (0.05-->7.02) (max @ vno 156697 --> 104453) face area 0.28 +- 0.13 (0.00-->3.30) mean absolute distance = 0.40 +- 0.60 4573 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2963455.2, rms=8.756 001: dt: 0.5000, sse=1847544.9, rms=6.365 (27.306%) 002: dt: 0.5000, sse=1299131.1, rms=4.734 (25.627%) 003: dt: 0.5000, sse=1017080.6, rms=3.621 (23.518%) 004: dt: 0.5000, sse=878388.4, rms=2.908 (19.670%) 005: dt: 0.5000, sse=818517.7, rms=2.512 (13.632%) 006: dt: 0.5000, sse=790514.9, rms=2.302 (8.351%) 007: dt: 0.5000, sse=774301.8, rms=2.204 (4.254%) 008: dt: 0.5000, sse=767529.8, rms=2.146 (2.628%) rms = 2.12, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=764616.9, rms=2.119 (1.253%) 010: dt: 0.2500, sse=701723.1, rms=1.414 (33.299%) 011: dt: 0.2500, sse=694262.4, rms=1.306 (7.627%) rms = 1.29, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=693306.5, rms=1.287 (1.418%) rms = 1.27, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=690876.4, rms=1.270 (1.351%) positioning took 2.2 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group mean border=90.5, 61 (12) missing vertices, mean dist -0.3 [0.5 (%72.9)->0.2 (%27.1))] %71 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=cc316, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.24 (0.09-->8.25) (max @ vno 104454 --> 104453) face area 0.36 +- 0.16 (0.00-->5.29) mean absolute distance = 0.29 +- 0.37 4267 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1320895.4, rms=4.086 014: dt: 0.5000, sse=1032642.9, rms=2.672 (34.604%) 015: dt: 0.5000, sse=945727.5, rms=2.122 (20.583%) 016: dt: 0.5000, sse=913407.4, rms=1.849 (12.866%) rms = 1.80, time step reduction 1 of 3 to 0.250... 017: dt: 0.5000, sse=903088.6, rms=1.804 (2.462%) 018: dt: 0.2500, sse=859688.3, rms=1.231 (31.732%) 019: dt: 0.2500, sse=853558.3, rms=1.118 (9.170%) rms = 1.11, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=851279.1, rms=1.105 (1.183%) rms = 1.09, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=851414.1, rms=1.091 (1.315%) positioning took 1.3 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=93.1, 54 (10) missing vertices, mean dist -0.2 [0.3 (%78.2)->0.2 (%21.8))] %86 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=cc316, 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 (0.07-->8.62) (max @ vno 104454 --> 104453) face area 0.34 +- 0.16 (0.00-->5.48) mean absolute distance = 0.19 +- 0.27 4002 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1102499.4, rms=3.294 022: dt: 0.5000, sse=879403.8, rms=1.828 (44.521%) 023: dt: 0.5000, sse=854618.7, rms=1.618 (11.457%) 024: dt: 0.5000, sse=846661.6, rms=1.564 (3.359%) rms = 1.72, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=817568.1, rms=1.172 (25.063%) 026: dt: 0.2500, sse=807632.1, rms=1.011 (13.756%) rms = 1.00, time step reduction 2 of 3 to 0.125... 027: dt: 0.2500, sse=806966.3, rms=1.004 (0.710%) rms = 0.99, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=806440.2, rms=0.994 (0.909%) positioning took 1.3 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=93.8, 58 (7) missing vertices, mean dist -0.1 [0.2 (%60.8)->0.2 (%39.2))] %90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=cc316, 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 /output_dir/freesurfer/sub-01/surf/lh.white.preaparc... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=815697.8, rms=1.377 029: dt: 0.5000, sse=788149.0, rms=0.970 (29.546%) rms = 1.28, time step reduction 1 of 3 to 0.250... 030: dt: 0.2500, sse=778826.1, rms=0.805 (16.980%) rms = 0.80, time step reduction 2 of 3 to 0.125... 031: dt: 0.2500, sse=778287.3, rms=0.798 (0.860%) rms = 0.78, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=776641.8, rms=0.781 (2.159%) positioning took 0.8 minutes generating cortex label... 21 non-cortical segments detected only using segment with 8559 vertices erasing segment 1 (vno[0] = 68660) erasing segment 2 (vno[0] = 71167) erasing segment 3 (vno[0] = 82384) erasing segment 4 (vno[0] = 84790) erasing segment 5 (vno[0] = 88279) erasing segment 6 (vno[0] = 89452) erasing segment 7 (vno[0] = 94001) erasing segment 8 (vno[0] = 101228) erasing segment 9 (vno[0] = 116603) erasing segment 10 (vno[0] = 117585) erasing segment 11 (vno[0] = 118604) erasing segment 12 (vno[0] = 118753) erasing segment 13 (vno[0] = 119775) erasing segment 14 (vno[0] = 119809) erasing segment 15 (vno[0] = 120871) erasing segment 16 (vno[0] = 120883) erasing segment 17 (vno[0] = 121035) erasing segment 18 (vno[0] = 121879) erasing segment 19 (vno[0] = 122980) erasing segment 20 (vno[0] = 124790) writing cortex label to /output_dir/freesurfer/sub-01/label/lh.cortex.label... writing curvature file /output_dir/freesurfer/sub-01/surf/lh.curv writing smoothed area to lh.area writing curvature file /output_dir/freesurfer/sub-01/surf/lh.area vertex spacing 0.89 +- 0.25 (0.02-->8.59) (max @ vno 104453 --> 104454) face area 0.33 +- 0.16 (0.00-->5.39) refinement took 8.4 minutes mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub-01 rh using white.preaparc as white matter name... only generating white matter surface using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /output_dir/freesurfer/sub-01/mri/filled.mgz... reading volume /output_dir/freesurfer/sub-01/mri/brain.finalsurfs.mgz... reading volume /output_dir/freesurfer/sub-01/mri/../mri/aseg.presurf.mgz... reading volume /output_dir/freesurfer/sub-01/mri/wm.mgz... 29674 bright wm thresholded. 67 bright non-wm voxels segmented. reading original surface position from /output_dir/freesurfer/sub-01/surf/rh.orig... computing class statistics... border white: 299912 voxels (1.79%) border gray 323525 voxels (1.93%) WM (104.0): 103.2 +- 6.1 [70.0 --> 110.0] GM (84.0) : 82.9 +- 9.9 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 71.1 (was 70) setting MAX_BORDER_WHITE to 113.1 (was 105) setting MIN_BORDER_WHITE to 81.0 (was 85) setting MAX_CSF to 61.1 (was 40) setting MAX_GRAY to 100.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 71.1 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 51.2 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.02-->3.70) (max @ vno 71193 --> 71234) face area 0.28 +- 0.12 (0.00-->2.60) mean absolute distance = 0.84 +- 1.01 4128 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=107+-3.5, GM=81+-6.1 mean inside = 100.0, mean outside = 86.3 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group mean border=88.6, 74 (74) missing vertices, mean dist 0.4 [0.7 (%30.1)->0.9 (%69.9))] %56 local maxima, %40 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=cc316, 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 0.93 +- 0.26 (0.09-->5.25) (max @ vno 154966 --> 66177) face area 0.28 +- 0.13 (0.00-->2.86) mean absolute distance = 0.40 +- 0.62 4147 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2791281.8, rms=8.487 001: dt: 0.5000, sse=1751302.0, rms=6.147 (27.567%) 002: dt: 0.5000, sse=1232538.6, rms=4.553 (25.942%) 003: dt: 0.5000, sse=976289.1, rms=3.486 (23.430%) 004: dt: 0.5000, sse=849948.1, rms=2.816 (19.218%) 005: dt: 0.5000, sse=795795.4, rms=2.459 (12.686%) 006: dt: 0.5000, sse=770325.0, rms=2.271 (7.622%) 007: dt: 0.5000, sse=760453.1, rms=2.186 (3.770%) 008: dt: 0.5000, sse=754458.4, rms=2.132 (2.483%) rms = 2.11, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=752619.8, rms=2.113 (0.857%) 010: dt: 0.2500, sse=693866.8, rms=1.451 (31.331%) 011: dt: 0.2500, sse=686954.4, rms=1.356 (6.554%) rms = 1.34, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=685417.1, rms=1.336 (1.443%) rms = 1.32, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=684312.1, rms=1.322 (1.096%) positioning took 2.2 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=91.1, 76 (22) missing vertices, mean dist -0.3 [0.5 (%71.9)->0.2 (%28.1))] %71 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=cc316, 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-->5.60) (max @ vno 154966 --> 66177) face area 0.36 +- 0.16 (0.00-->3.85) mean absolute distance = 0.30 +- 0.39 4157 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1251157.6, rms=3.880 014: dt: 0.5000, sse=983122.1, rms=2.479 (36.104%) 015: dt: 0.5000, sse=912767.1, rms=1.980 (20.143%) 016: dt: 0.5000, sse=885184.9, rms=1.750 (11.622%) rms = 1.74, time step reduction 1 of 3 to 0.250... 017: dt: 0.5000, sse=881959.6, rms=1.738 (0.695%) 018: dt: 0.2500, sse=843152.0, rms=1.215 (30.052%) 019: dt: 0.2500, sse=837449.6, rms=1.123 (7.601%) rms = 1.11, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=836404.6, rms=1.108 (1.345%) rms = 1.09, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=837515.7, rms=1.092 (1.469%) positioning took 1.3 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group mean border=93.6, 90 (14) missing vertices, mean dist -0.2 [0.3 (%77.5)->0.2 (%22.5))] %86 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=cc316, 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-->5.59) (max @ vno 154966 --> 66177) face area 0.34 +- 0.16 (0.00-->3.77) mean absolute distance = 0.20 +- 0.29 3673 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1065980.4, rms=3.178 022: dt: 0.5000, sse=860292.9, rms=1.775 (44.158%) 023: dt: 0.5000, sse=837299.2, rms=1.550 (12.676%) rms = 1.50, time step reduction 1 of 3 to 0.250... 024: dt: 0.5000, sse=828573.6, rms=1.501 (3.169%) 025: dt: 0.2500, sse=799601.4, rms=1.047 (30.237%) rms = 1.00, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=800547.7, rms=0.997 (4.747%) rms = 0.99, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=794074.1, rms=0.985 (1.202%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 1 vertex label from ripped group mean border=94.3, 80 (7) missing vertices, mean dist -0.1 [0.2 (%60.4)->0.2 (%39.6))] %90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=cc316, 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 /output_dir/freesurfer/sub-01/surf/rh.white.preaparc... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=800702.0, rms=1.347 028: dt: 0.5000, sse=775113.3, rms=0.939 (30.324%) rms = 1.24, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=766032.4, rms=0.801 (14.640%) rms = 0.80, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=765243.4, rms=0.797 (0.524%) rms = 0.79, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=768148.0, rms=0.785 (1.485%) positioning took 0.8 minutes generating cortex label... 8 non-cortical segments detected only using segment with 8624 vertices erasing segment 1 (vno[0] = 110592) erasing segment 2 (vno[0] = 113658) erasing segment 3 (vno[0] = 114565) erasing segment 4 (vno[0] = 114627) erasing segment 5 (vno[0] = 114741) erasing segment 6 (vno[0] = 118103) erasing segment 7 (vno[0] = 118137) writing cortex label to /output_dir/freesurfer/sub-01/label/rh.cortex.label... writing curvature file /output_dir/freesurfer/sub-01/surf/rh.curv writing smoothed area to rh.area writing curvature file /output_dir/freesurfer/sub-01/surf/rh.area vertex spacing 0.89 +- 0.25 (0.04-->5.57) (max @ vno 66177 --> 154966) face area 0.33 +- 0.15 (0.00-->3.78) refinement took 8.2 minutes PIDs (2591 2594) completed and logs appended. #-------------------------------------------- #@# Smooth2 lh Thu May 7 20:53:00 UTC 2020 /output_dir/freesurfer/sub-01/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm #-------------------------------------------- #@# Smooth2 rh Thu May 7 20:53:00 UTC 2020 /output_dir/freesurfer/sub-01/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm Waiting for PID 2633 of (2633 2636) to complete... Waiting for PID 2636 of (2633 2636) to complete... mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... PIDs (2633 2636) completed and logs appended. #-------------------------------------------- #@# Inflation2 lh Thu May 7 20:53:10 UTC 2020 /output_dir/freesurfer/sub-01/scripts mris_inflate -rusage /output_dir/freesurfer/sub-01/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated #-------------------------------------------- #@# Inflation2 rh Thu May 7 20:53:10 UTC 2020 /output_dir/freesurfer/sub-01/scripts mris_inflate -rusage /output_dir/freesurfer/sub-01/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Waiting for PID 2675 of (2675 2678) to complete... Waiting for PID 2678 of (2675 2678) to complete... mris_inflate -rusage /output_dir/freesurfer/sub-01/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 49.5 mm, total surface area = 95603 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.173 (target=0.015) step 005: RMS=0.123 (target=0.015) step 010: RMS=0.089 (target=0.015) step 015: RMS=0.073 (target=0.015) step 020: RMS=0.061 (target=0.015) step 025: RMS=0.050 (target=0.015) step 030: RMS=0.042 (target=0.015) step 035: RMS=0.036 (target=0.015) step 040: RMS=0.031 (target=0.015) step 045: RMS=0.028 (target=0.015) step 050: RMS=0.025 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.021 (target=0.015) inflation complete. inflation took 1.1 minutes mris_inflate utimesec 43.193628 mris_inflate stimesec 0.200313 mris_inflate ru_maxrss 205492 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 49845 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 11848 mris_inflate ru_oublock 0 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 136 mris_inflate ru_nivcsw 9200 mris_inflate -rusage /output_dir/freesurfer/sub-01/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 49.1 mm, total surface area = 94050 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.174 (target=0.015) step 005: RMS=0.122 (target=0.015) step 010: RMS=0.090 (target=0.015) step 015: RMS=0.072 (target=0.015) step 020: RMS=0.061 (target=0.015) step 025: RMS=0.051 (target=0.015) step 030: RMS=0.044 (target=0.015) step 035: RMS=0.037 (target=0.015) step 040: RMS=0.033 (target=0.015) step 045: RMS=0.029 (target=0.015) step 050: RMS=0.027 (target=0.015) step 055: RMS=0.025 (target=0.015) step 060: RMS=0.024 (target=0.015) inflation complete. inflation took 1.1 minutes mris_inflate utimesec 42.328009 mris_inflate stimesec 0.184174 mris_inflate ru_maxrss 203028 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 49297 mris_inflate ru_majflt 1 mris_inflate ru_nswap 0 mris_inflate ru_inblock 11952 mris_inflate ru_oublock 0 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 136 mris_inflate ru_nivcsw 9204 PIDs (2675 2678) completed and logs appended. #-------------------------------------------- #@# Curv .H and .K lh Thu May 7 20:54:17 UTC 2020 /output_dir/freesurfer/sub-01/surf mris_curvature -w lh.white.preaparc rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated #-------------------------------------------- #@# Curv .H and .K rh Thu May 7 20:54:17 UTC 2020 /output_dir/freesurfer/sub-01/surf mris_curvature -w rh.white.preaparc rm -f rh.white.H ln -s rh.white.preaparc.H rh.white.H rm -f rh.white.K ln -s rh.white.preaparc.K rh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated cd /output_dir/freesurfer/sub-01/surf reconbatchjobs /output_dir/freesurfer/sub-01/scripts/recon-all.log mris_curvature_white_lh.cmd rm_curvature_white_lh.H.cmd ln_curvature_white_lh.H.cmd rm_curvature_white_lh.K.cmd ln_curvature_white_lh.K.cmd mris_curvature_inflated_lh.cmd mris_curvature_white_rh.cmd rm_curvature_white_rh.H.cmd ln_curvature_white_rh.H.cmd rm_curvature_white_rh.K.cmd ln_curvature_white_rh.K.cmd mris_curvature_inflated_rh.cmd Waiting for PID 2748 of (2748 2751 2754 2757 2760 2763 2766 2769 2772 2775 2778 2781) to complete... Waiting for PID 2751 of (2748 2751 2754 2757 2760 2763 2766 2769 2772 2775 2778 2781) to complete... Waiting for PID 2754 of (2748 2751 2754 2757 2760 2763 2766 2769 2772 2775 2778 2781) to complete... Waiting for PID 2757 of (2748 2751 2754 2757 2760 2763 2766 2769 2772 2775 2778 2781) to complete... Waiting for PID 2760 of (2748 2751 2754 2757 2760 2763 2766 2769 2772 2775 2778 2781) to complete... Waiting for PID 2763 of (2748 2751 2754 2757 2760 2763 2766 2769 2772 2775 2778 2781) to complete... Waiting for PID 2766 of (2748 2751 2754 2757 2760 2763 2766 2769 2772 2775 2778 2781) to complete... Waiting for PID 2769 of (2748 2751 2754 2757 2760 2763 2766 2769 2772 2775 2778 2781) to complete... Waiting for PID 2772 of (2748 2751 2754 2757 2760 2763 2766 2769 2772 2775 2778 2781) to complete... Waiting for PID 2775 of (2748 2751 2754 2757 2760 2763 2766 2769 2772 2775 2778 2781) to complete... Waiting for PID 2778 of (2748 2751 2754 2757 2760 2763 2766 2769 2772 2775 2778 2781) to complete... Waiting for PID 2781 of (2748 2751 2754 2757 2760 2763 2766 2769 2772 2775 2778 2781) to complete... mris_curvature -w lh.white.preaparc total integrated curvature = 1.524*4pi (19.145) --> -1 handles ICI = 163.2, FI = 1989.6, variation=30361.852 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 204 vertices thresholded to be in k1 ~ [-0.36 0.59], k2 ~ [-0.19 0.10] total integrated curvature = 0.486*4pi (6.112) --> 1 handles ICI = 1.6, FI = 10.1, variation=172.602 165 vertices thresholded to be in [-0.04 0.02] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 141 vertices thresholded to be in [-0.14 0.26] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.015, std = 0.022 done. mris_curvature -w rh.white.preaparc total integrated curvature = 2.758*4pi (34.662) --> -2 handles ICI = 170.6, FI = 2005.0, variation=30807.982 writing Gaussian curvature to ./rh.white.preaparc.K...done. writing mean curvature to ./rh.white.preaparc.H...done. rm -f rh.white.H ln -s rh.white.preaparc.H rh.white.H rm -f rh.white.K ln -s rh.white.preaparc.K rh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 214 vertices thresholded to be in k1 ~ [-0.70 0.39], k2 ~ [-0.20 0.17] total integrated curvature = 0.508*4pi (6.384) --> 0 handles ICI = 1.6, FI = 9.9, variation=172.860 177 vertices thresholded to be in [-0.06 0.01] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 123 vertices thresholded to be in [-0.18 0.15] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.015, std = 0.022 done. PIDs (2748 2751 2754 2757 2760 2763 2766 2769 2772 2775 2778 2781) completed and logs appended. #----------------------------------------- #@# Curvature Stats lh Thu May 7 20:56:22 UTC 2020 /output_dir/freesurfer/sub-01/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub-01 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 [ sub-01/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 [ 287 ] Gb_filter = 0 WARN: S lookup min: -0.853360 WARN: S explicit min: 0.000000 vertex = 125 #----------------------------------------- #@# Curvature Stats rh Thu May 7 20:56:28 UTC 2020 /output_dir/freesurfer/sub-01/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm sub-01 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 [ sub-01/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 [ 302 ] Gb_filter = 0 WARN: S lookup min: -0.289835 WARN: S explicit min: 0.000000 vertex = 779 #-------------------------------------------- #@# Sphere lh Thu May 7 20:56:33 UTC 2020 /output_dir/freesurfer/sub-01/scripts mris_sphere -rusage /output_dir/freesurfer/sub-01/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere #-------------------------------------------- #@# Sphere rh Thu May 7 20:56:34 UTC 2020 /output_dir/freesurfer/sub-01/scripts mris_sphere -rusage /output_dir/freesurfer/sub-01/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere Waiting for PID 2876 of (2876 2879) to complete... Waiting for PID 2879 of (2876 2879) to complete... mris_sphere -rusage /output_dir/freesurfer/sub-01/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.288... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=cc316, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.33 pass 1: epoch 2 of 3 starting distance error %19.30 unfolding complete - removing small folds... starting distance error %19.25 removing remaining folds... final distance error %19.27 MRISunfold() return, current seed 1234 -01: dt=0.0000, 136 negative triangles 183: dt=0.9900, 136 negative triangles 184: dt=0.9900, 71 negative triangles 185: dt=0.9900, 54 negative triangles 186: dt=0.9900, 46 negative triangles 187: dt=0.9900, 42 negative triangles 188: dt=0.9900, 32 negative triangles 189: dt=0.9900, 25 negative triangles 190: dt=0.9900, 18 negative triangles 191: dt=0.9900, 18 negative triangles 192: dt=0.9900, 11 negative triangles 193: dt=0.9900, 8 negative triangles 194: dt=0.9900, 6 negative triangles 195: dt=0.9900, 6 negative triangles 196: dt=0.9900, 6 negative triangles 197: dt=0.9900, 3 negative triangles 198: dt=0.9900, 2 negative triangles 199: dt=0.9900, 1 negative triangles 200: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 1.35 hours mris_sphere utimesec 3181.903272 mris_sphere stimesec 6.066424 mris_sphere ru_maxrss 281280 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 68705 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 16976 mris_sphere ru_oublock 0 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 176 mris_sphere ru_nivcsw 640961 FSRUNTIME@ mris_sphere 1.3478 hours 1 threads mris_sphere -rusage /output_dir/freesurfer/sub-01/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.290... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=cc316, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.83 pass 1: epoch 2 of 3 starting distance error %19.80 unfolding complete - removing small folds... starting distance error %19.70 removing remaining folds... final distance error %19.72 MRISunfold() return, current seed 1234 -01: dt=0.0000, 156 negative triangles 198: dt=0.9900, 156 negative triangles 199: dt=0.9900, 87 negative triangles 200: dt=0.9900, 67 negative triangles 201: dt=0.9900, 77 negative triangles 202: dt=0.9900, 70 negative triangles 203: dt=0.9900, 53 negative triangles 204: dt=0.9900, 53 negative triangles 205: dt=0.9900, 52 negative triangles 206: dt=0.9900, 48 negative triangles 207: dt=0.9900, 44 negative triangles 208: dt=0.9900, 42 negative triangles 209: dt=0.9900, 47 negative triangles 210: dt=0.9900, 44 negative triangles 211: dt=0.9900, 45 negative triangles 212: dt=0.9900, 34 negative triangles 213: dt=0.9900, 34 negative triangles 214: dt=0.9900, 38 negative triangles 215: dt=0.9900, 38 negative triangles 216: dt=0.9900, 39 negative triangles 217: dt=0.9900, 33 negative triangles 218: dt=0.9900, 44 negative triangles 219: dt=0.9900, 41 negative triangles 220: dt=0.9900, 38 negative triangles 221: dt=0.9900, 40 negative triangles 222: dt=0.9900, 41 negative triangles 223: dt=0.9900, 38 negative triangles 224: dt=0.9900, 41 negative triangles 225: dt=0.9900, 40 negative triangles 226: dt=0.9900, 31 negative triangles 227: dt=0.9900, 30 negative triangles 228: dt=0.9900, 30 negative triangles 229: dt=0.9900, 31 negative triangles 230: dt=0.9900, 32 negative triangles 231: dt=0.9900, 24 negative triangles 232: dt=0.9900, 29 negative triangles 233: dt=0.9900, 26 negative triangles 234: dt=0.9900, 29 negative triangles 235: dt=0.9900, 22 negative triangles 236: dt=0.9900, 28 negative triangles 237: dt=0.9900, 26 negative triangles 238: dt=0.9900, 28 negative triangles 239: dt=0.9900, 21 negative triangles 240: dt=0.9900, 22 negative triangles 241: dt=0.9900, 26 negative triangles 242: dt=0.9900, 26 negative triangles 243: dt=0.9900, 14 negative triangles 244: dt=0.9900, 8 negative triangles 245: dt=0.9900, 12 negative triangles 246: dt=0.9900, 8 negative triangles 247: dt=0.9900, 13 negative triangles 248: dt=0.9900, 10 negative triangles 249: dt=0.9900, 4 negative triangles 250: dt=0.9900, 7 negative triangles 251: dt=0.9900, 6 negative triangles 252: dt=0.9900, 7 negative triangles 253: dt=0.9900, 5 negative triangles 254: dt=0.9900, 4 negative triangles 255: dt=0.9900, 5 negative triangles 256: dt=0.9900, 5 negative triangles 257: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 1.44 hours mris_sphere utimesec 3497.291777 mris_sphere stimesec 6.687831 mris_sphere ru_maxrss 278236 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 67951 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 16848 mris_sphere ru_oublock 0 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 225 mris_sphere ru_nivcsw 686099 FSRUNTIME@ mris_sphere 1.4363 hours 1 threads PIDs (2876 2879) completed and logs appended. #-------------------------------------------- #@# Surf Reg lh Thu May 7 22:22:44 UTC 2020 /output_dir/freesurfer/sub-01/scripts mris_register -curv -rusage /output_dir/freesurfer/sub-01/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /opt/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg #-------------------------------------------- #@# Surf Reg rh Thu May 7 22:22:45 UTC 2020 /output_dir/freesurfer/sub-01/scripts mris_register -curv -rusage /output_dir/freesurfer/sub-01/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /opt/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg Waiting for PID 2918 of (2918 2921) to complete... Waiting for PID 2921 of (2918 2921) to complete... mris_register -curv -rusage /output_dir/freesurfer/sub-01/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /opt/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /output_dir/freesurfer/sub-01/scripts cmdline mris_register -curv -rusage /output_dir/freesurfer/sub-01/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /opt/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /opt/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=cc316, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 0 randomSeed 0 tol=5.0e-01, sigma=0.0, host=cc316, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading lh.sulc curvature mean = 0.000, std = 5.535 curvature mean = 0.033, std = 0.818 curvature mean = 0.021, std = 0.846 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, -16.00) sse = 405132.7, tmin=1.5800 d=32.00 min @ (8.00, 8.00, 8.00) sse = 278214.7, tmin=3.2282 d=16.00 min @ (0.00, 0.00, -4.00) sse = 252505.0, tmin=4.8324 d=8.00 min @ (-2.00, 0.00, 0.00) sse = 240665.5, tmin=6.4098 d=4.00 min @ (0.00, 0.00, 1.00) sse = 239368.9, tmin=8.0497 d=2.00 min @ (0.00, 0.00, -0.50) sse = 239309.6, tmin=9.6686 d=1.00 min @ (0.00, 0.00, 0.25) sse = 239172.4, tmin=11.2724 d=0.50 min @ (-0.12, 0.00, 0.00) sse = 239164.8, tmin=12.9301 tol=1.0e+00, sigma=0.5, host=cc316, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 12.94 min curvature mean = 0.003, std = 0.832 curvature mean = 0.010, std = 0.940 curvature mean = -0.004, std = 0.840 curvature mean = 0.004, std = 0.975 curvature mean = -0.005, std = 0.841 curvature mean = 0.001, std = 0.989 2 Reading smoothwm curvature mean = -0.026, std = 0.292 curvature mean = 0.039, std = 0.247 curvature mean = 0.065, std = 0.335 curvature mean = 0.036, std = 0.305 curvature mean = 0.032, std = 0.526 curvature mean = 0.035, std = 0.328 curvature mean = 0.017, std = 0.672 curvature mean = 0.035, std = 0.340 curvature mean = 0.006, std = 0.782 MRISregister() return, current seed 0 -01: dt=0.0000, 75 negative triangles 125: dt=0.9900, 75 negative triangles expanding nbhd size to 1 126: dt=0.9900, 91 negative triangles 127: dt=0.9900, 71 negative triangles 128: dt=0.9900, 67 negative triangles 129: dt=0.9900, 65 negative triangles 130: dt=0.9900, 64 negative triangles 131: dt=0.9900, 60 negative triangles 132: dt=0.9900, 55 negative triangles 133: dt=0.9900, 53 negative triangles 134: dt=0.9900, 52 negative triangles 135: dt=0.9900, 57 negative triangles 136: dt=0.9900, 50 negative triangles 137: dt=0.9900, 47 negative triangles 138: dt=0.9900, 42 negative triangles 139: dt=0.9900, 40 negative triangles 140: dt=0.9900, 37 negative triangles 141: dt=0.9900, 31 negative triangles 142: dt=0.9900, 30 negative triangles 143: dt=0.9900, 30 negative triangles 144: dt=0.9900, 27 negative triangles 145: dt=0.9900, 27 negative triangles 146: dt=0.9900, 24 negative triangles 147: dt=0.9900, 23 negative triangles 148: dt=0.9900, 21 negative triangles 149: dt=0.9900, 22 negative triangles 150: dt=0.9900, 21 negative triangles 151: dt=0.9900, 18 negative triangles 152: dt=0.9900, 17 negative triangles 153: dt=0.9900, 15 negative triangles 154: dt=0.9900, 13 negative triangles 155: dt=0.9900, 13 negative triangles 156: dt=0.9900, 13 negative triangles 157: dt=0.9900, 12 negative triangles 158: dt=0.9900, 12 negative triangles 159: dt=0.9900, 11 negative triangles 160: dt=0.9900, 11 negative triangles 161: dt=0.9900, 11 negative triangles 162: dt=0.9900, 11 negative triangles 163: dt=0.9900, 11 negative triangles 164: dt=0.9900, 11 negative triangles 165: dt=0.9900, 10 negative triangles 166: dt=0.9900, 10 negative triangles 167: dt=0.9900, 9 negative triangles 168: dt=0.9900, 9 negative triangles 169: dt=0.9900, 9 negative triangles 170: dt=0.9900, 9 negative triangles 171: dt=0.9900, 9 negative triangles 172: dt=0.9900, 9 negative triangles 173: dt=0.9900, 8 negative triangles 174: dt=0.9900, 8 negative triangles 175: dt=0.9900, 7 negative triangles 176: dt=0.9900, 7 negative triangles 177: dt=0.9900, 6 negative triangles 178: dt=0.9900, 5 negative triangles 179: dt=0.9900, 6 negative triangles 180: dt=0.9900, 5 negative triangles 181: dt=0.9900, 3 negative triangles 182: dt=0.9900, 6 negative triangles 183: dt=0.9900, 3 negative triangles 184: dt=0.9900, 3 negative triangles 185: dt=0.9900, 3 negative triangles 186: dt=0.9900, 2 negative triangles 187: dt=0.9900, 1 negative triangles 188: dt=0.9900, 2 negative triangles 189: dt=0.9900, 2 negative triangles 190: dt=0.9900, 1 negative triangles 191: dt=0.9900, 3 negative triangles 192: dt=0.9900, 1 negative triangles 193: dt=0.9900, 1 negative triangles 194: dt=0.9900, 3 negative triangles 195: dt=0.9900, 1 negative triangles 196: dt=0.9900, 1 negative triangles 197: dt=0.9405, 1 negative triangles 198: dt=0.9405, 3 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 1.71 hours mris_register utimesec 4063.790591 mris_register stimesec 8.528329 mris_register ru_maxrss 260348 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 63357 mris_register ru_majflt 34 mris_register ru_nswap 0 mris_register ru_inblock 42864 mris_register ru_oublock 0 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 372 mris_register ru_nivcsw 792501 FSRUNTIME@ mris_register 1.7052 hours 1 threads mris_register -curv -rusage /output_dir/freesurfer/sub-01/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /opt/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment cwd /output_dir/freesurfer/sub-01/scripts cmdline mris_register -curv -rusage /output_dir/freesurfer/sub-01/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /opt/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /opt/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=cc316, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 1 randomSeed 0 tol=5.0e-01, sigma=0.0, host=cc316, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading rh.sulc curvature mean = -0.000, std = 5.611 curvature mean = 0.018, std = 0.810 curvature mean = 0.023, std = 0.850 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 0.00, 0.00) sse = 375956.3, tmin=1.5648 d=32.00 min @ (-8.00, -8.00, -8.00) sse = 286661.8, tmin=3.2273 d=16.00 min @ (4.00, 4.00, 4.00) sse = 259800.4, tmin=4.8360 d=8.00 min @ (-2.00, -2.00, -2.00) sse = 254046.4, tmin=6.4798 d=4.00 min @ (0.00, 1.00, 0.00) sse = 251741.7, tmin=8.2028 d=2.00 min @ (0.50, 0.00, 0.50) sse = 250844.9, tmin=9.8368 d=1.00 min @ (-0.25, 0.00, 0.00) sse = 250840.2, tmin=11.4463 d=0.50 min @ (0.12, 0.00, 0.00) sse = 250796.6, tmin=13.1289 tol=1.0e+00, sigma=0.5, host=cc316, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 13.13 min curvature mean = -0.016, std = 0.815 curvature mean = 0.009, std = 0.942 curvature mean = -0.023, std = 0.821 curvature mean = 0.004, std = 0.977 curvature mean = -0.024, std = 0.822 curvature mean = 0.001, std = 0.991 2 Reading smoothwm curvature mean = -0.027, std = 0.353 curvature mean = 0.030, std = 0.238 curvature mean = 0.055, std = 0.274 curvature mean = 0.028, std = 0.296 curvature mean = 0.029, std = 0.431 curvature mean = 0.027, std = 0.322 curvature mean = 0.014, std = 0.553 curvature mean = 0.027, std = 0.334 curvature mean = 0.004, std = 0.649 MRISregister() return, current seed 0 -01: dt=0.0000, 182 negative triangles 119: dt=0.9900, 182 negative triangles 120: dt=0.9405, 204 negative triangles expanding nbhd size to 1 121: dt=0.9900, 194 negative triangles 122: dt=0.9900, 175 negative triangles 123: dt=0.9900, 160 negative triangles 124: dt=0.9900, 160 negative triangles 125: dt=0.9900, 134 negative triangles 126: dt=0.9900, 118 negative triangles 127: dt=0.9900, 111 negative triangles 128: dt=0.9900, 115 negative triangles 129: dt=0.9900, 100 negative triangles 130: dt=0.9900, 94 negative triangles 131: dt=0.9900, 87 negative triangles 132: dt=0.9900, 76 negative triangles 133: dt=0.9900, 81 negative triangles 134: dt=0.9900, 77 negative triangles 135: dt=0.9900, 76 negative triangles 136: dt=0.9900, 69 negative triangles 137: dt=0.9900, 71 negative triangles 138: dt=0.9900, 71 negative triangles 139: dt=0.9900, 65 negative triangles 140: dt=0.9900, 61 negative triangles 141: dt=0.9900, 60 negative triangles 142: dt=0.9900, 61 negative triangles 143: dt=0.9900, 67 negative triangles 144: dt=0.9900, 54 negative triangles 145: dt=0.9900, 56 negative triangles 146: dt=0.9900, 56 negative triangles 147: dt=0.9900, 59 negative triangles 148: dt=0.9900, 61 negative triangles 149: dt=0.9900, 53 negative triangles 150: dt=0.9900, 48 negative triangles 151: dt=0.9900, 48 negative triangles 152: dt=0.9900, 49 negative triangles 153: dt=0.9900, 49 negative triangles 154: dt=0.9900, 44 negative triangles 155: dt=0.9900, 46 negative triangles 156: dt=0.9900, 43 negative triangles 157: dt=0.9900, 46 negative triangles 158: dt=0.9900, 46 negative triangles 159: dt=0.9900, 40 negative triangles 160: dt=0.9900, 37 negative triangles 161: dt=0.9900, 36 negative triangles 162: dt=0.9900, 33 negative triangles 163: dt=0.9900, 33 negative triangles 164: dt=0.9900, 28 negative triangles 165: dt=0.9900, 24 negative triangles 166: dt=0.9900, 27 negative triangles 167: dt=0.9900, 27 negative triangles 168: dt=0.9900, 28 negative triangles 169: dt=0.9900, 28 negative triangles 170: dt=0.9900, 22 negative triangles 171: dt=0.9900, 23 negative triangles 172: dt=0.9900, 25 negative triangles 173: dt=0.9900, 24 negative triangles 174: dt=0.9900, 21 negative triangles 175: dt=0.9900, 20 negative triangles 176: dt=0.9900, 24 negative triangles 177: dt=0.9900, 19 negative triangles 178: dt=0.9900, 20 negative triangles 179: dt=0.9900, 19 negative triangles 180: dt=0.9900, 17 negative triangles 181: dt=0.9900, 17 negative triangles 182: dt=0.9900, 16 negative triangles 183: dt=0.9900, 14 negative triangles 184: dt=0.9900, 12 negative triangles 185: dt=0.9900, 9 negative triangles 186: dt=0.9900, 11 negative triangles 187: dt=0.9900, 10 negative triangles 188: dt=0.9900, 10 negative triangles 189: dt=0.9900, 8 negative triangles 190: dt=0.9900, 9 negative triangles 191: dt=0.9900, 7 negative triangles 192: dt=0.9900, 9 negative triangles 193: dt=0.9900, 7 negative triangles 194: dt=0.9900, 6 negative triangles 195: dt=0.9900, 6 negative triangles 196: dt=0.9900, 7 negative triangles 197: dt=0.9900, 5 negative triangles 198: dt=0.9900, 3 negative triangles 199: dt=0.9900, 4 negative triangles 200: dt=0.9900, 2 negative triangles 201: dt=0.9900, 4 negative triangles 202: dt=0.9900, 2 negative triangles 203: dt=0.9900, 2 negative triangles 204: dt=0.9900, 1 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 1.67 hours mris_register utimesec 3936.887247 mris_register stimesec 8.213011 mris_register ru_maxrss 255700 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 62189 mris_register ru_majflt 4 mris_register ru_nswap 0 mris_register ru_inblock 35208 mris_register ru_oublock 0 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 339 mris_register ru_nivcsw 785691 FSRUNTIME@ mris_register 1.6670 hours 1 threads PIDs (2918 2921) completed and logs appended. #-------------------------------------------- #@# Jacobian white lh Fri May 8 00:05:04 UTC 2020 /output_dir/freesurfer/sub-01/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white #-------------------------------------------- #@# Jacobian white rh Fri May 8 00:05:04 UTC 2020 /output_dir/freesurfer/sub-01/scripts mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white Waiting for PID 2956 of (2956 2959) to complete... Waiting for PID 2959 of (2956 2959) to complete... mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white.preaparc... writing curvature file ../surf/lh.jacobian_white mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white.preaparc... writing curvature file ../surf/rh.jacobian_white PIDs (2956 2959) completed and logs appended. #-------------------------------------------- #@# AvgCurv lh Fri May 8 00:05:08 UTC 2020 /output_dir/freesurfer/sub-01/scripts mrisp_paint -a 5 /opt/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv #-------------------------------------------- #@# AvgCurv rh Fri May 8 00:05:08 UTC 2020 /output_dir/freesurfer/sub-01/scripts mrisp_paint -a 5 /opt/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv Waiting for PID 2998 of (2998 3001) to complete... Waiting for PID 3001 of (2998 3001) to complete... mrisp_paint -a 5 /opt/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /opt/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/lh.avg_curv... mrisp_paint -a 5 /opt/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /opt/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/rh.avg_curv... PIDs (2998 3001) completed and logs appended. #----------------------------------------- #@# Cortical Parc lh Fri May 8 00:05:11 UTC 2020 /output_dir/freesurfer/sub-01/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-01 lh ../surf/lh.sphere.reg /opt/freesurfer/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot #----------------------------------------- #@# Cortical Parc rh Fri May 8 00:05:11 UTC 2020 /output_dir/freesurfer/sub-01/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-01 rh ../surf/rh.sphere.reg /opt/freesurfer/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.annot Waiting for PID 3040 of (3040 3043) to complete... Waiting for PID 3043 of (3040 3043) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-01 lh ../surf/lh.sphere.reg /opt/freesurfer/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /opt/freesurfer/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.8 using min determinant for regularization = 0.006 0 singular and 342 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1628 labels changed using aseg relabeling using gibbs priors... 000: 3376 changed, 157189 examined... 001: 779 changed, 14182 examined... 002: 197 changed, 4332 examined... 003: 56 changed, 1151 examined... 004: 16 changed, 340 examined... 005: 8 changed, 100 examined... 006: 2 changed, 49 examined... 007: 0 changed, 15 examined... 231 labels changed using aseg 000: 126 total segments, 86 labels (336 vertices) changed 001: 41 total segments, 1 labels (1 vertices) changed 002: 40 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 7 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 2127 vertices marked for relabeling... 2127 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 27 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-01 rh ../surf/rh.sphere.reg /opt/freesurfer/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /opt/freesurfer/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.004 0 singular and 309 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1250 labels changed using aseg relabeling using gibbs priors... 000: 2957 changed, 155426 examined... 001: 702 changed, 12647 examined... 002: 164 changed, 3928 examined... 003: 46 changed, 1011 examined... 004: 24 changed, 303 examined... 005: 11 changed, 131 examined... 006: 3 changed, 69 examined... 007: 0 changed, 20 examined... 163 labels changed using aseg 000: 102 total segments, 58 labels (280 vertices) changed 001: 44 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 4 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 2013 vertices marked for relabeling... 2013 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 25 seconds. PIDs (3040 3043) completed and logs appended. #-------------------------------------------- #@# Make Pial Surf lh Fri May 8 00:05:38 UTC 2020 /output_dir/freesurfer/sub-01/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs sub-01 lh #-------------------------------------------- #@# Make Pial Surf rh Fri May 8 00:05:38 UTC 2020 /output_dir/freesurfer/sub-01/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs sub-01 rh Waiting for PID 3082 of (3082 3085) to complete... Waiting for PID 3085 of (3082 3085) to complete... mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs sub-01 lh using white.preaparc starting white location... using white.preaparc starting pial locations... using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /output_dir/freesurfer/sub-01/mri/filled.mgz... reading volume /output_dir/freesurfer/sub-01/mri/brain.finalsurfs.mgz... reading volume /output_dir/freesurfer/sub-01/mri/../mri/aseg.presurf.mgz... reading volume /output_dir/freesurfer/sub-01/mri/wm.mgz... 29674 bright wm thresholded. 67 bright non-wm voxels segmented. reading original surface position from /output_dir/freesurfer/sub-01/surf/lh.orig... computing class statistics... border white: 299912 voxels (1.79%) border gray 323525 voxels (1.93%) WM (104.0): 103.2 +- 6.1 [70.0 --> 110.0] GM (84.0) : 82.9 +- 9.9 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 70.1 (was 70) setting MAX_BORDER_WHITE to 113.1 (was 105) setting MIN_BORDER_WHITE to 80.0 (was 85) setting MAX_CSF to 60.1 (was 40) setting MAX_GRAY to 100.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 70.1 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 50.2 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=107+-3.5, GM=80+-6.1 mean inside = 100.0, mean outside = 85.9 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.89 +- 0.25 (0.02-->8.59) (max @ vno 104453 --> 104454) face area 0.33 +- 0.15 (0.00-->5.35) mean absolute distance = 0.78 +- 0.94 2791 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 3 with 7 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 6 with 10 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 3 points - only 0.00% unknown deleting segment 8 with 128 points - only 0.00% unknown mean border=87.8, 102 (102) missing vertices, mean dist 0.5 [1.3 (%10.6)->0.7 (%89.4))] %53 local maxima, %42 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=cc316, 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 0.93 +- 0.26 (0.12-->8.96) (max @ vno 104454 --> 104453) face area 0.33 +- 0.16 (0.00-->5.05) mean absolute distance = 0.39 +- 0.59 3009 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2358546.5, rms=7.322 001: dt: 0.5000, sse=1334288.5, rms=4.418 (39.655%) 002: dt: 0.5000, sse=984056.3, rms=2.823 (36.118%) 003: dt: 0.5000, sse=884918.4, rms=2.172 (23.048%) 004: dt: 0.5000, sse=851271.1, rms=1.897 (12.642%) rms = 1.86, time step reduction 1 of 3 to 0.250... 005: dt: 0.5000, sse=847522.2, rms=1.861 (1.902%) 006: dt: 0.2500, sse=810657.2, rms=1.387 (25.490%) 007: dt: 0.2500, sse=804734.8, rms=1.304 (5.977%) rms = 1.28, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=803356.6, rms=1.281 (1.751%) rms = 1.26, time step reduction 3 of 3 to 0.062... 009: dt: 0.1250, sse=802309.1, rms=1.262 (1.471%) positioning took 1.6 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 1 vertex label from ripped group deleting segment 6 with 1 points - only 0.00% unknown deleting segment 7 with 6 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown deleting segment 9 with 26 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 10 with 1 points - only 0.00% unknown mean border=90.5, 65 (12) missing vertices, mean dist -0.3 [0.5 (%71.8)->0.2 (%28.2))] %71 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=cc316, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.25 (0.03-->8.95) (max @ vno 104454 --> 104453) face area 0.36 +- 0.17 (0.00-->5.83) mean absolute distance = 0.29 +- 0.36 4368 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1292869.5, rms=3.970 010: dt: 0.5000, sse=1017072.9, rms=2.576 (35.113%) 011: dt: 0.5000, sse=932563.4, rms=1.982 (23.049%) 012: dt: 0.5000, sse=899712.4, rms=1.706 (13.959%) rms = 1.68, time step reduction 1 of 3 to 0.250... 013: dt: 0.5000, sse=894104.9, rms=1.681 (1.477%) 014: dt: 0.2500, sse=856403.4, rms=1.135 (32.475%) 015: dt: 0.2500, sse=852255.4, rms=1.055 (7.038%) rms = 1.05, time step reduction 2 of 3 to 0.125... 016: dt: 0.2500, sse=853693.4, rms=1.054 (0.053%) rms = 1.04, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=851342.1, rms=1.044 (1.021%) positioning took 1.3 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group deleting segment 5 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 7 with 9 points - only 0.00% unknown deleting segment 8 with 6 points - only 0.00% unknown deleting segment 9 with 21 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 10 with 1 points - only 0.00% unknown mean border=93.0, 63 (8) missing vertices, mean dist -0.2 [0.3 (%78.3)->0.2 (%21.7))] %86 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=cc316, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.10-->9.00) (max @ vno 104454 --> 104453) face area 0.34 +- 0.17 (0.00-->5.78) mean absolute distance = 0.19 +- 0.27 4077 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1102151.4, rms=3.280 018: dt: 0.5000, sse=882499.1, rms=1.802 (45.063%) 019: dt: 0.5000, sse=855123.1, rms=1.584 (12.074%) 020: dt: 0.5000, sse=852758.9, rms=1.531 (3.351%) rms = 1.69, time step reduction 1 of 3 to 0.250... 021: dt: 0.2500, sse=820998.1, rms=1.140 (25.549%) 022: dt: 0.2500, sse=810905.9, rms=0.983 (13.785%) rms = 0.98, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=809966.3, rms=0.975 (0.774%) rms = 0.97, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=808882.1, rms=0.965 (1.031%) positioning took 1.3 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group deleting segment 2 with 7 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 3 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 5 with 9 points - only 0.00% unknown deleting segment 6 with 31 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 7 with 4 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 8 with 1 points - only 0.00% unknown mean border=93.8, 61 (3) missing vertices, mean dist -0.1 [0.2 (%60.9)->0.2 (%39.1))] %90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=cc316, 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 /output_dir/freesurfer/sub-01/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=818594.9, rms=1.359 025: dt: 0.5000, sse=792629.4, rms=0.954 (29.802%) rms = 1.26, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=782638.6, rms=0.788 (17.399%) rms = 0.78, time step reduction 2 of 3 to 0.125... 027: dt: 0.2500, sse=781441.1, rms=0.779 (1.117%) rms = 0.76, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=780171.7, rms=0.762 (2.288%) positioning took 0.7 minutes generating cortex label... 21 non-cortical segments detected only using segment with 8574 vertices erasing segment 1 (vno[0] = 68660) erasing segment 2 (vno[0] = 81152) erasing segment 3 (vno[0] = 84790) erasing segment 4 (vno[0] = 88279) erasing segment 5 (vno[0] = 89452) erasing segment 6 (vno[0] = 92907) erasing segment 7 (vno[0] = 93996) erasing segment 8 (vno[0] = 101228) erasing segment 9 (vno[0] = 101758) erasing segment 10 (vno[0] = 117585) erasing segment 11 (vno[0] = 118604) erasing segment 12 (vno[0] = 118753) erasing segment 13 (vno[0] = 119775) erasing segment 14 (vno[0] = 119809) erasing segment 15 (vno[0] = 120871) erasing segment 16 (vno[0] = 120883) erasing segment 17 (vno[0] = 121879) erasing segment 18 (vno[0] = 122980) erasing segment 19 (vno[0] = 124790) erasing segment 20 (vno[0] = 156760) writing cortex label to /output_dir/freesurfer/sub-01/label/lh.cortex.label... writing curvature file /output_dir/freesurfer/sub-01/surf/lh.curv writing smoothed area to lh.area writing curvature file /output_dir/freesurfer/sub-01/surf/lh.area vertex spacing 0.89 +- 0.26 (0.02-->8.94) (max @ vno 104453 --> 104454) face area 0.34 +- 0.16 (0.00-->5.65) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 3 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 5 with 7 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 6 with 1 points - only 0.00% unknown deleting segment 7 with 12 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 9 with 3 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=67.6, 107 (107) missing vertices, mean dist 1.8 [0.2 (%0.0)->2.7 (%100.0))] %21 local maxima, %40 large gradients and %34 min vals, 182 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=cc316, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=22561458.0, rms=26.956 001: dt: 0.0500, sse=20336870.0, rms=25.545 (5.237%) 002: dt: 0.0500, sse=18741072.0, rms=24.482 (4.161%) 003: dt: 0.0500, sse=17516884.0, rms=23.634 (3.463%) 004: dt: 0.0500, sse=16525358.0, rms=22.924 (3.003%) 005: dt: 0.0500, sse=15690603.0, rms=22.309 (2.684%) 006: dt: 0.0500, sse=14966719.0, rms=21.761 (2.455%) 007: dt: 0.0500, sse=14325524.0, rms=21.264 (2.283%) 008: dt: 0.0500, sse=13748127.0, rms=20.807 (2.152%) 009: dt: 0.0500, sse=13221391.0, rms=20.380 (2.050%) 010: dt: 0.0500, sse=12736649.0, rms=19.979 (1.966%) positioning took 1.5 minutes mean border=67.4, 71 (51) missing vertices, mean dist 1.5 [0.1 (%0.0)->2.2 (%100.0))] %22 local maxima, %40 large gradients and %33 min vals, 159 gradients ignored tol=1.0e-04, sigma=2.0, host=cc316, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=13548689.0, rms=20.646 011: dt: 0.0500, sse=13096928.0, rms=20.278 (1.783%) 012: dt: 0.0500, sse=12675817.0, rms=19.929 (1.723%) 013: dt: 0.0500, sse=12281400.0, rms=19.596 (1.671%) 014: dt: 0.0500, sse=11910807.0, rms=19.277 (1.624%) 015: dt: 0.0500, sse=11561934.0, rms=18.973 (1.579%) 016: dt: 0.0500, sse=11232668.0, rms=18.681 (1.539%) 017: dt: 0.0500, sse=10921368.0, rms=18.401 (1.501%) 018: dt: 0.0500, sse=10626737.0, rms=18.131 (1.464%) 019: dt: 0.0500, sse=10347176.0, rms=17.872 (1.431%) 020: dt: 0.0500, sse=10081594.0, rms=17.622 (1.400%) positioning took 1.6 minutes mean border=67.3, 98 (44) missing vertices, mean dist 1.2 [0.1 (%0.6)->1.9 (%99.4))] %23 local maxima, %40 large gradients and %32 min vals, 153 gradients ignored tol=1.0e-04, sigma=2.0, host=cc316, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=10227542.0, rms=17.766 021: dt: 0.0500, sse=9968361.0, rms=17.520 (1.382%) 022: dt: 0.0500, sse=9721407.0, rms=17.283 (1.355%) 023: dt: 0.0500, sse=9484552.0, rms=17.052 (1.335%) 024: dt: 0.0500, sse=9258632.0, rms=16.829 (1.309%) 025: dt: 0.0500, sse=9043025.0, rms=16.613 (1.283%) 026: dt: 0.0500, sse=8836574.0, rms=16.403 (1.261%) 027: dt: 0.0500, sse=8637776.0, rms=16.199 (1.245%) 028: dt: 0.0500, sse=8444762.0, rms=15.998 (1.240%) 029: dt: 0.0500, sse=8257476.5, rms=15.801 (1.234%) 030: dt: 0.0500, sse=8075639.5, rms=15.607 (1.229%) positioning took 1.5 minutes mean border=67.2, 130 (38) missing vertices, mean dist 1.0 [0.1 (%5.2)->1.6 (%94.8))] %23 local maxima, %40 large gradients and %32 min vals, 155 gradients ignored tol=1.0e-04, sigma=2.0, host=cc316, 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=8183524.5, rms=15.723 031: dt: 0.5000, sse=6852342.5, rms=14.233 (9.475%) 032: dt: 0.5000, sse=5796611.0, rms=12.925 (9.189%) 033: dt: 0.5000, sse=4896347.0, rms=11.698 (9.492%) 034: dt: 0.5000, sse=4091358.0, rms=10.475 (10.457%) 035: dt: 0.5000, sse=3384878.8, rms=9.272 (11.481%) 036: dt: 0.5000, sse=2748438.2, rms=8.032 (13.375%) 037: dt: 0.5000, sse=2241619.5, rms=6.894 (14.174%) 038: dt: 0.5000, sse=1873077.1, rms=5.923 (14.080%) 039: dt: 0.5000, sse=1669721.2, rms=5.319 (10.194%) 040: dt: 0.5000, sse=1551952.1, rms=4.928 (7.361%) 041: dt: 0.5000, sse=1494567.2, rms=4.733 (3.961%) 042: dt: 0.5000, sse=1452978.9, rms=4.577 (3.294%) 043: dt: 0.5000, sse=1437462.5, rms=4.524 (1.160%) 044: dt: 0.5000, sse=1419903.9, rms=4.451 (1.598%) rms = 4.44, time step reduction 1 of 3 to 0.250... 045: dt: 0.5000, sse=1414968.0, rms=4.439 (0.268%) 046: dt: 0.2500, sse=1236544.1, rms=3.634 (18.145%) 047: dt: 0.2500, sse=1190230.2, rms=3.414 (6.059%) rms = 3.40, time step reduction 2 of 3 to 0.125... 048: dt: 0.2500, sse=1187854.0, rms=3.395 (0.538%) 049: dt: 0.1250, sse=1158007.1, rms=3.237 (4.649%) rms = 3.22, time step reduction 3 of 3 to 0.062... 050: dt: 0.1250, sse=1153691.8, rms=3.215 (0.692%) positioning took 4.0 minutes mean border=65.5, 2069 (13) missing vertices, mean dist 0.1 [0.2 (%39.0)->0.4 (%61.0))] %40 local maxima, %26 large gradients and %28 min vals, 99 gradients ignored tol=1.0e-04, sigma=1.0, host=cc316, 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=1585512.0, rms=4.248 051: dt: 0.5000, sse=1518701.9, rms=3.984 (6.218%) 052: dt: 0.5000, sse=1483547.0, rms=3.875 (2.727%) rms = 4.09, time step reduction 1 of 3 to 0.250... 053: dt: 0.2500, sse=1309920.8, rms=2.973 (23.283%) 054: dt: 0.2500, sse=1261356.9, rms=2.661 (10.499%) 055: dt: 0.2500, sse=1253175.1, rms=2.608 (1.994%) rms = 2.59, time step reduction 2 of 3 to 0.125... 056: dt: 0.2500, sse=1250362.5, rms=2.590 (0.675%) 057: dt: 0.1250, sse=1220583.1, rms=2.376 (8.264%) rms = 2.35, time step reduction 3 of 3 to 0.062... 058: dt: 0.1250, sse=1216029.1, rms=2.345 (1.309%) positioning took 2.0 minutes mean border=64.5, 2221 (12) missing vertices, mean dist 0.1 [0.1 (%38.7)->0.3 (%61.3))] %53 local maxima, %13 large gradients and %28 min vals, 124 gradients ignored tol=1.0e-04, sigma=0.5, host=cc316, 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=1291032.9, rms=2.841 rms = 3.50, time step reduction 1 of 3 to 0.250... 059: dt: 0.2500, sse=1232945.2, rms=2.463 (13.295%) 060: dt: 0.2500, sse=1220204.4, rms=2.375 (3.598%) rms = 2.37, time step reduction 2 of 3 to 0.125... 061: dt: 0.2500, sse=1217770.8, rms=2.368 (0.270%) 062: dt: 0.1250, sse=1206716.9, rms=2.282 (3.640%) rms = 2.27, time step reduction 3 of 3 to 0.062... 063: dt: 0.1250, sse=1204168.2, rms=2.266 (0.705%) positioning took 1.5 minutes mean border=63.9, 4153 (12) missing vertices, mean dist 0.0 [0.1 (%43.7)->0.2 (%56.3))] %56 local maxima, %10 large gradients and %27 min vals, 126 gradients ignored tol=1.0e-04, sigma=0.2, host=cc316, 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 /output_dir/freesurfer/sub-01/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=1221646.5, rms=2.395 rms = 2.87, time step reduction 1 of 3 to 0.250... 064: dt: 0.2500, sse=1204498.6, rms=2.266 (5.380%) rms = 2.24, time step reduction 2 of 3 to 0.125... 065: dt: 0.2500, sse=1199096.8, rms=2.240 (1.166%) rms = 2.20, time step reduction 3 of 3 to 0.062... 066: dt: 0.1250, sse=1193882.6, rms=2.196 (1.959%) positioning took 0.9 minutes writing curvature file /output_dir/freesurfer/sub-01/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /output_dir/freesurfer/sub-01/surf/lh.area.pial vertex spacing 1.01 +- 0.43 (0.04-->8.04) (max @ vno 156697 --> 104453) face area 0.40 +- 0.31 (0.00-->7.62) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 157189 vertices processed 25000 of 157189 vertices processed 50000 of 157189 vertices processed 75000 of 157189 vertices processed 100000 of 157189 vertices processed 125000 of 157189 vertices processed 150000 of 157189 vertices processed 0 of 157189 vertices processed 25000 of 157189 vertices processed 50000 of 157189 vertices processed 75000 of 157189 vertices processed 100000 of 157189 vertices processed 125000 of 157189 vertices processed 150000 of 157189 vertices processed thickness calculation complete, 370:798 truncations. 41275 vertices at 0 distance 117787 vertices at 1 distance 91300 vertices at 2 distance 34751 vertices at 3 distance 10556 vertices at 4 distance 3062 vertices at 5 distance 937 vertices at 6 distance 306 vertices at 7 distance 109 vertices at 8 distance 60 vertices at 9 distance 39 vertices at 10 distance 47 vertices at 11 distance 24 vertices at 12 distance 22 vertices at 13 distance 18 vertices at 14 distance 12 vertices at 15 distance 7 vertices at 16 distance 9 vertices at 17 distance 2 vertices at 18 distance 6 vertices at 19 distance 1 vertices at 20 distance writing curvature file /output_dir/freesurfer/sub-01/surf/lh.thickness positioning took 24.3 minutes mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs sub-01 rh using white.preaparc starting white location... using white.preaparc starting pial locations... using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /output_dir/freesurfer/sub-01/mri/filled.mgz... reading volume /output_dir/freesurfer/sub-01/mri/brain.finalsurfs.mgz... reading volume /output_dir/freesurfer/sub-01/mri/../mri/aseg.presurf.mgz... reading volume /output_dir/freesurfer/sub-01/mri/wm.mgz... 29674 bright wm thresholded. 67 bright non-wm voxels segmented. reading original surface position from /output_dir/freesurfer/sub-01/surf/rh.orig... computing class statistics... border white: 299912 voxels (1.79%) border gray 323525 voxels (1.93%) WM (104.0): 103.2 +- 6.1 [70.0 --> 110.0] GM (84.0) : 82.9 +- 9.9 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 71.1 (was 70) setting MAX_BORDER_WHITE to 113.1 (was 105) setting MIN_BORDER_WHITE to 81.0 (was 85) setting MAX_CSF to 61.1 (was 40) setting MAX_GRAY to 100.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 71.1 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 51.2 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=107+-3.5, GM=81+-6.1 mean inside = 100.0, mean outside = 86.3 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.89 +- 0.25 (0.04-->5.57) (max @ vno 66177 --> 154966) face area 0.33 +- 0.15 (0.00-->3.75) mean absolute distance = 0.76 +- 0.93 2820 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 3 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 4 with 1 points - only 0.00% unknown deleting segment 5 with 140 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 6 with 2 points - only 0.00% unknown deleting segment 7 with 18 points - only 0.00% unknown deleting segment 8 with 9 points - only 0.00% unknown removing 1 vertex label from ripped group mean border=88.6, 56 (56) missing vertices, mean dist 0.5 [1.3 (%10.6)->0.7 (%89.4))] %54 local maxima, %42 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=cc316, 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 0.93 +- 0.26 (0.06-->5.98) (max @ vno 154966 --> 66177) face area 0.33 +- 0.16 (0.00-->3.62) mean absolute distance = 0.39 +- 0.61 3374 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2180445.8, rms=6.951 001: dt: 0.5000, sse=1262289.5, rms=4.182 (39.826%) 002: dt: 0.5000, sse=949507.2, rms=2.690 (35.688%) 003: dt: 0.5000, sse=865419.4, rms=2.108 (21.635%) 004: dt: 0.5000, sse=846025.4, rms=1.854 (12.030%) rms = 1.82, time step reduction 1 of 3 to 0.250... 005: dt: 0.5000, sse=834973.6, rms=1.822 (1.726%) 006: dt: 0.2500, sse=812026.8, rms=1.367 (24.977%) 007: dt: 0.2500, sse=792888.1, rms=1.289 (5.682%) rms = 1.27, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=790281.6, rms=1.267 (1.732%) rms = 1.25, time step reduction 3 of 3 to 0.062... 009: dt: 0.1250, sse=810497.7, rms=1.250 (1.350%) positioning took 1.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 1 with 95 points - only 0.00% unknown deleting segment 2 with 9 points - only 0.00% unknown mean border=91.1, 74 (22) missing vertices, mean dist -0.3 [0.5 (%71.1)->0.2 (%28.9))] %71 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=cc316, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.08-->6.36) (max @ vno 154966 --> 66177) face area 0.36 +- 0.17 (0.00-->4.49) mean absolute distance = 0.30 +- 0.39 4297 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1240901.9, rms=3.738 010: dt: 0.5000, sse=966695.8, rms=2.349 (37.152%) 011: dt: 0.5000, sse=899600.0, rms=1.818 (22.604%) 012: dt: 0.5000, sse=874260.8, rms=1.595 (12.275%) rms = 1.62, time step reduction 1 of 3 to 0.250... 013: dt: 0.2500, sse=850442.2, rms=1.273 (20.205%) 014: dt: 0.2500, sse=841702.1, rms=1.086 (14.656%) rms = 1.05, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=847259.2, rms=1.050 (3.359%) rms = 1.04, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=836513.2, rms=1.038 (1.151%) positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 61 points - only 0.00% unknown deleting segment 1 with 43 points - only 0.00% unknown deleting segment 2 with 11 points - only 0.00% unknown deleting segment 4 with 9 points - only 0.00% unknown mean border=93.6, 70 (13) missing vertices, mean dist -0.2 [0.3 (%77.9)->0.2 (%22.1))] %86 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=cc316, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.05-->6.24) (max @ vno 154966 --> 66177) face area 0.34 +- 0.16 (0.00-->4.63) mean absolute distance = 0.20 +- 0.29 3678 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1069842.1, rms=3.181 017: dt: 0.5000, sse=865340.9, rms=1.765 (44.493%) 018: dt: 0.5000, sse=840674.5, rms=1.520 (13.882%) rms = 1.47, time step reduction 1 of 3 to 0.250... 019: dt: 0.5000, sse=832467.6, rms=1.471 (3.232%) 020: dt: 0.2500, sse=801509.0, rms=1.011 (31.251%) rms = 0.96, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=798529.8, rms=0.961 (4.940%) rms = 0.95, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=797207.4, rms=0.950 (1.240%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 119 points - only 0.00% unknown deleting segment 1 with 11 points - only 0.00% unknown deleting segment 2 with 8 points - only 0.00% unknown deleting segment 3 with 8 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 4 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 5 with 3 points - only 0.00% unknown mean border=94.3, 77 (11) missing vertices, mean dist -0.1 [0.2 (%60.3)->0.2 (%39.7))] %90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=cc316, 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 /output_dir/freesurfer/sub-01/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=803721.6, rms=1.330 023: dt: 0.5000, sse=778310.3, rms=0.923 (30.604%) rms = 1.21, time step reduction 1 of 3 to 0.250... 024: dt: 0.2500, sse=772619.9, rms=0.782 (15.333%) rms = 0.77, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=769475.9, rms=0.773 (1.075%) rms = 0.76, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=767420.2, rms=0.762 (1.507%) positioning took 0.8 minutes generating cortex label... 10 non-cortical segments detected only using segment with 8613 vertices erasing segment 1 (vno[0] = 110615) erasing segment 2 (vno[0] = 114565) erasing segment 3 (vno[0] = 114627) erasing segment 4 (vno[0] = 114686) erasing segment 5 (vno[0] = 114741) erasing segment 6 (vno[0] = 118103) erasing segment 7 (vno[0] = 118137) erasing segment 8 (vno[0] = 122501) erasing segment 9 (vno[0] = 123539) writing cortex label to /output_dir/freesurfer/sub-01/label/rh.cortex.label... writing curvature file /output_dir/freesurfer/sub-01/surf/rh.curv writing smoothed area to rh.area writing curvature file /output_dir/freesurfer/sub-01/surf/rh.area vertex spacing 0.89 +- 0.26 (0.04-->6.31) (max @ vno 66177 --> 154966) face area 0.33 +- 0.16 (0.00-->4.63) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 20 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 1 with 4 points - only 0.00% unknown deleting segment 3 with 10 points - only 0.00% unknown deleting segment 4 with 25 points - only 0.00% unknown deleting segment 8 with 51 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 9 with 1 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=68.6, 53 (53) missing vertices, mean dist 1.8 [1.5 (%0.0)->2.7 (%100.0))] %23 local maxima, %39 large gradients and %33 min vals, 212 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=cc316, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=21499110.0, rms=26.477 001: dt: 0.0500, sse=19420472.0, rms=25.117 (5.137%) 002: dt: 0.0500, sse=17930730.0, rms=24.095 (4.070%) 003: dt: 0.0500, sse=16788696.0, rms=23.280 (3.379%) 004: dt: 0.0500, sse=15865074.0, rms=22.601 (2.921%) 005: dt: 0.0500, sse=15086050.0, rms=22.011 (2.610%) 006: dt: 0.0500, sse=14410474.0, rms=21.486 (2.384%) 007: dt: 0.0500, sse=13811295.0, rms=21.009 (2.217%) 008: dt: 0.0500, sse=13270791.0, rms=20.570 (2.091%) 009: dt: 0.0500, sse=12777523.0, rms=20.161 (1.990%) 010: dt: 0.0500, sse=12322896.0, rms=19.776 (1.909%) positioning took 1.5 minutes mean border=68.4, 41 (18) missing vertices, mean dist 1.5 [0.1 (%0.0)->2.2 (%100.0))] %23 local maxima, %39 large gradients and %33 min vals, 197 gradients ignored tol=1.0e-04, sigma=2.0, host=cc316, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=13155898.0, rms=20.476 011: dt: 0.0500, sse=12731267.0, rms=20.123 (1.727%) 012: dt: 0.0500, sse=12334995.0, rms=19.787 (1.668%) 013: dt: 0.0500, sse=11963798.0, rms=19.467 (1.616%) 014: dt: 0.0500, sse=11614288.0, rms=19.161 (1.572%) 015: dt: 0.0500, sse=11284549.0, rms=18.868 (1.531%) 016: dt: 0.0500, sse=10972864.0, rms=18.586 (1.493%) 017: dt: 0.0500, sse=10677610.0, rms=18.315 (1.457%) 018: dt: 0.0500, sse=10397635.0, rms=18.055 (1.423%) 019: dt: 0.0500, sse=10131853.0, rms=17.804 (1.390%) 020: dt: 0.0500, sse=9879186.0, rms=17.562 (1.360%) positioning took 1.6 minutes mean border=68.3, 48 (15) missing vertices, mean dist 1.3 [0.1 (%0.4)->1.9 (%99.6))] %24 local maxima, %39 large gradients and %32 min vals, 195 gradients ignored tol=1.0e-04, sigma=2.0, host=cc316, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=10018070.0, rms=17.701 021: dt: 0.0500, sse=9772177.0, rms=17.464 (1.339%) 022: dt: 0.0500, sse=9537765.0, rms=17.235 (1.311%) 023: dt: 0.0500, sse=9313017.0, rms=17.012 (1.291%) 024: dt: 0.0500, sse=9098641.0, rms=16.797 (1.264%) 025: dt: 0.0500, sse=8893462.0, rms=16.588 (1.242%) 026: dt: 0.0500, sse=8696907.0, rms=16.386 (1.220%) 027: dt: 0.0500, sse=8507454.0, rms=16.188 (1.205%) 028: dt: 0.0500, sse=8323388.0, rms=15.994 (1.200%) 029: dt: 0.0500, sse=8144503.0, rms=15.803 (1.195%) 030: dt: 0.0500, sse=7970282.5, rms=15.614 (1.193%) positioning took 1.5 minutes mean border=68.1, 54 (11) missing vertices, mean dist 1.0 [0.1 (%5.1)->1.6 (%94.9))] %24 local maxima, %40 large gradients and %32 min vals, 176 gradients ignored tol=1.0e-04, sigma=2.0, host=cc316, 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=8079350.0, rms=15.733 031: dt: 0.5000, sse=6805581.0, rms=14.291 (9.166%) 032: dt: 0.5000, sse=5783166.0, rms=13.014 (8.935%) 033: dt: 0.5000, sse=4899918.0, rms=11.803 (9.307%) 034: dt: 0.5000, sse=4103876.5, rms=10.588 (10.289%) 035: dt: 0.5000, sse=3401907.0, rms=9.391 (11.311%) 036: dt: 0.5000, sse=2768565.8, rms=8.158 (13.128%) 037: dt: 0.5000, sse=2260197.8, rms=7.018 (13.977%) 038: dt: 0.5000, sse=1889988.8, rms=6.049 (13.804%) 039: dt: 0.5000, sse=1672382.5, rms=5.405 (10.649%) 040: dt: 0.5000, sse=1553208.4, rms=5.010 (7.313%) 041: dt: 0.5000, sse=1489432.6, rms=4.791 (4.367%) 042: dt: 0.5000, sse=1450152.9, rms=4.644 (3.069%) 043: dt: 0.5000, sse=1424344.5, rms=4.552 (1.983%) 044: dt: 0.5000, sse=1403479.1, rms=4.468 (1.832%) rms = 4.43, time step reduction 1 of 3 to 0.250... 045: dt: 0.5000, sse=1393393.6, rms=4.433 (0.791%) 046: dt: 0.2500, sse=1224008.4, rms=3.660 (17.438%) 047: dt: 0.2500, sse=1178747.2, rms=3.442 (5.951%) rms = 3.42, time step reduction 2 of 3 to 0.125... 048: dt: 0.2500, sse=1176228.4, rms=3.424 (0.532%) 049: dt: 0.1250, sse=1146973.4, rms=3.268 (4.546%) rms = 3.25, time step reduction 3 of 3 to 0.062... 050: dt: 0.1250, sse=1142733.1, rms=3.245 (0.695%) positioning took 4.0 minutes mean border=66.5, 1951 (5) missing vertices, mean dist 0.1 [0.2 (%38.4)->0.4 (%61.6))] %41 local maxima, %25 large gradients and %28 min vals, 87 gradients ignored tol=1.0e-04, sigma=1.0, host=cc316, 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=1584490.4, rms=4.323 051: dt: 0.5000, sse=1501009.2, rms=3.993 (7.623%) 052: dt: 0.5000, sse=1454306.2, rms=3.824 (4.227%) rms = 4.08, time step reduction 1 of 3 to 0.250... 053: dt: 0.2500, sse=1291038.6, rms=2.955 (22.740%) 054: dt: 0.2500, sse=1244697.4, rms=2.653 (10.223%) rms = 2.60, time step reduction 2 of 3 to 0.125... 055: dt: 0.2500, sse=1237305.1, rms=2.604 (1.847%) 056: dt: 0.1250, sse=1208281.4, rms=2.393 (8.078%) rms = 2.36, time step reduction 3 of 3 to 0.062... 057: dt: 0.1250, sse=1204204.6, rms=2.364 (1.207%) positioning took 1.7 minutes mean border=65.4, 2095 (4) missing vertices, mean dist 0.1 [0.1 (%37.8)->0.3 (%62.2))] %53 local maxima, %13 large gradients and %27 min vals, 109 gradients ignored tol=1.0e-04, sigma=0.5, host=cc316, 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=1281755.0, rms=2.872 rms = 3.47, time step reduction 1 of 3 to 0.250... 058: dt: 0.2500, sse=1226252.8, rms=2.512 (12.542%) 059: dt: 0.2500, sse=1212121.5, rms=2.414 (3.886%) rms = 2.40, time step reduction 2 of 3 to 0.125... 060: dt: 0.2500, sse=1208748.2, rms=2.402 (0.515%) 061: dt: 0.1250, sse=1198422.0, rms=2.321 (3.362%) rms = 2.31, time step reduction 3 of 3 to 0.062... 062: dt: 0.1250, sse=1196141.5, rms=2.307 (0.624%) positioning took 1.4 minutes mean border=64.9, 4263 (4) missing vertices, mean dist 0.0 [0.1 (%43.4)->0.2 (%56.6))] %56 local maxima, %10 large gradients and %27 min vals, 122 gradients ignored tol=1.0e-04, sigma=0.2, host=cc316, 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 /output_dir/freesurfer/sub-01/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=1210814.0, rms=2.409 rms = 2.83, time step reduction 1 of 3 to 0.250... 063: dt: 0.2500, sse=1195463.6, rms=2.293 (4.803%) rms = 2.26, time step reduction 2 of 3 to 0.125... 064: dt: 0.2500, sse=1189638.4, rms=2.264 (1.287%) rms = 2.22, time step reduction 3 of 3 to 0.062... 065: dt: 0.1250, sse=1184182.5, rms=2.218 (2.007%) positioning took 0.9 minutes writing curvature file /output_dir/freesurfer/sub-01/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /output_dir/freesurfer/sub-01/surf/rh.area.pial vertex spacing 1.01 +- 0.43 (0.06-->6.64) (max @ vno 92516 --> 93630) face area 0.40 +- 0.31 (0.00-->6.13) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 155426 vertices processed 25000 of 155426 vertices processed 50000 of 155426 vertices processed 75000 of 155426 vertices processed 100000 of 155426 vertices processed 125000 of 155426 vertices processed 150000 of 155426 vertices processed 0 of 155426 vertices processed 25000 of 155426 vertices processed 50000 of 155426 vertices processed 75000 of 155426 vertices processed 100000 of 155426 vertices processed 125000 of 155426 vertices processed 150000 of 155426 vertices processed thickness calculation complete, 449:916 truncations. 41107 vertices at 0 distance 113934 vertices at 1 distance 90095 vertices at 2 distance 35002 vertices at 3 distance 11049 vertices at 4 distance 3253 vertices at 5 distance 1050 vertices at 6 distance 339 vertices at 7 distance 117 vertices at 8 distance 67 vertices at 9 distance 51 vertices at 10 distance 34 vertices at 11 distance 25 vertices at 12 distance 21 vertices at 13 distance 19 vertices at 14 distance 14 vertices at 15 distance 17 vertices at 16 distance 17 vertices at 17 distance 13 vertices at 18 distance 8 vertices at 19 distance 10 vertices at 20 distance writing curvature file /output_dir/freesurfer/sub-01/surf/rh.thickness positioning took 23.8 minutes PIDs (3082 3085) completed and logs appended. #-------------------------------------------- #@# Surf Volume lh Fri May 8 00:29:59 UTC 2020 /output_dir/freesurfer/sub-01/surf /output_dir/freesurfer/sub-01/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume sub-01 lh /output_dir/freesurfer/sub-01/surf/lh.volume masking with /output_dir/freesurfer/sub-01/label/lh.cortex.label Total face volume 289420 Total vertex volume 285513 (mask=0) #@# sub-01 lh 285513 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Fri May 8 00:30:03 UTC 2020 /output_dir/freesurfer/sub-01/surf /output_dir/freesurfer/sub-01/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume sub-01 rh /output_dir/freesurfer/sub-01/surf/rh.volume masking with /output_dir/freesurfer/sub-01/label/rh.cortex.label Total face volume 287251 Total vertex volume 283664 (mask=0) #@# sub-01 rh 283664 vertexvol Done #-------------------------------------------- #@# Cortical ribbon mask Fri May 8 00:30:08 UTC 2020 /output_dir/freesurfer/sub-01/mri mris_volmask --aseg_name aseg.presurf --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon sub-01 SUBJECTS_DIR is /output_dir/freesurfer loading input data... computing distance to left white surface computing distance to left pial surface computing distance to right white surface computing distance to right pial surface hemi masks overlap voxels = 27 writing volume /output_dir/freesurfer/sub-01/mri/ribbon.mgz mris_volmask took 16.67 minutes writing ribbon files #----------------------------------------- #@# Parcellation Stats lh Fri May 8 00:46:49 UTC 2020 /output_dir/freesurfer/sub-01/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab sub-01 lh white mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab sub-01 lh pial #----------------------------------------- #@# Parcellation Stats rh Fri May 8 00:46:49 UTC 2020 /output_dir/freesurfer/sub-01/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab sub-01 rh white mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab sub-01 rh pial Waiting for PID 3198 of (3198 3201 3204 3207) to complete... Waiting for PID 3201 of (3198 3201 3204 3207) to complete... Waiting for PID 3204 of (3198 3201 3204 3207) to complete... Waiting for PID 3207 of (3198 3201 3204 3207) to complete... mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab sub-01 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /output_dir/freesurfer/sub-01/mri/wm.mgz... reading input surface /output_dir/freesurfer/sub-01/surf/lh.white... reading input pial surface /output_dir/freesurfer/sub-01/surf/lh.pial... reading input white surface /output_dir/freesurfer/sub-01/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 289420 Total vertex volume 285513 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1886972 mm^3 (det: 1.032398 ) lhCtxGM: 284964.013 284602.000 diff= 362.0 pctdiff= 0.127 rhCtxGM: 282764.340 282639.000 diff= 125.3 pctdiff= 0.044 lhCtxWM: 264716.121 264809.000 diff= -92.9 pctdiff=-0.035 rhCtxWM: 260828.970 261515.000 diff= -686.0 pctdiff=-0.263 SubCortGMVol 69603.000 SupraTentVol 1186125.445 (1183773.000) diff=2352.445 pctdiff=0.198 SupraTentVolNotVent 1165563.445 (1163211.000) diff=2352.445 pctdiff=0.202 BrainSegVol 1348873.000 (1345092.000) diff=3781.000 pctdiff=0.280 BrainSegVolNotVent 1323161.000 (1322654.445) diff=506.555 pctdiff=0.038 BrainSegVolNotVent 1323161.000 CerebellumVol 159735.000 VentChorVol 20562.000 3rd4th5thCSF 5150.000 CSFVol 1369.000, OptChiasmVol 215.000 MaskVol 1897316.000 1347 977 2202 2.352 0.344 0.073 0.008 5 0.4 bankssts 960 635 2004 2.946 0.607 0.112 0.017 11 0.7 caudalanteriorcingulate 3923 2594 7752 2.768 0.449 0.110 0.018 35 3.0 caudalmiddlefrontal 2641 1708 3485 1.918 0.407 0.150 0.038 39 4.1 cuneus 553 412 2214 3.689 0.625 0.123 0.035 7 0.7 entorhinal 5390 3681 11933 2.842 0.608 0.134 0.031 85 6.5 fusiform 6689 4495 11916 2.456 0.448 0.125 0.025 85 6.5 inferiorparietal 5457 3750 11980 2.747 0.662 0.127 0.028 89 6.1 inferiortemporal 2308 1487 3714 2.283 0.912 0.133 0.034 38 2.7 isthmuscingulate 9226 5863 13831 2.121 0.573 0.133 0.029 116 10.6 lateraloccipital 4260 2912 8845 2.833 0.585 0.130 0.029 60 4.9 lateralorbitofrontal 5068 3424 7774 2.074 0.652 0.141 0.035 73 7.3 lingual 3157 2084 6534 2.722 0.813 0.129 0.037 61 4.2 medialorbitofrontal 5671 3853 13779 2.896 0.665 0.125 0.027 80 5.8 middletemporal 1185 773 2517 2.749 0.726 0.078 0.012 6 0.6 parahippocampal 2137 1408 3903 2.575 0.569 0.098 0.016 14 1.4 paracentral 2456 1687 5208 2.718 0.469 0.117 0.021 27 1.9 parsopercularis 948 665 2378 2.773 0.526 0.158 0.036 18 1.4 parsorbitalis 2194 1478 4541 2.600 0.511 0.127 0.024 30 2.1 parstriangularis 2169 1452 2143 1.663 0.390 0.136 0.030 25 2.5 pericalcarine 7093 4549 10836 2.146 0.639 0.105 0.018 66 5.3 postcentral 2162 1464 4314 2.642 0.724 0.147 0.030 37 2.6 posteriorcingulate 9434 5791 17319 2.722 0.524 0.100 0.020 82 8.2 precentral 7053 4880 12746 2.379 0.493 0.125 0.025 92 6.9 precuneus 1299 854 3289 3.357 0.824 0.129 0.029 19 1.5 rostralanteriorcingulate 8820 5987 17596 2.540 0.534 0.134 0.028 130 9.9 rostralmiddlefrontal 12244 8137 26937 2.865 0.511 0.116 0.022 135 10.7 superiorfrontal 10642 7115 18225 2.279 0.481 0.123 0.023 127 9.4 superiorparietal 6900 4577 14827 2.800 0.602 0.107 0.025 94 5.7 superiortemporal 8347 5560 16240 2.602 0.531 0.122 0.022 101 7.4 supramarginal 450 305 1292 3.284 0.570 0.188 0.042 12 0.9 frontalpole 709 520 2900 3.701 0.776 0.155 0.056 19 1.4 temporalpole 1104 692 1842 2.342 0.352 0.093 0.019 9 0.8 transversetemporal 4023 2645 8473 3.147 0.715 0.119 0.032 46 4.9 insula mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab sub-01 lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /output_dir/freesurfer/sub-01/mri/wm.mgz... reading input surface /output_dir/freesurfer/sub-01/surf/lh.pial... reading input pial surface /output_dir/freesurfer/sub-01/surf/lh.pial... reading input white surface /output_dir/freesurfer/sub-01/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 289420 Total vertex volume 285513 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1886972 mm^3 (det: 1.032398 ) lhCtxGM: 284964.013 284602.000 diff= 362.0 pctdiff= 0.127 rhCtxGM: 282764.340 282639.000 diff= 125.3 pctdiff= 0.044 lhCtxWM: 264716.121 264809.000 diff= -92.9 pctdiff=-0.035 rhCtxWM: 260828.970 261515.000 diff= -686.0 pctdiff=-0.263 SubCortGMVol 69603.000 SupraTentVol 1186125.445 (1183773.000) diff=2352.445 pctdiff=0.198 SupraTentVolNotVent 1165563.445 (1163211.000) diff=2352.445 pctdiff=0.202 BrainSegVol 1348873.000 (1345092.000) diff=3781.000 pctdiff=0.280 BrainSegVolNotVent 1323161.000 (1322654.445) diff=506.555 pctdiff=0.038 BrainSegVolNotVent 1323161.000 CerebellumVol 159735.000 VentChorVol 20562.000 3rd4th5thCSF 5150.000 CSFVol 1369.000, OptChiasmVol 215.000 MaskVol 1897316.000 1347 909 2202 2.352 0.344 0.087 0.016 11 0.9 bankssts 960 809 2004 2.946 0.607 0.144 0.027 33 1.0 caudalanteriorcingulate 3923 2918 7752 2.768 0.449 0.107 0.019 40 3.0 caudalmiddlefrontal 2641 2044 3485 1.918 0.407 0.144 0.035 38 4.1 cuneus 553 810 2214 3.689 0.625 0.207 0.038 7 1.0 entorhinal 5390 4594 11933 2.842 0.608 0.145 0.035 85 8.3 fusiform 6689 5143 11916 2.456 0.448 0.129 0.027 97 8.8 inferiorparietal 5457 4800 11980 2.747 0.662 0.144 0.036 117 8.2 inferiortemporal 2308 1718 3714 2.283 0.912 0.144 0.046 70 3.8 isthmuscingulate 9226 7055 13831 2.121 0.573 0.125 0.027 122 11.4 lateraloccipital 4260 3282 8845 2.833 0.585 0.130 0.030 57 5.4 lateralorbitofrontal 5068 4111 7774 2.074 0.652 0.136 0.032 70 7.1 lingual 3157 2615 6534 2.722 0.813 0.146 0.038 62 5.1 medialorbitofrontal 5671 5386 13779 2.896 0.665 0.141 0.026 71 6.4 middletemporal 1185 1083 2517 2.749 0.726 0.121 0.025 8 1.5 parahippocampal 2137 1593 3903 2.575 0.569 0.107 0.021 17 1.9 paracentral 2456 2063 5208 2.718 0.469 0.132 0.026 27 2.5 parsopercularis 948 989 2378 2.773 0.526 0.173 0.037 17 1.6 parsorbitalis 2194 1913 4541 2.600 0.511 0.150 0.030 29 2.8 parstriangularis 2169 1191 2143 1.663 0.390 0.110 0.028 32 2.5 pericalcarine 7093 5499 10836 2.146 0.639 0.111 0.019 52 5.6 postcentral 2162 1716 4314 2.642 0.724 0.150 0.042 55 3.2 posteriorcingulate 9434 6747 17319 2.722 0.524 0.103 0.019 86 7.6 precentral 7053 5693 12746 2.379 0.493 0.136 0.027 97 8.4 precuneus 1299 1140 3289 3.357 0.824 0.153 0.037 14 2.1 rostralanteriorcingulate 8820 7563 17596 2.540 0.534 0.151 0.032 137 11.9 rostralmiddlefrontal 12244 10132 26937 2.865 0.511 0.125 0.026 139 13.2 superiorfrontal 10642 8557 18225 2.279 0.481 0.130 0.024 127 10.5 superiorparietal 6900 5675 14827 2.800 0.602 0.125 0.025 86 7.5 superiortemporal 8347 6694 16240 2.602 0.531 0.128 0.027 108 9.2 supramarginal 450 471 1292 3.284 0.570 0.183 0.033 5 0.7 frontalpole 709 980 2900 3.701 0.776 0.204 0.033 10 1.2 temporalpole 1104 923 1842 2.342 0.352 0.109 0.019 7 0.9 transversetemporal 4023 2544 8473 3.147 0.715 0.123 0.032 72 5.0 insula mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab sub-01 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /output_dir/freesurfer/sub-01/mri/wm.mgz... reading input surface /output_dir/freesurfer/sub-01/surf/rh.white... reading input pial surface /output_dir/freesurfer/sub-01/surf/rh.pial... reading input white surface /output_dir/freesurfer/sub-01/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 287251 Total vertex volume 283664 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1886972 mm^3 (det: 1.032398 ) lhCtxGM: 284964.013 284602.000 diff= 362.0 pctdiff= 0.127 rhCtxGM: 282764.340 282639.000 diff= 125.3 pctdiff= 0.044 lhCtxWM: 264716.121 264809.000 diff= -92.9 pctdiff=-0.035 rhCtxWM: 260828.970 261515.000 diff= -686.0 pctdiff=-0.263 SubCortGMVol 69603.000 SupraTentVol 1186125.445 (1183773.000) diff=2352.445 pctdiff=0.198 SupraTentVolNotVent 1165563.445 (1163211.000) diff=2352.445 pctdiff=0.202 BrainSegVol 1348873.000 (1345092.000) diff=3781.000 pctdiff=0.280 BrainSegVolNotVent 1323161.000 (1322654.445) diff=506.555 pctdiff=0.038 BrainSegVolNotVent 1323161.000 CerebellumVol 159735.000 VentChorVol 20562.000 3rd4th5thCSF 5150.000 CSFVol 1369.000, OptChiasmVol 215.000 MaskVol 1897316.000 1347 959 2487 2.614 0.424 0.098 0.016 9 0.9 bankssts 998 657 2251 3.202 0.622 0.140 0.029 18 1.2 caudalanteriorcingulate 4015 2691 8160 2.699 0.498 0.109 0.019 36 3.0 caudalmiddlefrontal 2718 1650 3522 1.895 0.539 0.134 0.033 39 3.6 cuneus 386 281 1653 3.871 0.548 0.116 0.029 4 0.5 entorhinal 5191 3505 12082 2.894 0.618 0.126 0.026 68 5.5 fusiform 9527 6199 17196 2.536 0.479 0.124 0.025 113 9.3 inferiorparietal 5498 3657 12368 2.817 0.653 0.135 0.033 87 7.8 inferiortemporal 1783 1153 3148 2.331 0.921 0.125 0.034 28 2.0 isthmuscingulate 8047 4977 12564 2.234 0.586 0.134 0.030 105 9.6 lateraloccipital 4166 2852 8458 2.590 0.889 0.136 0.038 64 6.4 lateralorbitofrontal 5032 3335 7806 2.102 0.669 0.145 0.040 71 8.3 lingual 3255 2134 6752 2.620 0.714 0.140 0.045 78 5.9 medialorbitofrontal 6294 4340 15565 2.949 0.611 0.126 0.026 82 6.7 middletemporal 1121 740 2038 2.447 0.684 0.083 0.014 6 0.6 parahippocampal 2547 1660 4445 2.522 0.492 0.100 0.015 16 1.6 paracentral 2119 1463 4192 2.627 0.396 0.119 0.022 25 1.7 parsopercularis 1328 872 2961 2.705 0.574 0.133 0.024 19 1.4 parsorbitalis 2659 1805 5325 2.534 0.504 0.129 0.027 38 3.0 parstriangularis 2535 1665 2401 1.613 0.399 0.124 0.031 30 3.8 pericalcarine 7104 4552 11028 2.199 0.578 0.109 0.021 71 5.9 postcentral 1870 1229 3562 2.664 0.559 0.127 0.029 27 2.0 posteriorcingulate 8925 5622 16571 2.693 0.570 0.098 0.017 64 5.9 precentral 6814 4627 12271 2.468 0.517 0.126 0.027 87 7.0 precuneus 775 518 1890 3.230 0.543 0.143 0.036 14 1.2 rostralanteriorcingulate 9487 6425 18357 2.490 0.504 0.131 0.027 136 10.4 rostralmiddlefrontal 11077 7515 24435 2.818 0.572 0.120 0.024 124 11.1 superiorfrontal 10834 7044 17728 2.296 0.454 0.113 0.020 116 8.9 superiorparietal 6023 4078 14092 3.057 0.554 0.116 0.022 68 5.8 superiortemporal 7290 4784 14261 2.647 0.488 0.122 0.025 88 7.1 supramarginal 502 350 1258 2.886 0.652 0.213 0.068 18 1.3 frontalpole 670 515 3126 3.873 0.784 0.153 0.049 13 1.3 temporalpole 623 350 1120 2.697 0.291 0.113 0.017 7 0.4 transversetemporal 3846 2602 8577 3.150 0.804 0.119 0.029 41 4.8 insula mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab sub-01 rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /output_dir/freesurfer/sub-01/mri/wm.mgz... reading input surface /output_dir/freesurfer/sub-01/surf/rh.pial... reading input pial surface /output_dir/freesurfer/sub-01/surf/rh.pial... reading input white surface /output_dir/freesurfer/sub-01/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 287251 Total vertex volume 283664 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1886972 mm^3 (det: 1.032398 ) lhCtxGM: 284964.013 284602.000 diff= 362.0 pctdiff= 0.127 rhCtxGM: 282764.340 282639.000 diff= 125.3 pctdiff= 0.044 lhCtxWM: 264716.121 264809.000 diff= -92.9 pctdiff=-0.035 rhCtxWM: 260828.970 261515.000 diff= -686.0 pctdiff=-0.263 SubCortGMVol 69603.000 SupraTentVol 1186125.445 (1183773.000) diff=2352.445 pctdiff=0.198 SupraTentVolNotVent 1165563.445 (1163211.000) diff=2352.445 pctdiff=0.202 BrainSegVol 1348873.000 (1345092.000) diff=3781.000 pctdiff=0.280 BrainSegVolNotVent 1323161.000 (1322654.445) diff=506.555 pctdiff=0.038 BrainSegVolNotVent 1323161.000 CerebellumVol 159735.000 VentChorVol 20562.000 3rd4th5thCSF 5150.000 CSFVol 1369.000, OptChiasmVol 215.000 MaskVol 1897316.000 1347 968 2487 2.614 0.424 0.107 0.026 15 1.4 bankssts 998 810 2251 3.202 0.622 0.135 0.035 28 1.7 caudalanteriorcingulate 4015 3168 8160 2.699 0.498 0.113 0.020 40 3.2 caudalmiddlefrontal 2718 2097 3522 1.895 0.539 0.133 0.029 31 3.3 cuneus 386 562 1653 3.871 0.548 0.195 0.038 3 0.8 entorhinal 5191 4563 12082 2.894 0.618 0.141 0.034 80 7.5 fusiform 9527 7217 17196 2.536 0.479 0.129 0.026 123 11.1 inferiorparietal 5498 4913 12368 2.817 0.653 0.151 0.034 96 8.6 inferiortemporal 1783 1416 3148 2.331 0.921 0.131 0.035 47 2.4 isthmuscingulate 8047 6096 12564 2.234 0.586 0.127 0.029 110 10.8 lateraloccipital 4166 3422 8458 2.590 0.889 0.158 0.052 102 11.4 lateralorbitofrontal 5032 4029 7806 2.102 0.669 0.140 0.035 67 7.9 lingual 3255 2919 6752 2.620 0.714 0.163 0.040 45 5.9 medialorbitofrontal 6294 6008 15565 2.949 0.611 0.146 0.026 73 7.6 middletemporal 1121 942 2038 2.447 0.684 0.123 0.027 10 1.4 parahippocampal 2547 1823 4445 2.522 0.492 0.107 0.017 24 1.9 paracentral 2119 1653 4192 2.627 0.396 0.133 0.027 34 2.3 parsopercularis 1328 1310 2961 2.705 0.574 0.162 0.028 26 1.7 parsorbitalis 2659 2335 5325 2.534 0.504 0.156 0.030 32 3.7 parstriangularis 2535 1412 2401 1.613 0.399 0.100 0.026 39 2.6 pericalcarine 7104 5527 11028 2.199 0.578 0.117 0.020 53 6.2 postcentral 1870 1458 3562 2.664 0.559 0.139 0.030 46 2.3 posteriorcingulate 8925 6550 16571 2.693 0.570 0.102 0.017 74 6.5 precentral 6814 5211 12271 2.468 0.517 0.130 0.029 119 8.2 precuneus 775 705 1890 3.230 0.543 0.183 0.044 23 1.5 rostralanteriorcingulate 9487 8154 18357 2.490 0.504 0.150 0.028 126 12.2 rostralmiddlefrontal 11077 9269 24435 2.818 0.572 0.135 0.045 194 24.9 superiorfrontal 10834 8221 17728 2.296 0.454 0.121 0.022 114 10.1 superiorparietal 6023 5107 14092 3.057 0.554 0.131 0.026 87 7.1 superiortemporal 7290 5763 14261 2.647 0.488 0.134 0.028 94 8.8 supramarginal 502 511 1258 2.886 0.652 0.191 0.039 7 0.9 frontalpole 670 995 3126 3.873 0.784 0.206 0.036 6 1.3 temporalpole 623 488 1120 2.697 0.291 0.106 0.021 3 0.6 transversetemporal 3846 2493 8577 3.150 0.804 0.124 0.031 62 4.9 insula PIDs (3198 3201 3204 3207) completed and logs appended. #----------------------------------------- #@# Cortical Parc 2 lh Fri May 8 00:49:51 UTC 2020 /output_dir/freesurfer/sub-01/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-01 lh ../surf/lh.sphere.reg /opt/freesurfer/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot #----------------------------------------- #@# Cortical Parc 2 rh Fri May 8 00:49:51 UTC 2020 /output_dir/freesurfer/sub-01/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-01 rh ../surf/rh.sphere.reg /opt/freesurfer/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.a2009s.annot Waiting for PID 3250 of (3250 3253) to complete... Waiting for PID 3253 of (3250 3253) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-01 lh ../surf/lh.sphere.reg /opt/freesurfer/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /opt/freesurfer/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 2.9 using min determinant for regularization = 0.086 0 singular and 762 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 12 labels changed using aseg relabeling using gibbs priors... 000: 10195 changed, 157189 examined... 001: 2351 changed, 39567 examined... 002: 724 changed, 12371 examined... 003: 333 changed, 4002 examined... 004: 151 changed, 1842 examined... 005: 81 changed, 844 examined... 006: 41 changed, 452 examined... 007: 28 changed, 242 examined... 008: 14 changed, 157 examined... 009: 6 changed, 76 examined... 010: 4 changed, 34 examined... 011: 1 changed, 20 examined... 012: 0 changed, 7 examined... 0 labels changed using aseg 000: 288 total segments, 204 labels (2521 vertices) changed 001: 98 total segments, 15 labels (65 vertices) changed 002: 83 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 29 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1415 vertices marked for relabeling... 1415 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 32 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-01 rh ../surf/rh.sphere.reg /opt/freesurfer/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /opt/freesurfer/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 1.4 using min determinant for regularization = 0.020 0 singular and 719 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 43 labels changed using aseg relabeling using gibbs priors... 000: 9957 changed, 155426 examined... 001: 2283 changed, 39358 examined... 002: 692 changed, 11980 examined... 003: 315 changed, 3972 examined... 004: 143 changed, 1838 examined... 005: 56 changed, 819 examined... 006: 33 changed, 326 examined... 007: 30 changed, 188 examined... 008: 23 changed, 174 examined... 009: 7 changed, 99 examined... 010: 6 changed, 40 examined... 011: 5 changed, 37 examined... 012: 4 changed, 26 examined... 013: 0 changed, 17 examined... 18 labels changed using aseg 000: 285 total segments, 194 labels (2465 vertices) changed 001: 104 total segments, 16 labels (160 vertices) changed 002: 90 total segments, 2 labels (15 vertices) changed 003: 88 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 32 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1567 vertices marked for relabeling... 1567 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 34 seconds. PIDs (3250 3253) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 2 lh Fri May 8 00:50:25 UTC 2020 /output_dir/freesurfer/sub-01/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab sub-01 lh white #----------------------------------------- #@# Parcellation Stats 2 rh Fri May 8 00:50:25 UTC 2020 /output_dir/freesurfer/sub-01/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab sub-01 rh white Waiting for PID 3292 of (3292 3295) to complete... Waiting for PID 3295 of (3292 3295) to complete... mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab sub-01 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /output_dir/freesurfer/sub-01/mri/wm.mgz... reading input surface /output_dir/freesurfer/sub-01/surf/lh.white... reading input pial surface /output_dir/freesurfer/sub-01/surf/lh.pial... reading input white surface /output_dir/freesurfer/sub-01/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 289420 Total vertex volume 285513 (mask=0) reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1886972 mm^3 (det: 1.032398 ) lhCtxGM: 284964.013 284602.000 diff= 362.0 pctdiff= 0.127 rhCtxGM: 282764.340 282639.000 diff= 125.3 pctdiff= 0.044 lhCtxWM: 264716.121 264809.000 diff= -92.9 pctdiff=-0.035 rhCtxWM: 260828.970 261515.000 diff= -686.0 pctdiff=-0.263 SubCortGMVol 69603.000 SupraTentVol 1186125.445 (1183773.000) diff=2352.445 pctdiff=0.198 SupraTentVolNotVent 1165563.445 (1163211.000) diff=2352.445 pctdiff=0.202 BrainSegVol 1348873.000 (1345092.000) diff=3781.000 pctdiff=0.280 BrainSegVolNotVent 1323161.000 (1322654.445) diff=506.555 pctdiff=0.038 BrainSegVolNotVent 1323161.000 CerebellumVol 159735.000 VentChorVol 20562.000 3rd4th5thCSF 5150.000 CSFVol 1369.000, OptChiasmVol 215.000 MaskVol 1897316.000 1636 1112 3198 2.637 0.507 0.146 0.030 25 2.0 G&S_frontomargin 2168 1454 4509 2.486 0.655 0.130 0.026 28 2.4 G&S_occipital_inf 1759 1031 3087 2.461 0.603 0.105 0.020 17 1.4 G&S_paracentral 1952 1318 4627 2.851 0.456 0.136 0.027 27 2.1 G&S_subcentral 1039 708 2558 2.838 0.709 0.170 0.041 25 1.9 G&S_transv_frontopol 2390 1651 5342 3.006 0.557 0.123 0.029 30 2.7 G&S_cingul-Ant 1247 883 2592 2.821 0.478 0.107 0.020 11 0.9 G&S_cingul-Mid-Ant 1653 1121 3177 2.737 0.517 0.131 0.029 19 1.9 G&S_cingul-Mid-Post 865 594 2299 2.979 0.614 0.171 0.044 19 1.7 G_cingul-Post-dorsal 557 344 1106 2.654 0.823 0.132 0.036 10 0.6 G_cingul-Post-ventral 2472 1578 3370 1.846 0.481 0.162 0.041 44 4.2 G_cuneus 1362 891 3499 2.985 0.395 0.124 0.026 19 1.3 G_front_inf-Opercular 461 301 1266 2.852 0.475 0.151 0.039 9 0.7 G_front_inf-Orbital 1509 1003 3638 2.744 0.493 0.146 0.030 29 1.9 G_front_inf-Triangul 4325 2747 10455 2.860 0.515 0.131 0.028 70 4.8 G_front_middle 8345 5400 20687 2.998 0.510 0.122 0.024 110 7.7 G_front_sup 922 593 2028 3.297 0.722 0.134 0.044 14 1.5 G_Ins_lg&S_cent_ins 857 547 2858 3.681 0.771 0.138 0.044 18 1.4 G_insular_short 2589 1586 5005 2.485 0.482 0.138 0.028 39 2.9 G_occipital_middle 2080 1313 3242 2.176 0.579 0.151 0.031 33 2.6 G_occipital_sup 2301 1519 5716 2.899 0.540 0.144 0.035 46 3.2 G_oc-temp_lat-fusifor 3512 2316 5845 2.091 0.717 0.152 0.041 60 5.9 G_oc-temp_med-Lingual 1423 962 4188 3.183 0.809 0.103 0.027 14 1.5 G_oc-temp_med-Parahip 2357 1597 6049 2.890 0.551 0.138 0.032 47 3.0 G_orbital 2693 1756 6143 2.671 0.501 0.138 0.027 49 2.9 G_pariet_inf-Angular 4108 2710 9545 2.793 0.545 0.132 0.026 65 4.2 G_pariet_inf-Supramar 4357 2921 8735 2.400 0.515 0.126 0.025 62 4.1 G_parietal_sup 2546 1554 4177 2.230 0.545 0.109 0.019 28 2.0 G_postcentral 3555 1947 7726 2.983 0.483 0.097 0.022 35 3.4 G_precentral 3702 2517 7724 2.455 0.507 0.138 0.030 67 4.3 G_precuneus 991 648 2767 2.979 0.677 0.155 0.046 29 2.1 G_rectus 719 438 1309 2.562 1.191 0.090 0.043 10 0.7 G_subcallosal 838 522 1622 2.460 0.379 0.103 0.023 9 0.8 G_temp_sup-G_T_transv 2397 1485 7002 3.108 0.585 0.130 0.044 66 2.8 G_temp_sup-Lateral 749 549 2345 3.551 0.628 0.083 0.014 3 0.4 G_temp_sup-Plan_polar 1243 870 2292 2.462 0.463 0.075 0.010 7 0.5 G_temp_sup-Plan_tempo 2843 1870 6766 2.732 0.704 0.136 0.038 61 4.6 G_temporal_inf 3009 1919 8684 3.161 0.596 0.128 0.028 49 3.0 G_temporal_middle 325 216 461 2.221 0.413 0.102 0.012 2 0.1 Lat_Fis-ant-Horizont 376 269 532 2.274 0.332 0.093 0.012 1 0.2 Lat_Fis-ant-Vertical 1444 984 1906 2.461 0.395 0.114 0.021 11 1.2 Lat_Fis-post 2451 1453 2818 1.788 0.455 0.140 0.033 35 3.3 Pole_occipital 1789 1318 6304 3.305 0.729 0.147 0.043 41 2.7 Pole_temporal 2657 1825 2967 1.871 0.560 0.124 0.026 23 2.9 S_calcarine 3942 2616 4754 2.021 0.604 0.093 0.018 27 3.1 S_central 1362 955 2020 2.315 0.432 0.089 0.011 6 0.7 S_cingul-Marginalis 596 421 1043 2.857 0.400 0.094 0.016 2 0.4 S_circular_insula_ant 1469 998 2344 2.838 0.568 0.088 0.014 6 0.9 S_circular_insula_inf 1946 1342 2901 2.694 0.430 0.103 0.016 10 1.4 S_circular_insula_sup 1169 795 2444 3.146 0.771 0.128 0.028 16 1.4 S_collat_transv_ant 526 389 716 2.270 0.425 0.160 0.038 7 0.7 S_collat_transv_post 2164 1500 3244 2.310 0.319 0.109 0.018 19 1.6 S_front_inf 1768 1238 3039 2.346 0.477 0.128 0.026 21 1.8 S_front_middle 3631 2544 6192 2.521 0.422 0.105 0.017 26 2.8 S_front_sup 308 216 454 2.489 0.454 0.117 0.018 2 0.3 S_interm_prim-Jensen 3696 2545 5076 2.222 0.340 0.100 0.014 23 2.2 S_intrapariet&P_trans 1185 811 1332 1.887 0.353 0.131 0.028 11 1.4 S_oc_middle&Lunatus 1885 1286 2411 2.055 0.388 0.126 0.022 17 1.7 S_oc_sup&transversal 850 573 1136 2.295 0.271 0.098 0.015 4 0.5 S_occipital_ant 1309 922 2325 2.723 0.434 0.113 0.022 12 1.1 S_oc-temp_lat 2506 1726 3624 2.277 0.467 0.114 0.023 23 2.2 S_oc-temp_med&Lingual 260 185 431 2.446 0.443 0.157 0.042 3 0.4 S_orbital_lateral 717 505 1004 2.316 0.585 0.114 0.017 5 0.4 S_orbital_med-olfact 1678 1139 3159 2.911 0.660 0.134 0.029 21 2.0 S_orbital-H_Shaped 2626 1795 3982 2.266 0.471 0.118 0.022 26 2.3 S_parieto_occipital 1689 1004 1548 2.045 1.177 0.128 0.025 32 1.4 S_pericallosal 3649 2425 5085 2.164 0.438 0.103 0.017 28 2.6 S_postcentral 1937 1334 3228 2.592 0.368 0.103 0.014 12 1.1 S_precentral-inf-part 1999 1358 3259 2.611 0.385 0.101 0.016 13 1.3 S_precentral-sup-part 790 552 1495 2.766 0.701 0.139 0.026 11 0.8 S_suborbital 1355 954 2102 2.406 0.374 0.113 0.018 10 1.0 S_subparietal 1797 1310 2687 2.443 0.502 0.114 0.016 13 1.3 S_temporal_inf 5858 4102 9445 2.454 0.399 0.103 0.019 48 4.1 S_temporal_sup 716 487 873 2.248 0.286 0.100 0.012 5 0.4 S_temporal_transverse mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab sub-01 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /output_dir/freesurfer/sub-01/mri/wm.mgz... reading input surface /output_dir/freesurfer/sub-01/surf/rh.white... reading input pial surface /output_dir/freesurfer/sub-01/surf/rh.pial... reading input white surface /output_dir/freesurfer/sub-01/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 287251 Total vertex volume 283664 (mask=0) reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1886972 mm^3 (det: 1.032398 ) lhCtxGM: 284964.013 284602.000 diff= 362.0 pctdiff= 0.127 rhCtxGM: 282764.340 282639.000 diff= 125.3 pctdiff= 0.044 lhCtxWM: 264716.121 264809.000 diff= -92.9 pctdiff=-0.035 rhCtxWM: 260828.970 261515.000 diff= -686.0 pctdiff=-0.263 SubCortGMVol 69603.000 SupraTentVol 1186125.445 (1183773.000) diff=2352.445 pctdiff=0.198 SupraTentVolNotVent 1165563.445 (1163211.000) diff=2352.445 pctdiff=0.202 BrainSegVol 1348873.000 (1345092.000) diff=3781.000 pctdiff=0.280 BrainSegVolNotVent 1323161.000 (1322654.445) diff=506.555 pctdiff=0.038 BrainSegVolNotVent 1323161.000 CerebellumVol 159735.000 VentChorVol 20562.000 3rd4th5thCSF 5150.000 CSFVol 1369.000, OptChiasmVol 215.000 MaskVol 1897316.000 1045 736 1961 2.513 0.551 0.168 0.043 23 1.8 G&S_frontomargin 1332 843 2910 2.753 0.669 0.129 0.029 18 1.5 G&S_occipital_inf 1565 872 2509 2.392 0.589 0.089 0.016 13 0.9 G&S_paracentral 1917 1281 4029 2.746 0.527 0.139 0.030 29 2.2 G&S_subcentral 1254 876 2904 2.640 0.580 0.172 0.044 32 2.3 G&S_transv_frontopol 3173 2188 6559 2.747 0.581 0.137 0.034 54 4.8 G&S_cingul-Ant 1320 901 2647 2.731 0.605 0.114 0.027 17 1.4 G&S_cingul-Mid-Ant 1467 988 2713 2.679 0.372 0.110 0.024 15 1.4 G&S_cingul-Mid-Post 769 512 2154 3.104 0.426 0.158 0.036 15 1.1 G_cingul-Post-dorsal 328 202 811 3.065 0.749 0.138 0.031 7 0.4 G_cingul-Post-ventral 2502 1506 3279 1.851 0.554 0.138 0.036 40 3.6 G_cuneus 1329 902 3369 2.770 0.394 0.129 0.027 22 1.4 G_front_inf-Opercular 398 261 868 2.549 0.384 0.127 0.038 7 0.5 G_front_inf-Orbital 1414 918 3481 2.812 0.429 0.144 0.033 28 1.8 G_front_inf-Triangul 5385 3487 13028 2.743 0.550 0.129 0.026 89 5.7 G_front_middle 7413 4896 18783 3.013 0.560 0.129 0.028 100 8.6 G_front_sup 741 506 2039 3.526 0.653 0.134 0.037 11 0.9 G_Ins_lg&S_cent_ins 1082 710 2975 3.330 1.056 0.146 0.048 21 2.6 G_insular_short 2610 1646 5308 2.570 0.497 0.141 0.033 39 3.4 G_occipital_middle 2299 1349 3456 2.148 0.526 0.124 0.026 30 2.2 G_occipital_sup 2570 1665 6745 3.067 0.554 0.136 0.028 43 3.1 G_oc-temp_lat-fusifor 3190 2044 5245 2.120 0.746 0.147 0.045 50 5.5 G_oc-temp_med-Lingual 1082 723 3372 3.158 0.908 0.099 0.023 8 0.9 G_oc-temp_med-Parahip 2652 1767 7192 2.974 0.595 0.146 0.036 53 4.1 G_orbital 4101 2513 9093 2.723 0.506 0.135 0.031 71 4.8 G_pariet_inf-Angular 3625 2350 8284 2.777 0.509 0.125 0.027 52 3.8 G_pariet_inf-Supramar 3124 2016 6206 2.453 0.437 0.110 0.020 38 2.6 G_parietal_sup 2366 1429 4342 2.370 0.494 0.112 0.021 27 1.9 G_postcentral 3454 1933 7714 3.009 0.428 0.094 0.016 29 2.2 G_precentral 3481 2260 7484 2.585 0.485 0.140 0.033 68 4.2 G_precuneus 801 516 2064 2.706 0.532 0.153 0.058 28 2.0 G_rectus 833 449 949 1.819 1.344 0.100 0.047 15 1.2 G_subcallosal 452 238 917 2.841 0.379 0.123 0.021 7 0.3 G_temp_sup-G_T_transv 2072 1367 6118 3.233 0.590 0.136 0.031 34 3.1 G_temp_sup-Lateral 862 606 2575 3.661 0.623 0.094 0.017 5 0.6 G_temp_sup-Plan_polar 1003 666 2083 2.890 0.382 0.123 0.023 13 0.8 G_temp_sup-Plan_tempo 3217 2047 8008 2.905 0.675 0.140 0.039 63 5.3 G_temporal_inf 3521 2382 10372 3.126 0.595 0.134 0.030 56 4.3 G_temporal_middle 436 303 589 2.171 0.392 0.115 0.018 3 0.3 Lat_Fis-ant-Horizont 328 242 505 2.517 0.241 0.094 0.012 1 0.2 Lat_Fis-ant-Vertical 1448 975 2137 2.685 0.444 0.126 0.024 12 1.5 Lat_Fis-post 3540 2112 4434 1.873 0.487 0.141 0.035 50 5.3 Pole_occipital 2078 1533 7541 3.329 0.739 0.151 0.044 40 3.8 Pole_temporal 2561 1718 2948 1.957 0.613 0.126 0.031 26 3.8 S_calcarine 3506 2391 4266 2.016 0.590 0.092 0.016 17 2.4 S_central 1596 1126 2391 2.259 0.359 0.086 0.011 6 0.8 S_cingul-Marginalis 551 403 1098 3.132 0.505 0.100 0.018 2 0.4 S_circular_insula_ant 1296 866 2027 2.881 0.531 0.078 0.010 4 0.5 S_circular_insula_inf 1743 1208 2664 2.590 0.459 0.097 0.015 8 1.1 S_circular_insula_sup 1050 751 1890 2.708 0.531 0.111 0.018 7 0.7 S_collat_transv_ant 668 458 901 2.301 0.267 0.132 0.028 6 0.8 S_collat_transv_post 2262 1576 3504 2.326 0.380 0.117 0.020 20 1.7 S_front_inf 2596 1797 3906 2.340 0.383 0.113 0.021 18 2.1 S_front_middle 2618 1844 4222 2.499 0.381 0.096 0.015 14 1.6 S_front_sup 671 457 876 2.330 0.324 0.107 0.014 4 0.5 S_interm_prim-Jensen 5300 3609 7821 2.288 0.397 0.109 0.017 43 3.6 S_intrapariet&P_trans 884 595 943 1.914 0.269 0.126 0.020 8 0.8 S_oc_middle&Lunatus 1658 1133 2203 2.133 0.380 0.124 0.021 16 1.5 S_oc_sup&transversal 619 422 912 2.404 0.424 0.105 0.016 4 0.4 S_occipital_ant 907 632 1648 2.729 0.588 0.116 0.020 7 0.7 S_oc-temp_lat 2711 1936 4018 2.238 0.469 0.111 0.019 20 2.3 S_oc-temp_med&Lingual 444 324 571 2.074 0.444 0.129 0.023 4 0.4 S_orbital_lateral 778 569 1182 2.122 0.581 0.115 0.026 6 0.7 S_orbital_med-olfact 1374 943 2452 2.588 0.568 0.136 0.034 18 2.0 S_orbital-H_Shaped 2441 1653 3386 2.291 0.562 0.118 0.022 20 2.2 S_parieto_occipital 1493 892 1428 2.154 1.025 0.126 0.035 27 1.3 S_pericallosal 3071 2073 4085 2.189 0.456 0.106 0.020 22 2.6 S_postcentral 1716 1194 2733 2.472 0.409 0.101 0.016 10 1.1 S_precentral-inf-part 1887 1310 2859 2.459 0.427 0.104 0.016 13 1.3 S_precentral-sup-part 431 314 916 2.795 0.973 0.152 0.022 5 0.4 S_suborbital 1293 928 2113 2.396 0.389 0.113 0.020 10 1.0 S_subparietal 1584 1114 2204 2.417 0.423 0.119 0.017 12 1.2 S_temporal_inf 6748 4599 11153 2.606 0.465 0.110 0.019 53 5.3 S_temporal_sup 367 266 592 2.827 0.406 0.117 0.015 2 0.2 S_temporal_transverse PIDs (3292 3295) completed and logs appended. #----------------------------------------- #@# Cortical Parc 3 lh Fri May 8 00:52:07 UTC 2020 /output_dir/freesurfer/sub-01/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-01 lh ../surf/lh.sphere.reg /opt/freesurfer/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot #----------------------------------------- #@# Cortical Parc 3 rh Fri May 8 00:52:07 UTC 2020 /output_dir/freesurfer/sub-01/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-01 rh ../surf/rh.sphere.reg /opt/freesurfer/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.DKTatlas.annot Waiting for PID 3334 of (3334 3337) to complete... Waiting for PID 3337 of (3334 3337) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-01 lh ../surf/lh.sphere.reg /opt/freesurfer/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /opt/freesurfer/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 1.4 using min determinant for regularization = 0.020 0 singular and 383 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1687 labels changed using aseg relabeling using gibbs priors... 000: 2267 changed, 157189 examined... 001: 505 changed, 10379 examined... 002: 130 changed, 2840 examined... 003: 57 changed, 768 examined... 004: 28 changed, 338 examined... 005: 18 changed, 167 examined... 006: 17 changed, 116 examined... 007: 12 changed, 92 examined... 008: 9 changed, 60 examined... 009: 9 changed, 51 examined... 010: 5 changed, 49 examined... 011: 6 changed, 32 examined... 012: 4 changed, 33 examined... 013: 5 changed, 19 examined... 014: 5 changed, 25 examined... 015: 5 changed, 26 examined... 016: 4 changed, 30 examined... 017: 5 changed, 27 examined... 018: 4 changed, 20 examined... 019: 3 changed, 22 examined... 020: 4 changed, 11 examined... 021: 1 changed, 16 examined... 022: 2 changed, 6 examined... 023: 2 changed, 10 examined... 024: 3 changed, 12 examined... 025: 3 changed, 13 examined... 026: 3 changed, 16 examined... 027: 3 changed, 20 examined... 028: 5 changed, 22 examined... 029: 6 changed, 28 examined... 030: 2 changed, 29 examined... 031: 2 changed, 11 examined... 032: 3 changed, 9 examined... 033: 4 changed, 19 examined... 034: 3 changed, 16 examined... 035: 3 changed, 21 examined... 036: 1 changed, 17 examined... 037: 0 changed, 7 examined... 288 labels changed using aseg 000: 67 total segments, 34 labels (356 vertices) changed 001: 34 total segments, 1 labels (8 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 7 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 867 vertices marked for relabeling... 867 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 30 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-01 rh ../surf/rh.sphere.reg /opt/freesurfer/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.DKTatlas.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /opt/freesurfer/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.009 0 singular and 325 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1552 labels changed using aseg relabeling using gibbs priors... 000: 2281 changed, 155426 examined... 001: 530 changed, 10203 examined... 002: 158 changed, 2984 examined... 003: 57 changed, 852 examined... 004: 26 changed, 308 examined... 005: 15 changed, 142 examined... 006: 13 changed, 89 examined... 007: 6 changed, 57 examined... 008: 4 changed, 38 examined... 009: 2 changed, 21 examined... 010: 3 changed, 14 examined... 011: 4 changed, 19 examined... 012: 1 changed, 20 examined... 013: 2 changed, 5 examined... 014: 1 changed, 10 examined... 015: 1 changed, 8 examined... 016: 2 changed, 7 examined... 017: 1 changed, 10 examined... 018: 3 changed, 7 examined... 019: 5 changed, 13 examined... 020: 2 changed, 19 examined... 021: 1 changed, 11 examined... 022: 2 changed, 7 examined... 023: 2 changed, 11 examined... 024: 2 changed, 9 examined... 025: 3 changed, 10 examined... 026: 2 changed, 15 examined... 027: 3 changed, 14 examined... 028: 4 changed, 16 examined... 029: 2 changed, 16 examined... 030: 2 changed, 9 examined... 031: 1 changed, 15 examined... 032: 0 changed, 7 examined... 263 labels changed using aseg 000: 53 total segments, 20 labels (263 vertices) changed 001: 34 total segments, 1 labels (1 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 5 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 997 vertices marked for relabeling... 997 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 30 seconds. PIDs (3334 3337) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 3 lh Fri May 8 00:52:37 UTC 2020 /output_dir/freesurfer/sub-01/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas.stats -b -a ../label/lh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab sub-01 lh white #----------------------------------------- #@# Parcellation Stats 3 rh Fri May 8 00:52:38 UTC 2020 /output_dir/freesurfer/sub-01/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab sub-01 rh white Waiting for PID 3376 of (3376 3379) to complete... Waiting for PID 3379 of (3376 3379) to complete... mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas.stats -b -a ../label/lh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab sub-01 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /output_dir/freesurfer/sub-01/mri/wm.mgz... reading input surface /output_dir/freesurfer/sub-01/surf/lh.white... reading input pial surface /output_dir/freesurfer/sub-01/surf/lh.pial... reading input white surface /output_dir/freesurfer/sub-01/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 289420 Total vertex volume 285513 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1886972 mm^3 (det: 1.032398 ) lhCtxGM: 284964.013 284602.000 diff= 362.0 pctdiff= 0.127 rhCtxGM: 282764.340 282639.000 diff= 125.3 pctdiff= 0.044 lhCtxWM: 264716.121 264809.000 diff= -92.9 pctdiff=-0.035 rhCtxWM: 260828.970 261515.000 diff= -686.0 pctdiff=-0.263 SubCortGMVol 69603.000 SupraTentVol 1186125.445 (1183773.000) diff=2352.445 pctdiff=0.198 SupraTentVolNotVent 1165563.445 (1163211.000) diff=2352.445 pctdiff=0.202 BrainSegVol 1348873.000 (1345092.000) diff=3781.000 pctdiff=0.280 BrainSegVolNotVent 1323161.000 (1322654.445) diff=506.555 pctdiff=0.038 BrainSegVolNotVent 1323161.000 CerebellumVol 159735.000 VentChorVol 20562.000 3rd4th5thCSF 5150.000 CSFVol 1369.000, OptChiasmVol 215.000 MaskVol 1897316.000 1465 994 2887 2.863 0.549 0.114 0.017 16 1.0 caudalanteriorcingulate 4201 2773 8361 2.768 0.450 0.110 0.018 39 3.1 caudalmiddlefrontal 3553 2306 5039 1.988 0.487 0.144 0.034 51 5.0 cuneus 573 426 2236 3.656 0.654 0.127 0.042 8 0.8 entorhinal 4847 3268 9771 2.757 0.602 0.130 0.030 69 5.3 fusiform 6625 4451 11970 2.472 0.450 0.126 0.024 87 6.2 inferiorparietal 5634 3888 13485 2.830 0.672 0.131 0.032 102 7.1 inferiortemporal 2285 1476 3701 2.306 0.900 0.134 0.035 38 2.7 isthmuscingulate 9367 5961 14239 2.132 0.582 0.134 0.028 118 10.9 lateraloccipital 4867 3283 10324 2.843 0.619 0.133 0.032 73 6.2 lateralorbitofrontal 5105 3449 7870 2.078 0.652 0.142 0.035 73 7.4 lingual 2368 1573 5291 2.774 0.828 0.134 0.037 51 3.2 medialorbitofrontal 7265 5004 16686 2.801 0.658 0.121 0.025 98 7.1 middletemporal 1259 829 2664 2.741 0.730 0.080 0.012 7 0.6 parahippocampal 2595 1691 4894 2.638 0.578 0.098 0.017 16 1.7 paracentral 2327 1580 4842 2.735 0.456 0.116 0.021 25 1.8 parsopercularis 956 671 2078 2.612 0.519 0.130 0.027 12 1.0 parsorbitalis 2562 1752 5391 2.593 0.503 0.129 0.024 35 2.5 parstriangularis 2149 1439 2119 1.661 0.392 0.135 0.030 25 2.5 pericalcarine 8050 5164 12406 2.185 0.638 0.109 0.019 77 6.3 postcentral 2345 1575 4500 2.615 0.740 0.145 0.030 39 2.8 posteriorcingulate 9253 5697 16982 2.722 0.525 0.101 0.021 80 8.2 precentral 7134 4931 12985 2.370 0.493 0.127 0.025 95 7.2 precuneus 1848 1209 4118 3.152 0.876 0.125 0.030 25 2.0 rostralanteriorcingulate 6029 4039 12162 2.576 0.535 0.135 0.028 91 7.0 rostralmiddlefrontal 13880 9305 30584 2.812 0.544 0.121 0.024 173 13.3 superiorfrontal 8652 5812 14717 2.280 0.452 0.119 0.022 99 7.4 superiorparietal 8572 5762 18917 2.826 0.663 0.107 0.026 112 7.5 superiortemporal 7741 5152 15047 2.612 0.541 0.120 0.022 90 6.8 supramarginal 1083 680 1820 2.339 0.353 0.092 0.019 9 0.8 transversetemporal 3366 2227 7424 3.190 0.700 0.116 0.028 38 3.6 insula mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab sub-01 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /output_dir/freesurfer/sub-01/mri/wm.mgz... reading input surface /output_dir/freesurfer/sub-01/surf/rh.white... reading input pial surface /output_dir/freesurfer/sub-01/surf/rh.pial... reading input white surface /output_dir/freesurfer/sub-01/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 287251 Total vertex volume 283664 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1886972 mm^3 (det: 1.032398 ) lhCtxGM: 284964.013 284602.000 diff= 362.0 pctdiff= 0.127 rhCtxGM: 282764.340 282639.000 diff= 125.3 pctdiff= 0.044 lhCtxWM: 264716.121 264809.000 diff= -92.9 pctdiff=-0.035 rhCtxWM: 260828.970 261515.000 diff= -686.0 pctdiff=-0.263 SubCortGMVol 69603.000 SupraTentVol 1186125.445 (1183773.000) diff=2352.445 pctdiff=0.198 SupraTentVolNotVent 1165563.445 (1163211.000) diff=2352.445 pctdiff=0.202 BrainSegVol 1348873.000 (1345092.000) diff=3781.000 pctdiff=0.280 BrainSegVolNotVent 1323161.000 (1322654.445) diff=506.555 pctdiff=0.038 BrainSegVolNotVent 1323161.000 CerebellumVol 159735.000 VentChorVol 20562.000 3rd4th5thCSF 5150.000 CSFVol 1369.000, OptChiasmVol 215.000 MaskVol 1897316.000 1030 687 2298 3.164 0.624 0.143 0.030 19 1.3 caudalanteriorcingulate 4181 2791 8379 2.698 0.487 0.111 0.020 38 3.2 caudalmiddlefrontal 3246 1983 4245 1.911 0.522 0.131 0.032 45 4.2 cuneus 376 268 1576 3.866 0.553 0.112 0.029 3 0.4 entorhinal 4785 3230 10642 2.849 0.582 0.125 0.024 61 4.8 fusiform 9692 6318 17428 2.532 0.482 0.124 0.025 115 9.5 inferiorparietal 5959 3973 13892 2.853 0.677 0.133 0.033 94 8.3 inferiortemporal 1772 1160 3130 2.322 0.933 0.125 0.035 28 2.0 isthmuscingulate 8271 5107 12823 2.213 0.589 0.137 0.031 112 10.2 lateraloccipital 4340 3015 9607 2.746 0.664 0.147 0.042 78 7.9 lateralorbitofrontal 4897 3242 7652 2.109 0.670 0.145 0.040 69 8.0 lingual 2600 1650 4991 2.379 1.034 0.136 0.045 61 4.6 medialorbitofrontal 7274 5021 17487 2.922 0.591 0.125 0.025 90 7.5 middletemporal 1183 777 2110 2.439 0.675 0.083 0.015 6 0.6 parahippocampal 2685 1756 4756 2.524 0.491 0.099 0.015 16 1.7 paracentral 2516 1727 5020 2.615 0.391 0.117 0.021 30 2.0 parsopercularis 1027 682 2300 2.690 0.470 0.126 0.023 14 1.0 parsorbitalis 2594 1768 5096 2.510 0.520 0.136 0.029 39 3.0 parstriangularis 2476 1631 2338 1.609 0.393 0.120 0.029 27 3.4 pericalcarine 7759 5000 11936 2.191 0.573 0.110 0.021 78 6.5 postcentral 2032 1325 3749 2.639 0.583 0.125 0.030 30 2.2 posteriorcingulate 8615 5412 16173 2.709 0.572 0.099 0.017 63 5.9 precentral 7014 4722 12668 2.462 0.522 0.128 0.027 96 7.3 precuneus 1093 739 2516 3.115 0.555 0.132 0.032 17 1.6 rostralanteriorcingulate 6947 4701 12968 2.434 0.481 0.127 0.024 93 6.9 rostralmiddlefrontal 14272 9669 31097 2.776 0.576 0.126 0.027 187 15.7 superiorfrontal 9167 5996 15282 2.336 0.441 0.109 0.019 90 7.2 superiorparietal 7588 5211 18842 3.076 0.648 0.117 0.025 86 8.1 superiortemporal 6786 4460 13423 2.658 0.488 0.121 0.024 81 6.6 supramarginal 647 369 1175 2.711 0.296 0.117 0.018 8 0.4 transversetemporal 3579 2422 8066 3.181 0.790 0.115 0.025 35 3.9 insula PIDs (3376 3379) completed and logs appended. #----------------------------------------- #@# WM/GM Contrast lh Fri May 8 00:54:11 UTC 2020 /output_dir/freesurfer/sub-01/scripts pctsurfcon --s sub-01 --lh-only #----------------------------------------- #@# WM/GM Contrast rh Fri May 8 00:54:11 UTC 2020 /output_dir/freesurfer/sub-01/scripts pctsurfcon --s sub-01 --rh-only Waiting for PID 3418 of (3418 3421) to complete... Waiting for PID 3421 of (3418 3421) to complete... pctsurfcon --s sub-01 --lh-only Log file is /output_dir/freesurfer/sub-01/scripts/pctsurfcon.log Fri May 8 00:54:12 UTC 2020 setenv SUBJECTS_DIR /output_dir/freesurfer cd /output_dir/freesurfer/sub-01/scripts /opt/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux cc31617c633f 4.19.76-linuxkit #1 SMP Thu Oct 17 19:31:58 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /opt/freesurfer mri_vol2surf --mov /output_dir/freesurfer/sub-01/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /output_dir/freesurfer/sub-01/surf/tmp.pctsurfcon.3418/lh.wm.mgh --regheader sub-01 --cortex srcvol = /output_dir/freesurfer/sub-01/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /output_dir/freesurfer/sub-01/mri/orig.mgz as target reference. -------- original matrix ----------- -1.00000 0.00000 0.00000 0.00001; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /output_dir/freesurfer/sub-01/label/lh.cortex.label Reading surface /output_dir/freesurfer/sub-01/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 85190 Masking with /output_dir/freesurfer/sub-01/label/lh.cortex.label Writing to /output_dir/freesurfer/sub-01/surf/tmp.pctsurfcon.3418/lh.wm.mgh Dim: 157189 1 1 mri_vol2surf --mov /output_dir/freesurfer/sub-01/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /output_dir/freesurfer/sub-01/surf/tmp.pctsurfcon.3418/lh.gm.mgh --projfrac 0.3 --regheader sub-01 --cortex srcvol = /output_dir/freesurfer/sub-01/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /output_dir/freesurfer/sub-01/mri/orig.mgz as target reference. -------- original matrix ----------- -1.00000 0.00000 0.00000 0.00001; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /output_dir/freesurfer/sub-01/label/lh.cortex.label Reading surface /output_dir/freesurfer/sub-01/surf/lh.white Done reading source surface Reading thickness /output_dir/freesurfer/sub-01/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 104877 Masking with /output_dir/freesurfer/sub-01/label/lh.cortex.label Writing to /output_dir/freesurfer/sub-01/surf/tmp.pctsurfcon.3418/lh.gm.mgh Dim: 157189 1 1 mri_concat /output_dir/freesurfer/sub-01/surf/tmp.pctsurfcon.3418/lh.wm.mgh /output_dir/freesurfer/sub-01/surf/tmp.pctsurfcon.3418/lh.gm.mgh --paired-diff-norm --mul 100 --o /output_dir/freesurfer/sub-01/surf/lh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /output_dir/freesurfer/sub-01/surf/lh.w-g.pct.mgh mri_segstats --in /output_dir/freesurfer/sub-01/surf/lh.w-g.pct.mgh --annot sub-01 lh aparc --sum /output_dir/freesurfer/sub-01/stats/lh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --in /output_dir/freesurfer/sub-01/surf/lh.w-g.pct.mgh --annot sub-01 lh aparc --sum /output_dir/freesurfer/sub-01/stats/lh.w-g.pct.stats --snr sysname Linux hostname cc31617c633f machine x86_64 user root UseRobust 0 Constructing seg from annotation Reading annotation /output_dir/freesurfer/sub-01/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Seg base 1000 Loading /output_dir/freesurfer/sub-01/surf/lh.w-g.pct.mgh Vertex Area is 0.664905 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up pctsurfcon --s sub-01 --rh-only Log file is /output_dir/freesurfer/sub-01/scripts/pctsurfcon.log Fri May 8 00:54:12 UTC 2020 setenv SUBJECTS_DIR /output_dir/freesurfer cd /output_dir/freesurfer/sub-01/scripts /opt/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux cc31617c633f 4.19.76-linuxkit #1 SMP Thu Oct 17 19:31:58 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /opt/freesurfer mri_vol2surf --mov /output_dir/freesurfer/sub-01/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /output_dir/freesurfer/sub-01/surf/tmp.pctsurfcon.3421/rh.wm.mgh --regheader sub-01 --cortex srcvol = /output_dir/freesurfer/sub-01/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /output_dir/freesurfer/sub-01/mri/orig.mgz as target reference. -------- original matrix ----------- -1.00000 0.00000 0.00000 0.00001; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /output_dir/freesurfer/sub-01/label/rh.cortex.label Reading surface /output_dir/freesurfer/sub-01/surf/rh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 84230 Masking with /output_dir/freesurfer/sub-01/label/rh.cortex.label Writing to /output_dir/freesurfer/sub-01/surf/tmp.pctsurfcon.3421/rh.wm.mgh Dim: 155426 1 1 mri_vol2surf --mov /output_dir/freesurfer/sub-01/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /output_dir/freesurfer/sub-01/surf/tmp.pctsurfcon.3421/rh.gm.mgh --projfrac 0.3 --regheader sub-01 --cortex srcvol = /output_dir/freesurfer/sub-01/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /output_dir/freesurfer/sub-01/mri/orig.mgz as target reference. -------- original matrix ----------- -1.00000 0.00000 0.00000 0.00001; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /output_dir/freesurfer/sub-01/label/rh.cortex.label Reading surface /output_dir/freesurfer/sub-01/surf/rh.white Done reading source surface Reading thickness /output_dir/freesurfer/sub-01/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 103602 Masking with /output_dir/freesurfer/sub-01/label/rh.cortex.label Writing to /output_dir/freesurfer/sub-01/surf/tmp.pctsurfcon.3421/rh.gm.mgh Dim: 155426 1 1 mri_concat /output_dir/freesurfer/sub-01/surf/tmp.pctsurfcon.3421/rh.wm.mgh /output_dir/freesurfer/sub-01/surf/tmp.pctsurfcon.3421/rh.gm.mgh --paired-diff-norm --mul 100 --o /output_dir/freesurfer/sub-01/surf/rh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /output_dir/freesurfer/sub-01/surf/rh.w-g.pct.mgh mri_segstats --in /output_dir/freesurfer/sub-01/surf/rh.w-g.pct.mgh --annot sub-01 rh aparc --sum /output_dir/freesurfer/sub-01/stats/rh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --in /output_dir/freesurfer/sub-01/surf/rh.w-g.pct.mgh --annot sub-01 rh aparc --sum /output_dir/freesurfer/sub-01/stats/rh.w-g.pct.stats --snr sysname Linux hostname cc31617c633f machine x86_64 user root UseRobust 0 Constructing seg from annotation Reading annotation /output_dir/freesurfer/sub-01/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Seg base 2000 Loading /output_dir/freesurfer/sub-01/surf/rh.w-g.pct.mgh Vertex Area is 0.66192 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up PIDs (3418 3421) completed and logs appended. #----------------------------------------- #@# Relabel Hypointensities Fri May 8 00:54:25 UTC 2020 /output_dir/freesurfer/sub-01/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 3864 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 3860 voxels changed to hypointensity... 7493 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg aparc Fri May 8 00:54:56 UTC 2020 /output_dir/freesurfer/sub-01 mri_aparc2aseg --s sub-01 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt #----------------------------------------- #@# AParc-to-ASeg a2009s Fri May 8 00:54:56 UTC 2020 /output_dir/freesurfer/sub-01 mri_aparc2aseg --s sub-01 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --a2009s #----------------------------------------- #@# AParc-to-ASeg DKTatlas Fri May 8 00:54:57 UTC 2020 /output_dir/freesurfer/sub-01 mri_aparc2aseg --s sub-01 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --annot aparc.DKTatlas --o mri/aparc.DKTatlas+aseg.mgz Waiting for PID 3562 of (3562 3565 3568) to complete... /opt/freesurfer/bin/reconbatchjobs: line 81: 3562 Killed exec $JOB >> $LOG 2>&1 /opt/freesurfer/bin/reconbatchjobs: line 81: 3565 Killed exec $JOB >> $LOG 2>&1 Waiting for PID 3565 of (3562 3565 3568) to complete... Waiting for PID 3568 of (3562 3565 3568) to complete... mri_aparc2aseg --s sub-01 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /output_dir/freesurfer subject sub-01 outvol /output_dir/freesurfer/sub-01/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /output_dir/freesurfer/sub-01/surf/lh.white Reading lh pial surface /output_dir/freesurfer/sub-01/surf/lh.pial Loading lh annotations from /output_dir/freesurfer/sub-01/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading rh white surface /output_dir/freesurfer/sub-01/surf/rh.white Reading rh pial surface /output_dir/freesurfer/sub-01/surf/rh.pial Loading rh annotations from /output_dir/freesurfer/sub-01/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) mri_aparc2aseg --s sub-01 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --a2009s relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /output_dir/freesurfer subject sub-01 outvol /output_dir/freesurfer/sub-01/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /output_dir/freesurfer/sub-01/surf/lh.white Reading lh pial surface /output_dir/freesurfer/sub-01/surf/lh.pial Loading lh annotations from /output_dir/freesurfer/sub-01/label/lh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Reading rh white surface /output_dir/freesurfer/sub-01/surf/rh.white Reading rh pial surface /output_dir/freesurfer/sub-01/surf/rh.pial Loading rh annotations from /output_dir/freesurfer/sub-01/label/rh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) mri_aparc2aseg --s sub-01 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --annot aparc.DKTatlas --o mri/aparc.DKTatlas+aseg.mgz relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /output_dir/freesurfer subject sub-01 outvol mri/aparc.DKTatlas+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /output_dir/freesurfer/sub-01/surf/lh.white Reading lh pial surface /output_dir/freesurfer/sub-01/surf/lh.pial Loading lh annotations from /output_dir/freesurfer/sub-01/label/lh.aparc.DKTatlas.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading rh white surface /output_dir/freesurfer/sub-01/surf/rh.white Reading rh pial surface /output_dir/freesurfer/sub-01/surf/rh.pial Loading rh annotations from /output_dir/freesurfer/sub-01/label/rh.aparc.DKTatlas.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /output_dir/freesurfer/sub-01/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /output_dir/freesurfer/sub-01/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 8.08 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 104 rescaling Left_Cerebral_Cortex from 61 --> 75 rescaling Left_Lateral_Ventricle from 13 --> 32 rescaling Left_Inf_Lat_Vent from 34 --> 33 rescaling Left_Cerebellum_White_Matter from 86 --> 95 rescaling Left_Cerebellum_Cortex from 60 --> 76 rescaling Left_Thalamus from 94 --> 103 rescaling Left_Thalamus_Proper from 84 --> 98 rescaling Left_Caudate from 75 --> 90 rescaling Left_Putamen from 80 --> 93 rescaling Left_Pallidum from 98 --> 100 rescaling Third_Ventricle from 25 --> 49 rescaling Fourth_Ventricle from 22 --> 32 rescaling Brain_Stem from 81 --> 89 rescaling Left_Hippocampus from 57 --> 69 rescaling Left_Amygdala from 56 --> 73 rescaling CSF from 32 --> 71 rescaling Left_Accumbens_area from 62 --> 72 rescaling Left_VentralDC from 87 --> 96 rescaling Right_Cerebral_White_Matter from 105 --> 103 rescaling Right_Cerebral_Cortex from 58 --> 75 rescaling Right_Lateral_Ventricle from 13 --> 28 rescaling Right_Inf_Lat_Vent from 25 --> 31 rescaling Right_Cerebellum_White_Matter from 87 --> 95 rescaling Right_Cerebellum_Cortex from 59 --> 77 rescaling Right_Thalamus_Proper from 85 --> 95 rescaling Right_Caudate from 62 --> 83 rescaling Right_Putamen from 80 --> 88 rescaling Right_Pallidum from 97 --> 100 rescaling Right_Hippocampus from 53 --> 75 rescaling Right_Amygdala from 55 --> 74 rescaling Right_Accumbens_area from 65 --> 82 rescaling Right_VentralDC from 86 --> 98 rescaling Fifth_Ventricle from 40 --> 59 rescaling WM_hypointensities from 78 --> 76 rescaling non_WM_hypointensities from 40 --> 43 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 566344 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 273 changed. pass 2: 13 changed. pass 3: 1 changed. pass 4: 0 changed. nchanged = 0 Writing output aseg to mri/aparc.DKTatlas+aseg.mgz PIDs (3562 3565 3568) completed and logs appended. Linux cc31617c633f 4.19.76-linuxkit #1 SMP Thu Oct 17 19:31:58 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-01 exited with ERRORS at Fri May 8 01:04:29 UTC 2020 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting