Mon Mar 29 22:23:38 UTC 2021 /out/out/freesurfer/sub-05 /opt/freesurfer/bin/recon-all -autorecon1 -i /data/sub-05/anat/sub-05_T1w.nii.gz -noskullstrip -openmp 8 -subjid sub-05 -sd /out/out/freesurfer subjid sub-05 setenv SUBJECTS_DIR /out/out/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 83ec93b3099f 5.4.0-67-generic #75~18.04.1-Ubuntu SMP Tue Feb 23 19:17:50 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize unlimited memoryuse unlimited vmemoryuse unlimited descriptors 1048576 memorylocked 65536 kbytes maxproc unlimited maxlocks unlimited maxsignal 62787 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 16122748 7624192 254612 978548 8243944 6825400 Swap: 31999996 731136 31268860 ######################################## 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: 2021/03/29-22:23:38-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic 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: 2021/03/29-22:23:38-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-22:23:38-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/03/29-22:23:38-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-22:23:38-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-22:23:38-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/03/29-22:23:38-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/03/29-22:23:38-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/03/29-22:23:38-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/03/29-22:23:38-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/03/29-22:23:38-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/03/29-22:23:38-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-22:23:38-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-22:23:39-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/03/29-22:23:39-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-22:23:39-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-22:23:39-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-22:23:39-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-22:23:39-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-22:23:39-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-22:23:39-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/03/29-22:23:39-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-22:23:39-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-22:23:39-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-22:23:39-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/03/29-22:23:39-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-22:23:39-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2021/03/29-22:23:39-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-22:23:39-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-22:23:39-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-22:23:39-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-22:23:39-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic 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: 2021/03/29-22:23:39-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic 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: 2021/03/29-22:23:39-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-22:23:39-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-22:23:39-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-22:23:39-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-22:23:39-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-22:23:39-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic 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 ####################################### /out/out/freesurfer/sub-05 mri_convert /data/sub-05/anat/sub-05_T1w.nii.gz /out/out/freesurfer/sub-05/mri/orig/001.mgz mri_convert.bin /data/sub-05/anat/sub-05_T1w.nii.gz /out/out/freesurfer/sub-05/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /data/sub-05/anat/sub-05_T1w.nii.gz... TR=2250.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.999468, 0.0314122, 0.00873194) j_ras = (-0.0314134, 0.999506, -1.80917e-08) k_ras = (-0.00872763, -0.000274282, 0.999962) writing to /out/out/freesurfer/sub-05/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Mon Mar 29 22:23:43 UTC 2021 Found 1 runs /out/out/freesurfer/sub-05/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 /out/out/freesurfer/sub-05/mri/orig/001.mgz /out/out/freesurfer/sub-05/mri/rawavg.mgz /out/out/freesurfer/sub-05 mri_convert /out/out/freesurfer/sub-05/mri/rawavg.mgz /out/out/freesurfer/sub-05/mri/orig.mgz --conform mri_convert.bin /out/out/freesurfer/sub-05/mri/rawavg.mgz /out/out/freesurfer/sub-05/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /out/out/freesurfer/sub-05/mri/rawavg.mgz... TR=2250.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.999468, 0.0314122, 0.00873194) j_ras = (-0.0314134, 0.999506, -1.80917e-08) k_ras = (-0.00872763, -0.000274282, 0.999962) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /out/out/freesurfer/sub-05/mri/orig.mgz... mri_add_xform_to_header -c /out/out/freesurfer/sub-05/mri/transforms/talairach.xfm /out/out/freesurfer/sub-05/mri/orig.mgz /out/out/freesurfer/sub-05/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Mon Mar 29 22:23:50 UTC 2021 /out/out/freesurfer/sub-05/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /out/out/freesurfer/sub-05/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 83ec93b3099f 5.4.0-67-generic #75~18.04.1-Ubuntu SMP Tue Feb 23 19:17:50 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux Mon Mar 29 22:23:50 UTC 2021 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.714 /out/out/freesurfer/sub-05/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.714/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.714/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=2250.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.19848e-09, 9.31323e-10) j_ras = (-9.31323e-10, -2.91038e-11, -1) k_ras = (-1.52681e-09, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.714/nu0.mnc... -------------------------------------------------------- Iteration 1 Mon Mar 29 22:23:52 UTC 2021 nu_correct -clobber ./tmp.mri_nu_correct.mni.714/nu0.mnc ./tmp.mri_nu_correct.mni.714/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.714/0/ -iterations 1000 -distance 50 [root@83ec93b3099f:/out/out/freesurfer/sub-05/mri/] [2021-03-29 22:23:52] 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.714/0/ ./tmp.mri_nu_correct.mni.714/nu0.mnc ./tmp.mri_nu_correct.mni.714/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 Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 66 CV of field change: 0.000957212 mri_convert ./tmp.mri_nu_correct.mni.714/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.714/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.714/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.19848e-09, 9.31323e-10) j_ras = (-9.31323e-10, -2.91038e-11, -1) k_ras = (-1.52681e-09, 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... Mon Mar 29 22:24:43 UTC 2021 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 Mon Mar 29 22:24:43 UTC 2021 Ended at Mon Mar 29 22:24:58 UTC 2021 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Mon Mar 29 22:25:00 UTC 2021 /out/out/freesurfer/sub-05/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7312, pval=0.6675 >= threshold=0.0050) awk -f /opt/freesurfer/bin/extract_talairach_avi_QA.awk /out/out/freesurfer/sub-05/mri/transforms/talairach_avi.log tal_QC_AZS /out/out/freesurfer/sub-05/mri/transforms/talairach_avi.log TalAviQA: 0.97821 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Mon Mar 29 22:25:00 UTC 2021 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /out/out/freesurfer/sub-05/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 83ec93b3099f 5.4.0-67-generic #75~18.04.1-Ubuntu SMP Tue Feb 23 19:17:50 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux Mon Mar 29 22:25:00 UTC 2021 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.7201 /out/out/freesurfer/sub-05/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.7201/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.7201/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=2250.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.19848e-09, 9.31323e-10) j_ras = (-9.31323e-10, -2.91038e-11, -1) k_ras = (-1.52681e-09, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.7201/nu0.mnc... -------------------------------------------------------- Iteration 1 Mon Mar 29 22:25:01 UTC 2021 nu_correct -clobber ./tmp.mri_nu_correct.mni.7201/nu0.mnc ./tmp.mri_nu_correct.mni.7201/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.7201/0/ [root@83ec93b3099f:/out/out/freesurfer/sub-05/mri/] [2021-03-29 22:25:01] 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.7201/0/ ./tmp.mri_nu_correct.mni.7201/nu0.mnc ./tmp.mri_nu_correct.mni.7201/nu1.imp Processing:.................................................................Done 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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: 50 CV of field change: 0.00141006 -------------------------------------------------------- Iteration 2 Mon Mar 29 22:25:32 UTC 2021 nu_correct -clobber ./tmp.mri_nu_correct.mni.7201/nu1.mnc ./tmp.mri_nu_correct.mni.7201/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.7201/1/ [root@83ec93b3099f:/out/out/freesurfer/sub-05/mri/] [2021-03-29 22:25:32] 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.7201/1/ ./tmp.mri_nu_correct.mni.7201/nu1.mnc ./tmp.mri_nu_correct.mni.7201/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 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: 28 CV of field change: 0.000990677 mri_binarize --i ./tmp.mri_nu_correct.mni.7201/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.7201/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /out/out/freesurfer/sub-05/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.7201/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.7201/ones.mgz sysname Linux hostname 83ec93b3099f machine x86_64 user root input ./tmp.mri_nu_correct.mni.7201/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.7201/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.7201/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.7201/sum.junk --avgwf ./tmp.mri_nu_correct.mni.7201/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.7201/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.7201/sum.junk --avgwf ./tmp.mri_nu_correct.mni.7201/input.mean.dat sysname Linux hostname 83ec93b3099f machine x86_64 user root UseRobust 0 Loading ./tmp.mri_nu_correct.mni.7201/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.7201/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.7201/ones.mgz --i ./tmp.mri_nu_correct.mni.7201/nu2.mnc --sum ./tmp.mri_nu_correct.mni.7201/sum.junk --avgwf ./tmp.mri_nu_correct.mni.7201/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.7201/ones.mgz --i ./tmp.mri_nu_correct.mni.7201/nu2.mnc --sum ./tmp.mri_nu_correct.mni.7201/sum.junk --avgwf ./tmp.mri_nu_correct.mni.7201/output.mean.dat sysname Linux hostname 83ec93b3099f machine x86_64 user root UseRobust 0 Loading ./tmp.mri_nu_correct.mni.7201/ones.mgz Loading ./tmp.mri_nu_correct.mni.7201/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.7201/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.7201/nu2.mnc ./tmp.mri_nu_correct.mni.7201/nu2.mnc mul 1.01774553892868457541 Saving result to './tmp.mri_nu_correct.mni.7201/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.7201/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.7201/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.7201/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.19848e-09, 9.31323e-10) j_ras = (-9.31323e-10, -2.91038e-11, -1) k_ras = (-1.52681e-09, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 4 seconds. mapping ( 6, 112) to ( 3, 110) Mon Mar 29 22:26:13 UTC 2021 mri_nu_correct.mni done mri_add_xform_to_header -c /out/out/freesurfer/sub-05/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Mon Mar 29 22:26:13 UTC 2021 /out/out/freesurfer/sub-05/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 1.08199 0.01147 0.00305 0.00005; -0.02166 0.98572 0.27064 -23.82175; -0.01016 -0.21196 1.03983 -12.19084; 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 71 (71), valley at 34 (34) csf peak at 36, setting threshold to 59 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 70 (70), valley at 24 (24) csf peak at 35, setting threshold to 58 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 0 minutes and 55 seconds. Started at Mon Mar 29 22:23:38 UTC 2021 Ended at Mon Mar 29 22:27:08 UTC 2021 #@#%# recon-all-run-time-hours 0.058 recon-all -s sub-05 finished without error at Mon Mar 29 22:27:08 UTC 2021 New invocation of recon-all Mon Mar 29 22:35:31 UTC 2021 /out/out/freesurfer/sub-05 /opt/freesurfer/bin/recon-all -autorecon2-volonly -openmp 8 -subjid sub-05 -sd /out/out/freesurfer subjid sub-05 setenv SUBJECTS_DIR /out/out/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 83ec93b3099f 5.4.0-67-generic #75~18.04.1-Ubuntu SMP Tue Feb 23 19:17:50 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize unlimited memoryuse unlimited vmemoryuse unlimited descriptors 1048576 memorylocked 65536 kbytes maxproc unlimited maxlocks unlimited maxsignal 62787 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 16122748 7366944 2403504 969968 6352300 7090332 Swap: 31999996 740352 31259644 ######################################## 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: 2021/03/29-22:35:31-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic 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: 2021/03/29-22:35:31-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-22:35:31-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/03/29-22:35:31-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-22:35:31-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-22:35:31-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/03/29-22:35:31-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/03/29-22:35:31-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/03/29-22:35:31-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/03/29-22:35:31-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/03/29-22:35:31-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/03/29-22:35:31-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-22:35:31-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-22:35:31-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/03/29-22:35:31-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-22:35:31-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-22:35:31-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-22:35:31-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-22:35:31-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-22:35:31-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-22:35:31-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/03/29-22:35:31-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-22:35:31-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-22:35:31-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-22:35:31-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/03/29-22:35:31-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-22:35:31-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2021/03/29-22:35:31-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-22:35:31-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-22:35:31-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-22:35:31-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-22:35:31-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic 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: 2021/03/29-22:35:31-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic 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: 2021/03/29-22:35:31-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-22:35:31-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-22:35:31-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-22:35:31-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-22:35:31-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/03/29-22:35:31-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: 83ec93b3099f Platform: Linux PlatformVersion: 5.4.0-67-generic 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 ####################################### #------------------------------------- #@# EM Registration Mon Mar 29 22:35:31 UTC 2021 /out/out/freesurfer/sub-05/mri mri_em_register -rusage /out/out/freesurfer/sub-05/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 = 8 == 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'... INFO: MRImask() using MRImaskDifferentGeometry() INFO: MRImask() using MRImaskDifferentGeometry() INFO: MRImask() using MRImaskDifferentGeometry() INFO: MRImask() using MRImaskDifferentGeometry() INFO: MRImask() using MRImaskDifferentGeometry() 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=29.9 skull bounding box = (62, 51, 37) --> (192, 185, 201) using (105, 96, 119) as brain centroid... mean wm in atlas = 107, using box (89,80,99) --> (120, 112,139) to find MRI wm before smoothing, mri peak at 107 robust fit to distribution - 108 +- 3.7 after smoothing, mri peak at 108, scaling input intensities by 0.991 scaling channel 0 by 0.990741 initial log_p = -3.991 ************************************************ First Search limited to translation only. ************************************************ max log p = -3.930322 @ (-9.091, 9.091, -9.091) max log p = -3.791455 @ (4.545, -4.545, 4.545) max log p = -3.680316 @ (2.273, 2.273, -6.818) max log p = -3.667144 @ (-1.136, -1.136, 1.136) max log p = -3.661307 @ (1.705, 1.705, 0.568) max log p = -3.661307 @ (0.000, 0.000, 0.000) Found translation: (-1.7, 7.4, -9.7): log p = -3.661 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.518, old_max_log_p =-3.661 (thresh=-3.7) 1.07500 0.00000 0.00000 -11.33768; 0.00000 1.06580 0.14032 -16.12809; 0.00000 -0.13053 0.99144 5.93199; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.518, old_max_log_p =-3.518 (thresh=-3.5) 1.07500 0.00000 0.00000 -11.33768; 0.00000 1.06580 0.14032 -16.12809; 0.00000 -0.13053 0.99144 5.93199; 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=-3.401, old_max_log_p =-3.518 (thresh=-3.5) 1.07442 0.03488 0.00451 -15.67781; -0.03583 1.08536 0.14038 -13.47109; 0.00000 -0.12826 0.95408 11.84613; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.394, old_max_log_p =-3.401 (thresh=-3.4) 1.07448 0.00224 -0.03040 -8.08282; -0.00066 1.08963 0.10815 -14.82054; 0.03335 -0.08977 0.93984 4.86701; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.394, old_max_log_p =-3.394 (thresh=-3.4) 1.07448 0.00224 -0.03040 -8.08282; 0.00152 1.08142 0.16938 -19.23647; 0.03394 -0.16386 0.94821 14.01128; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.376, old_max_log_p =-3.394 (thresh=-3.4) 1.07226 0.01721 -0.01208 -11.48435; -0.01604 1.08002 0.16941 -15.88917; 0.01634 -0.16369 0.94746 17.27280; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.372, old_max_log_p =-3.376 (thresh=-3.4) 1.07100 0.01719 -0.01206 -11.32237; -0.01620 1.08259 0.16184 -15.78961; 0.01622 -0.15503 0.94993 15.59646; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.371, old_max_log_p =-3.372 (thresh=-3.4) 1.07226 0.01721 -0.01208 -11.48415; -0.01620 1.08259 0.16184 -15.78961; 0.01624 -0.15521 0.95104 15.49117; 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 1.07226 0.01721 -0.01208 -11.48415; -0.01620 1.08259 0.16184 -15.78961; 0.01624 -0.15521 0.95104 15.49117; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.07226 0.01721 -0.01208 -11.48415; -0.01620 1.08259 0.16184 -15.78961; 0.01624 -0.15521 0.95104 15.49117; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.07226 0.01721 -0.01208 -11.48415; -0.01620 1.08259 0.16184 -15.78961; 0.01624 -0.15521 0.95104 15.49117; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.371 (old=-3.991) transform before final EM align: 1.07226 0.01721 -0.01208 -11.48415; -0.01620 1.08259 0.16184 -15.78961; 0.01624 -0.15521 0.95104 15.49117; 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 1.07226 0.01721 -0.01208 -11.48415; -0.01620 1.08259 0.16184 -15.78961; 0.01624 -0.15521 0.95104 15.49117; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 1.07226 0.01721 -0.01208 -11.48415; -0.01620 1.08259 0.16184 -15.78961; 0.01624 -0.15521 0.95104 15.49117; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 012: -log(p) = 3.9 tol 0.000000 final transform: 1.07226 0.01721 -0.01208 -11.48415; -0.01620 1.08259 0.16184 -15.78961; 0.01624 -0.15521 0.95104 15.49117; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 711.609371 mri_em_register stimesec 0.875952 mri_em_register ru_maxrss 602888 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 166755 mri_em_register ru_majflt 13 mri_em_register ru_nswap 0 mri_em_register ru_inblock 151360 mri_em_register ru_oublock 16 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 108 mri_em_register ru_nivcsw 1028 registration took 1 minutes and 47 seconds. #-------------------------------------- #@# CA Normalize Mon Mar 29 22:37:18 UTC 2021 /out/out/freesurfer/sub-05/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... INFO: MRImask() using MRImaskDifferentGeometry() resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=29.9 skull bounding box = (62, 51, 37) --> (192, 185, 201) using (105, 96, 119) as brain centroid... mean wm in atlas = 107, using box (89,80,99) --> (120, 112,139) to find MRI wm before smoothing, mri peak at 107 robust fit to distribution - 108 +- 3.7 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 1.07226 0.01721 -0.01208 -11.48415; -0.01620 1.08259 0.16184 -15.78961; 0.01624 -0.15521 0.95104 15.49117; 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 (126, 49, 30) --> (189, 155, 203) Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 132.0 5 of 5708 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (68, 50, 29) --> (130, 155, 203) Right_Cerebral_White_Matter: limiting intensities to 95.0 --> 132.0 1 of 7035 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (128, 132, 57) --> (173, 172, 114) Left_Cerebellum_White_Matter: limiting intensities to 98.0 --> 132.0 0 of 166 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (86, 132, 55) --> (127, 169, 115) Right_Cerebellum_White_Matter: limiting intensities to 97.0 --> 132.0 0 of 141 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (112, 120, 95) --> (144, 185, 126) Brain_Stem: limiting intensities to 93.0 --> 132.0 0 of 36 (0.0%) samples deleted using 13086 total control points for intensity normalization... bias field = 0.984 +- 0.043 197 of 13080 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (126, 49, 30) --> (189, 155, 203) Left_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0 4 of 6208 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (68, 50, 29) --> (130, 155, 203) Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 1 of 7326 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (128, 132, 57) --> (173, 172, 114) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 3 of 246 (1.2%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (86, 132, 55) --> (127, 169, 115) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 3 of 226 (1.3%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (112, 120, 95) --> (144, 185, 126) Brain_Stem: limiting intensities to 88.0 --> 132.0 1 of 112 (0.9%) samples deleted using 14118 total control points for intensity normalization... bias field = 1.026 +- 0.039 92 of 13990 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (126, 49, 30) --> (189, 155, 203) Left_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0 11 of 6194 (0.2%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (68, 50, 29) --> (130, 155, 203) Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 5 of 7314 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (128, 132, 57) --> (173, 172, 114) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 60 of 310 (19.4%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (86, 132, 55) --> (127, 169, 115) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 51 of 291 (17.5%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (112, 120, 95) --> (144, 185, 126) Brain_Stem: limiting intensities to 88.0 --> 132.0 45 of 188 (23.9%) samples deleted using 14297 total control points for intensity normalization... bias field = 1.021 +- 0.034 57 of 13976 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 0 minutes and 46 seconds. #-------------------------------------- #@# CA Reg Mon Mar 29 22:38:04 UTC 2021 /out/out/freesurfer/sub-05/mri mri_ca_register -rusage /out/out/freesurfer/sub-05/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 = 8 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... INFO: MRImask() using MRImaskDifferentGeometry() INFO: MRImask() using MRImaskDifferentGeometry() INFO: MRImask() using MRImaskDifferentGeometry() INFO: MRImask() using MRImaskDifferentGeometry() INFO: MRImask() using MRImaskDifferentGeometry() reading GCA '/opt/freesurfer/average/RB_all_2016-05-10.vc700.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.13 (predicted orig area = 7.1) 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=0.820, neg=0, invalid=762 0001: dt=221.952000, rms=0.731 (10.890%), neg=0, invalid=762 0002: dt=147.361345, rms=0.711 (2.657%), neg=0, invalid=762 0003: dt=295.936000, rms=0.698 (1.857%), neg=0, invalid=762 0004: dt=110.976000, rms=0.694 (0.614%), neg=0, invalid=762 0005: dt=1183.744000, rms=0.683 (1.487%), neg=0, invalid=762 0006: dt=92.480000, rms=0.681 (0.364%), neg=0, invalid=762 0007: dt=443.904000, rms=0.679 (0.320%), neg=0, invalid=762 0008: dt=369.920000, rms=0.676 (0.400%), neg=0, invalid=762 0009: dt=73.984000, rms=0.675 (0.099%), neg=0, invalid=762 0010: dt=73.984000, rms=0.675 (0.022%), neg=0, invalid=762 0011: dt=73.984000, rms=0.675 (0.040%), neg=0, invalid=762 0012: dt=73.984000, rms=0.674 (0.075%), neg=0, invalid=762 0013: dt=73.984000, rms=0.673 (0.135%), neg=0, invalid=762 0014: dt=73.984000, rms=0.672 (0.185%), neg=0, invalid=762 0015: dt=73.984000, rms=0.671 (0.199%), neg=0, invalid=762 0016: dt=73.984000, rms=0.670 (0.185%), neg=0, invalid=762 0017: dt=73.984000, rms=0.669 (0.145%), neg=0, invalid=762 0018: dt=73.984000, rms=0.668 (0.111%), neg=0, invalid=762 0019: dt=73.984000, rms=0.667 (0.088%), neg=0, invalid=762 0020: dt=369.920000, rms=0.667 (0.062%), neg=0, invalid=762 0021: dt=369.920000, rms=0.667 (-0.232%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.667, neg=0, invalid=762 0022: dt=221.952000, rms=0.664 (0.507%), neg=0, invalid=762 0023: dt=221.952000, rms=0.663 (0.116%), neg=0, invalid=762 0024: dt=221.952000, rms=0.663 (0.069%), neg=0, invalid=762 0025: dt=221.952000, rms=0.662 (0.134%), neg=0, invalid=762 0026: dt=221.952000, rms=0.661 (0.190%), neg=0, invalid=762 0027: dt=221.952000, rms=0.660 (0.150%), neg=0, invalid=762 0028: dt=221.952000, rms=0.659 (0.148%), neg=0, invalid=762 0029: dt=221.952000, rms=0.657 (0.171%), neg=0, invalid=762 0030: dt=221.952000, rms=0.656 (0.166%), neg=0, invalid=762 0031: dt=221.952000, rms=0.656 (0.118%), neg=0, invalid=762 0032: dt=221.952000, rms=0.655 (0.097%), neg=0, invalid=762 0033: dt=369.920000, rms=0.654 (0.097%), neg=0, invalid=762 0034: dt=369.920000, rms=0.654 (-0.318%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.659, neg=0, invalid=762 0035: dt=62.208000, rms=0.655 (0.522%), neg=0, invalid=762 0036: dt=331.776000, rms=0.642 (1.957%), neg=0, invalid=762 0037: dt=158.165605, rms=0.635 (1.152%), neg=0, invalid=762 0038: dt=63.778035, rms=0.632 (0.548%), neg=0, invalid=762 0039: dt=145.152000, rms=0.630 (0.291%), neg=0, invalid=762 0040: dt=109.639344, rms=0.627 (0.445%), neg=0, invalid=762 0041: dt=36.288000, rms=0.626 (0.159%), neg=0, invalid=762 0042: dt=36.288000, rms=0.625 (0.088%), neg=0, invalid=762 0043: dt=36.288000, rms=0.624 (0.146%), neg=0, invalid=762 0044: dt=36.288000, rms=0.623 (0.234%), neg=0, invalid=762 0045: dt=36.288000, rms=0.621 (0.313%), neg=0, invalid=762 0046: dt=36.288000, rms=0.619 (0.346%), neg=0, invalid=762 0047: dt=36.288000, rms=0.617 (0.346%), neg=0, invalid=762 0048: dt=36.288000, rms=0.615 (0.331%), neg=0, invalid=762 0049: dt=36.288000, rms=0.613 (0.308%), neg=0, invalid=762 0050: dt=36.288000, rms=0.611 (0.300%), neg=0, invalid=762 0051: dt=36.288000, rms=0.609 (0.305%), neg=0, invalid=762 0052: dt=36.288000, rms=0.607 (0.300%), neg=0, invalid=762 0053: dt=36.288000, rms=0.606 (0.269%), neg=0, invalid=762 0054: dt=36.288000, rms=0.604 (0.233%), neg=0, invalid=762 0055: dt=36.288000, rms=0.603 (0.205%), neg=0, invalid=762 0056: dt=36.288000, rms=0.602 (0.181%), neg=0, invalid=762 0057: dt=36.288000, rms=0.601 (0.168%), neg=0, invalid=762 0058: dt=36.288000, rms=0.600 (0.155%), neg=0, invalid=762 0059: dt=36.288000, rms=0.599 (0.150%), neg=0, invalid=762 0060: dt=36.288000, rms=0.598 (0.133%), neg=0, invalid=762 0061: dt=36.288000, rms=0.598 (0.115%), neg=0, invalid=762 0062: dt=36.288000, rms=0.597 (0.100%), neg=0, invalid=762 0063: dt=145.152000, rms=0.597 (0.031%), neg=0, invalid=762 0064: dt=145.152000, rms=0.597 (-0.029%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.597, neg=0, invalid=762 0065: dt=103.680000, rms=0.594 (0.608%), neg=0, invalid=762 0066: dt=36.288000, rms=0.593 (0.063%), neg=0, invalid=762 0067: dt=36.288000, rms=0.593 (0.028%), neg=0, invalid=762 0068: dt=36.288000, rms=0.593 (0.041%), neg=0, invalid=762 0069: dt=36.288000, rms=0.593 (0.063%), neg=0, invalid=762 0070: dt=36.288000, rms=0.592 (0.078%), neg=0, invalid=762 0071: dt=36.288000, rms=0.592 (0.066%), neg=0, invalid=762 0072: dt=36.288000, rms=0.591 (0.042%), neg=0, invalid=762 0073: dt=0.567000, rms=0.591 (0.001%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.616, neg=0, invalid=762 0074: dt=2.800000, rms=0.615 (0.130%), neg=0, invalid=762 0075: dt=2.800000, rms=0.615 (0.014%), neg=0, invalid=762 0076: dt=2.800000, rms=0.615 (0.003%), neg=0, invalid=762 0077: dt=2.800000, rms=0.615 (-0.046%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.616, neg=0, invalid=762 0078: dt=1.600000, rms=0.615 (0.096%), neg=0, invalid=762 0079: dt=0.175000, rms=0.615 (-0.001%), neg=0, invalid=762 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.680, neg=0, invalid=762 0080: dt=5.942446, rms=0.661 (2.843%), neg=0, invalid=762 0081: dt=3.456000, rms=0.660 (0.139%), neg=0, invalid=762 0082: dt=3.456000, rms=0.660 (-0.046%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.661, neg=0, invalid=762 0083: dt=0.000000, rms=0.660 (0.078%), neg=0, invalid=762 0084: dt=0.000000, rms=0.660 (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=0.720, neg=0, invalid=762 0085: dt=0.768000, rms=0.718 (0.298%), neg=0, invalid=762 0086: dt=1.792000, rms=0.715 (0.396%), neg=0, invalid=762 0087: dt=2.220339, rms=0.712 (0.458%), neg=0, invalid=762 0088: dt=1.024000, rms=0.711 (0.044%), neg=0, invalid=762 0089: dt=1.024000, rms=0.711 (0.056%), neg=0, invalid=762 0090: dt=1.024000, rms=0.711 (0.047%), neg=0, invalid=762 0091: dt=1.024000, rms=0.711 (-0.042%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.711, neg=0, invalid=762 0092: dt=1.536000, rms=0.710 (0.204%), neg=0, invalid=762 0093: dt=0.000000, rms=0.710 (0.000%), neg=0, invalid=762 0094: dt=0.100000, rms=0.710 (-0.003%), 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=0.671, neg=0, invalid=762 0095: dt=0.819227, rms=0.655 (2.454%), neg=0, invalid=762 0096: dt=0.080000, rms=0.654 (0.137%), neg=0, invalid=762 0097: dt=0.080000, rms=0.654 (-0.073%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.654, neg=0, invalid=762 0098: dt=0.028000, rms=0.654 (0.094%), neg=0, invalid=762 0099: dt=0.001500, rms=0.654 (-0.002%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.14576 (23) Left_Lateral_Ventricle (4): linear fit = 1.23 x + 0.0 (1229 voxels, overlap=0.686) Left_Lateral_Ventricle (4): linear fit = 1.23 x + 0.0 (1229 voxels, peak = 24), gca=24.5 gca peak = 0.15565 (16) mri peak = 0.09541 (24) Right_Lateral_Ventricle (43): linear fit = 1.59 x + 0.0 (679 voxels, overlap=0.231) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (679 voxels, peak = 25), gca=24.0 gca peak = 0.26829 (96) mri peak = 0.13641 (100) Right_Pallidum (52): linear fit = 1.03 x + 0.0 (1006 voxels, overlap=0.986) Right_Pallidum (52): linear fit = 1.03 x + 0.0 (1006 voxels, peak = 99), gca=99.4 gca peak = 0.20183 (93) mri peak = 0.08776 (100) Left_Pallidum (13): linear fit = 1.03 x + 0.0 (924 voxels, overlap=1.002) Left_Pallidum (13): linear fit = 1.03 x + 0.0 (924 voxels, peak = 96), gca=96.3 gca peak = 0.21683 (55) mri peak = 0.09467 (71) Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (1170 voxels, overlap=0.026) Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (1170 voxels, peak = 67), gca=67.4 gca peak = 0.30730 (58) mri peak = 0.07715 (70) Left_Hippocampus (17): linear fit = 1.18 x + 0.0 (891 voxels, overlap=0.020) Left_Hippocampus (17): linear fit = 1.18 x + 0.0 (891 voxels, peak = 69), gca=68.7 gca peak = 0.11430 (101) mri peak = 0.17753 (106) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (69055 voxels, overlap=0.619) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (69055 voxels, peak = 105), gca=104.5 gca peak = 0.12076 (102) mri peak = 0.12701 (105) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (70477 voxels, overlap=0.587) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (70477 voxels, peak = 106), gca=105.6 gca peak = 0.14995 (59) mri peak = 0.04148 (63) Left_Cerebral_Cortex (3): linear fit = 1.12 x + 0.0 (33686 voxels, overlap=0.684) Left_Cerebral_Cortex (3): linear fit = 1.12 x + 0.0 (33686 voxels, peak = 66), gca=66.4 gca peak = 0.15082 (58) mri peak = 0.04065 (65) Right_Cerebral_Cortex (42): linear fit = 1.14 x + 0.0 (35279 voxels, overlap=0.670) Right_Cerebral_Cortex (42): linear fit = 1.14 x + 0.0 (35279 voxels, peak = 66), gca=66.4 gca peak = 0.14161 (67) mri peak = 0.09666 (76) Right_Caudate (50): linear fit = 1.13 x + 0.0 (869 voxels, overlap=0.333) Right_Caudate (50): linear fit = 1.13 x + 0.0 (869 voxels, peak = 76), gca=76.0 gca peak = 0.15243 (71) mri peak = 0.10220 (79) Left_Caudate (11): linear fit = 1.08 x + 0.0 (1084 voxels, overlap=0.651) Left_Caudate (11): linear fit = 1.08 x + 0.0 (1084 voxels, peak = 76), gca=76.3 gca peak = 0.13336 (57) mri peak = 0.04967 (67) Left_Cerebellum_Cortex (8): linear fit = 1.22 x + 0.0 (28387 voxels, overlap=0.319) Left_Cerebellum_Cortex (8): linear fit = 1.22 x + 0.0 (28387 voxels, peak = 69), gca=69.3 gca peak = 0.13252 (56) mri peak = 0.05466 (68) Right_Cerebellum_Cortex (47): linear fit = 1.21 x + 0.0 (33198 voxels, overlap=0.182) Right_Cerebellum_Cortex (47): linear fit = 1.21 x + 0.0 (33198 voxels, peak = 67), gca=67.5 gca peak = 0.18181 (84) mri peak = 0.10145 (89) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (10925 voxels, overlap=0.377) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (10925 voxels, peak = 89), gca=89.5 gca peak = 0.20573 (83) mri peak = 0.11005 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (9627 voxels, overlap=0.457) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (9627 voxels, peak = 89), gca=89.2 gca peak = 0.21969 (57) mri peak = 0.10137 (70) Left_Amygdala (18): linear fit = 1.21 x + 0.0 (471 voxels, overlap=0.334) Left_Amygdala (18): linear fit = 1.21 x + 0.0 (471 voxels, peak = 69), gca=68.7 gca peak = 0.39313 (56) mri peak = 0.10129 (66) Right_Amygdala (54): linear fit = 1.16 x + 0.0 (622 voxels, overlap=0.132) Right_Amygdala (54): linear fit = 1.16 x + 0.0 (622 voxels, peak = 65), gca=65.2 gca peak = 0.14181 (85) mri peak = 0.06476 (94) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (6002 voxels, overlap=0.764) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (6002 voxels, peak = 91), gca=90.5 gca peak = 0.11978 (83) mri peak = 0.06886 (91) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (5148 voxels, overlap=0.541) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (5148 voxels, peak = 93), gca=92.5 gca peak = 0.13399 (79) mri peak = 0.06420 (84) Left_Putamen (12): linear fit = 1.10 x + 0.0 (2648 voxels, overlap=0.691) Left_Putamen (12): linear fit = 1.10 x + 0.0 (2648 voxels, peak = 87), gca=86.5 gca peak = 0.14159 (79) mri peak = 0.06982 (85) Right_Putamen (51): linear fit = 1.10 x + 0.0 (2688 voxels, overlap=0.914) Right_Putamen (51): linear fit = 1.10 x + 0.0 (2688 voxels, peak = 87), gca=86.5 gca peak = 0.10025 (80) mri peak = 0.09458 (90) Brain_Stem (16): linear fit = 1.12 x + 0.0 (13840 voxels, overlap=0.303) Brain_Stem (16): linear fit = 1.12 x + 0.0 (13840 voxels, peak = 89), gca=89.2 gca peak = 0.13281 (86) mri peak = 0.10725 (96) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1502 voxels, overlap=0.431) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1502 voxels, peak = 93), gca=93.3 gca peak = 0.12801 (89) mri peak = 0.08705 (97) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1567 voxels, overlap=0.537) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1567 voxels, peak = 97), gca=97.5 gca peak = 0.20494 (23) mri peak = 0.08258 (23) gca peak = 0.15061 (21) mri peak = 0.10368 (27) Fourth_Ventricle (15): linear fit = 1.37 x + 0.0 (407 voxels, overlap=0.506) Fourth_Ventricle (15): linear fit = 1.37 x + 0.0 (407 voxels, peak = 29), gca=28.7 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18056 (32) gca peak Left_Thalamus = 0.64095 (94) gca peak Third_Ventricle = 0.20494 (23) 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 1.17 x + 0.0 estimating mean wm scale to be 1.03 x + 0.0 estimating mean csf scale to be 1.36 x + 0.0 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=0.646, neg=0, invalid=762 0100: dt=130.729517, rms=0.630 (2.463%), neg=0, invalid=762 0101: dt=295.936000, rms=0.625 (0.892%), neg=0, invalid=762 0102: dt=129.472000, rms=0.622 (0.427%), neg=0, invalid=762 0103: dt=129.472000, rms=0.621 (0.166%), neg=0, invalid=762 0104: dt=517.888000, rms=0.618 (0.440%), neg=0, invalid=762 0105: dt=73.984000, rms=0.617 (0.181%), neg=0, invalid=762 0106: dt=443.904000, rms=0.616 (0.111%), neg=0, invalid=762 0107: dt=129.472000, rms=0.615 (0.218%), neg=0, invalid=762 0108: dt=92.480000, rms=0.615 (0.024%), neg=0, invalid=762 0109: dt=92.480000, rms=0.615 (0.047%), neg=0, invalid=762 0110: dt=92.480000, rms=0.614 (0.081%), neg=0, invalid=762 0111: dt=92.480000, rms=0.613 (0.103%), neg=0, invalid=762 0112: dt=92.480000, rms=0.613 (0.112%), neg=0, invalid=762 0113: dt=92.480000, rms=0.612 (0.123%), neg=0, invalid=762 0114: dt=92.480000, rms=0.611 (0.124%), neg=0, invalid=762 0115: dt=92.480000, rms=0.610 (0.124%), neg=0, invalid=762 0116: dt=92.480000, rms=0.610 (0.111%), neg=0, invalid=762 0117: dt=92.480000, rms=0.609 (0.102%), neg=0, invalid=762 0118: dt=92.480000, rms=0.609 (0.100%), neg=0, invalid=762 0119: dt=92.480000, rms=0.608 (0.100%), neg=0, invalid=762 0120: dt=92.480000, rms=0.607 (0.101%), neg=0, invalid=762 0121: dt=92.480000, rms=0.607 (0.099%), neg=0, invalid=762 0122: dt=92.480000, rms=0.606 (0.091%), neg=0, invalid=762 0123: dt=92.480000, rms=0.606 (0.083%), neg=0, invalid=762 0124: dt=92.480000, rms=0.605 (0.084%), neg=0, invalid=762 0125: dt=92.480000, rms=0.605 (0.079%), neg=0, invalid=762 0126: dt=92.480000, rms=0.604 (0.074%), neg=0, invalid=762 0127: dt=92.480000, rms=0.604 (0.067%), neg=0, invalid=762 0128: dt=92.480000, rms=0.603 (0.061%), neg=0, invalid=762 0129: dt=92.480000, rms=0.603 (0.057%), neg=0, invalid=762 0130: dt=92.480000, rms=0.603 (0.055%), neg=0, invalid=762 0131: dt=92.480000, rms=0.602 (0.056%), neg=0, invalid=762 0132: dt=92.480000, rms=0.602 (0.055%), neg=0, invalid=762 0133: dt=92.480000, rms=0.602 (0.051%), neg=0, invalid=762 0134: dt=92.480000, rms=0.601 (0.049%), neg=0, invalid=762 0135: dt=92.480000, rms=0.601 (0.046%), neg=0, invalid=762 0136: dt=92.480000, rms=0.601 (0.046%), neg=0, invalid=762 0137: dt=92.480000, rms=0.601 (0.048%), neg=0, invalid=762 0138: dt=92.480000, rms=0.600 (0.049%), neg=0, invalid=762 0139: dt=92.480000, rms=0.600 (0.044%), neg=0, invalid=762 0140: dt=92.480000, rms=0.600 (0.041%), neg=0, invalid=762 0141: dt=92.480000, rms=0.600 (0.043%), neg=0, invalid=762 0142: dt=92.480000, rms=0.599 (0.042%), neg=0, invalid=762 0143: dt=92.480000, rms=0.599 (0.042%), neg=0, invalid=762 0144: dt=92.480000, rms=0.599 (0.037%), neg=0, invalid=762 0145: dt=92.480000, rms=0.599 (0.034%), neg=0, invalid=762 0146: dt=92.480000, rms=0.598 (0.037%), neg=0, invalid=762 0147: dt=92.480000, rms=0.598 (0.038%), neg=0, invalid=762 0148: dt=92.480000, rms=0.598 (0.033%), neg=0, invalid=762 0149: dt=92.480000, rms=0.598 (0.029%), neg=0, invalid=762 0150: dt=92.480000, rms=0.598 (0.028%), neg=0, invalid=762 0151: dt=92.480000, rms=0.598 (0.027%), neg=0, invalid=762 0152: dt=92.480000, rms=0.597 (0.027%), neg=0, invalid=762 0153: dt=92.480000, rms=0.597 (0.024%), neg=0, invalid=762 0154: dt=92.480000, rms=0.597 (0.023%), neg=0, invalid=762 0155: dt=32.368000, rms=0.597 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.597, neg=0, invalid=762 0156: dt=295.936000, rms=0.596 (0.214%), neg=0, invalid=762 0157: dt=129.472000, rms=0.596 (0.046%), neg=0, invalid=762 0158: dt=129.472000, rms=0.596 (0.022%), neg=0, invalid=762 0159: dt=129.472000, rms=0.596 (0.035%), neg=0, invalid=762 0160: dt=129.472000, rms=0.595 (0.042%), neg=0, invalid=762 0161: dt=129.472000, rms=0.595 (0.041%), neg=0, invalid=762 0162: dt=129.472000, rms=0.595 (0.036%), neg=0, invalid=762 0163: dt=129.472000, rms=0.595 (0.029%), neg=0, invalid=762 0164: dt=129.472000, rms=0.595 (0.024%), neg=0, invalid=762 0165: dt=129.472000, rms=0.594 (0.021%), neg=0, invalid=762 0166: dt=1183.744000, rms=0.594 (0.026%), neg=0, invalid=762 0167: dt=129.472000, rms=0.594 (0.015%), neg=0, invalid=762 0168: dt=129.472000, rms=0.594 (-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=0.595, neg=0, invalid=762 0169: dt=130.909091, rms=0.591 (0.668%), neg=0, invalid=762 0170: dt=172.775665, rms=0.584 (1.212%), neg=0, invalid=762 0171: dt=60.327869, rms=0.581 (0.513%), neg=0, invalid=762 0172: dt=414.720000, rms=0.574 (1.308%), neg=0, invalid=762 0173: dt=55.024390, rms=0.570 (0.592%), neg=0, invalid=762 0174: dt=497.664000, rms=0.565 (0.955%), neg=0, invalid=762 0175: dt=53.797101, rms=0.562 (0.495%), neg=0, invalid=762 0176: dt=145.152000, rms=0.560 (0.270%), neg=0, invalid=762 0177: dt=82.944000, rms=0.560 (0.124%), neg=0, invalid=762 0178: dt=145.152000, rms=0.558 (0.270%), neg=0, invalid=762 0179: dt=36.288000, rms=0.558 (0.095%), neg=0, invalid=762 0180: dt=331.776000, rms=0.556 (0.239%), neg=0, invalid=762 0181: dt=36.288000, rms=0.555 (0.270%), neg=0, invalid=762 0182: dt=331.776000, rms=0.553 (0.304%), neg=0, invalid=762 0183: dt=36.288000, rms=0.552 (0.174%), neg=0, invalid=762 0184: dt=82.944000, rms=0.552 (0.062%), neg=0, invalid=762 0185: dt=36.288000, rms=0.552 (0.061%), neg=0, invalid=762 0186: dt=36.288000, rms=0.551 (0.039%), neg=0, invalid=762 0187: dt=18.144000, rms=0.551 (0.019%), neg=0, invalid=762 0188: dt=1.134000, rms=0.551 (0.001%), neg=0, invalid=762 0189: dt=0.567000, rms=0.551 (0.001%), neg=0, invalid=762 0190: dt=0.141750, rms=0.551 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.552, neg=0, invalid=762 0191: dt=145.152000, rms=0.549 (0.556%), neg=0, invalid=762 0192: dt=36.288000, rms=0.548 (0.127%), neg=0, invalid=762 0193: dt=145.152000, rms=0.547 (0.151%), neg=0, invalid=762 0194: dt=124.416000, rms=0.546 (0.146%), neg=0, invalid=762 0195: dt=36.288000, rms=0.546 (0.070%), neg=0, invalid=762 0196: dt=9.072000, rms=0.546 (0.009%), neg=0, invalid=762 0197: dt=9.072000, rms=0.546 (0.010%), neg=0, invalid=762 0198: dt=1.134000, rms=0.546 (0.001%), neg=0, invalid=762 0199: dt=0.567000, rms=0.546 (0.001%), neg=0, invalid=762 0200: dt=0.283500, rms=0.546 (0.000%), neg=0, invalid=762 0201: dt=0.101250, rms=0.546 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.551, neg=0, invalid=762 0202: dt=0.000000, rms=0.551 (0.077%), neg=0, invalid=762 0203: dt=0.000000, rms=0.551 (0.000%), neg=0, invalid=762 0204: dt=0.000004, rms=0.551 (0.000%), neg=0, invalid=762 0205: dt=0.000001, rms=0.551 (0.000%), neg=0, invalid=762 0206: dt=0.000000, rms=0.551 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.551, neg=0, invalid=762 0207: dt=0.000000, rms=0.551 (0.077%), neg=0, invalid=762 0208: dt=0.000000, rms=0.551 (0.000%), neg=0, invalid=762 0209: dt=0.000015, rms=0.551 (0.000%), neg=0, invalid=762 0210: dt=0.000004, rms=0.551 (0.000%), neg=0, invalid=762 0211: dt=0.000002, rms=0.551 (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=0.568, neg=0, invalid=762 0212: dt=0.000000, rms=0.567 (0.073%), neg=0, invalid=762 0213: dt=0.000000, rms=0.567 (0.000%), neg=0, invalid=762 0214: dt=0.000000, rms=0.567 (0.000%), neg=0, invalid=762 0215: dt=0.000000, rms=0.567 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.568, neg=0, invalid=762 0216: dt=16.128000, rms=0.534 (5.860%), neg=0, invalid=762 0217: dt=4.032000, rms=0.532 (0.472%), neg=0, invalid=762 0218: dt=4.032000, rms=0.530 (0.377%), neg=0, invalid=762 0219: dt=4.032000, rms=0.528 (0.311%), neg=0, invalid=762 0220: dt=4.032000, rms=0.527 (0.262%), neg=0, invalid=762 0221: dt=4.032000, rms=0.526 (0.222%), neg=0, invalid=762 0222: dt=1.008000, rms=0.525 (0.051%), neg=0, invalid=762 0223: dt=1.008000, rms=0.525 (0.046%), neg=0, invalid=762 0224: dt=0.126000, rms=0.525 (0.006%), neg=0, invalid=762 0225: dt=0.063000, rms=0.525 (0.003%), neg=0, invalid=762 0226: dt=0.031500, rms=0.525 (0.002%), neg=0, invalid=762 0227: dt=0.015750, rms=0.525 (0.001%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.552, neg=0, invalid=762 0228: dt=0.000000, rms=0.551 (0.069%), neg=0, invalid=762 0229: dt=0.000000, rms=0.551 (0.000%), neg=0, invalid=762 0230: dt=0.100000, rms=0.551 (-0.036%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.552, neg=0, invalid=762 0231: dt=0.000000, rms=0.551 (0.069%), neg=0, invalid=762 0232: dt=0.000000, rms=0.551 (0.000%), neg=0, invalid=762 0233: dt=0.100000, rms=0.551 (-0.022%), 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=0.507, neg=0, invalid=762 0234: dt=0.112000, rms=0.504 (0.701%), neg=0, invalid=762 0235: dt=0.384000, rms=0.495 (1.665%), neg=0, invalid=762 0236: dt=0.448000, rms=0.492 (0.674%), neg=0, invalid=762 0237: dt=0.448000, rms=0.490 (0.320%), neg=0, invalid=762 0238: dt=0.448000, rms=0.489 (0.210%), neg=0, invalid=762 0239: dt=0.448000, rms=0.489 (0.155%), neg=0, invalid=762 0240: dt=0.448000, rms=0.488 (0.116%), neg=0, invalid=762 0241: dt=0.448000, rms=0.488 (0.093%), neg=0, invalid=762 0242: dt=0.448000, rms=0.487 (0.074%), neg=0, invalid=762 0243: dt=0.448000, rms=0.487 (0.061%), neg=0, invalid=762 0244: dt=0.448000, rms=0.487 (0.053%), neg=0, invalid=762 0245: dt=0.448000, rms=0.487 (0.043%), neg=0, invalid=762 0246: dt=0.448000, rms=0.486 (0.038%), neg=0, invalid=762 0247: dt=0.448000, rms=0.486 (0.065%), neg=0, invalid=762 0248: dt=0.448000, rms=0.486 (0.025%), neg=0, invalid=762 0249: dt=0.448000, rms=0.486 (0.045%), neg=0, invalid=762 0250: dt=0.448000, rms=0.486 (0.017%), neg=0, invalid=762 0251: dt=0.448000, rms=0.485 (0.031%), neg=0, invalid=762 0252: dt=0.448000, rms=0.485 (0.012%), neg=0, invalid=762 0253: dt=0.448000, rms=0.485 (0.021%), neg=0, invalid=762 0254: dt=0.448000, rms=0.485 (0.026%), neg=0, invalid=762 0255: dt=0.448000, rms=0.485 (0.034%), neg=0, invalid=762 0256: dt=0.448000, rms=0.485 (0.004%), neg=0, invalid=762 0257: dt=0.448000, rms=0.485 (0.007%), neg=0, invalid=762 0258: dt=0.224000, rms=0.485 (0.003%), neg=0, invalid=762 0259: dt=0.448000, rms=0.485 (0.002%), neg=0, invalid=762 0260: dt=0.224000, rms=0.485 (0.005%), neg=0, invalid=762 0261: dt=0.224000, rms=0.485 (0.001%), neg=0, invalid=762 0262: dt=0.224000, rms=0.485 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.485, neg=0, invalid=762 0263: dt=0.448000, rms=0.482 (0.745%), neg=0, invalid=762 0264: dt=0.448000, rms=0.481 (0.063%), neg=0, invalid=762 0265: dt=0.448000, rms=0.481 (0.020%), neg=0, invalid=762 0266: dt=0.448000, rms=0.481 (0.001%), neg=0, invalid=762 0267: dt=0.448000, rms=0.481 (-0.001%), 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=0.479, neg=0, invalid=762 0268: dt=0.000000, rms=0.479 (0.092%), neg=0, invalid=762 0269: dt=0.000000, rms=0.479 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.479, neg=0, invalid=762 0270: dt=55.488000, rms=0.479 (0.096%), neg=0, invalid=762 0271: dt=73.984000, rms=0.479 (0.002%), neg=0, invalid=762 0272: dt=73.984000, rms=0.479 (0.002%), neg=0, invalid=762 0273: dt=73.984000, rms=0.479 (0.000%), neg=0, invalid=762 0274: dt=73.984000, rms=0.479 (-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=0.479, neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0275: dt=25.920000, rms=0.479 (0.124%), neg=0, invalid=762 0276: dt=25.920000, rms=0.479 (0.016%), neg=0, invalid=762 0277: dt=25.920000, rms=0.479 (0.017%), neg=0, invalid=762 0278: dt=25.920000, rms=0.479 (0.015%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 8 iterations, nbhd size=1, neg = 0 0279: dt=25.920000, rms=0.479 (-0.005%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.479, neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0280: dt=103.680000, rms=0.476 (0.539%), neg=0, invalid=762 0281: dt=36.288000, rms=0.476 (0.116%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 7 iterations, nbhd size=1, neg = 0 0282: dt=36.288000, rms=0.476 (0.047%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0283: dt=36.288000, rms=0.475 (0.087%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0284: dt=36.288000, rms=0.475 (0.112%), neg=0, invalid=762 0285: dt=36.288000, rms=0.474 (0.129%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0286: dt=36.288000, rms=0.473 (0.127%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0287: dt=36.288000, rms=0.473 (0.113%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0288: dt=36.288000, rms=0.472 (0.103%), neg=0, invalid=762 0289: dt=145.152000, rms=0.472 (0.035%), neg=0, invalid=762 0290: dt=145.152000, rms=0.472 (-0.030%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.473, neg=0, invalid=762 iter 0, gcam->neg = 11 after 1 iterations, nbhd size=0, neg = 0 0291: dt=38.400000, rms=0.470 (0.603%), neg=0, invalid=762 iter 0, gcam->neg = 16 after 9 iterations, nbhd size=1, neg = 0 0292: dt=71.724138, rms=0.466 (0.806%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0293: dt=21.705882, rms=0.465 (0.345%), neg=0, invalid=762 0294: dt=44.800000, rms=0.463 (0.348%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0295: dt=32.000000, rms=0.462 (0.228%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 0296: dt=32.000000, rms=0.461 (0.214%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 8 iterations, nbhd size=1, neg = 0 0297: dt=32.000000, rms=0.460 (0.316%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 7 iterations, nbhd size=1, neg = 0 0298: dt=32.000000, rms=0.458 (0.288%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 1 iterations, nbhd size=0, neg = 0 0299: dt=32.000000, rms=0.457 (0.394%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 10 iterations, nbhd size=1, neg = 0 0300: dt=32.000000, rms=0.455 (0.317%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 10 iterations, nbhd size=1, neg = 0 0301: dt=32.000000, rms=0.454 (0.308%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 8 iterations, nbhd size=1, neg = 0 0302: dt=32.000000, rms=0.453 (0.211%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 7 iterations, nbhd size=1, neg = 0 0303: dt=32.000000, rms=0.452 (0.249%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 8 iterations, nbhd size=1, neg = 0 0304: dt=32.000000, rms=0.451 (0.212%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 7 iterations, nbhd size=1, neg = 0 0305: dt=32.000000, rms=0.450 (0.166%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 9 iterations, nbhd size=1, neg = 0 0306: dt=32.000000, rms=0.450 (0.082%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 9 iterations, nbhd size=1, neg = 0 0307: dt=32.000000, rms=0.449 (0.122%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0308: dt=32.000000, rms=0.449 (0.115%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0309: dt=11.200000, rms=0.448 (0.043%), neg=0, invalid=762 0310: dt=11.200000, rms=0.448 (0.033%), neg=0, invalid=762 0311: dt=11.200000, rms=0.448 (0.007%), neg=0, invalid=762 0312: dt=11.200000, rms=0.448 (0.015%), neg=0, invalid=762 0313: dt=11.200000, rms=0.448 (0.027%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 3 iterations, nbhd size=0, neg = 0 0314: dt=11.200000, rms=0.448 (0.024%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.448, neg=0, invalid=762 0315: dt=44.800000, rms=0.445 (0.712%), neg=0, invalid=762 0316: dt=25.600000, rms=0.444 (0.144%), neg=0, invalid=762 0317: dt=25.600000, rms=0.444 (0.098%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0318: dt=25.600000, rms=0.444 (0.115%), neg=0, invalid=762 0319: dt=25.600000, rms=0.443 (0.108%), neg=0, invalid=762 0320: dt=25.600000, rms=0.443 (0.069%), neg=0, invalid=762 0321: dt=11.200000, rms=0.443 (0.029%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.452, neg=0, invalid=762 0322: dt=1.008000, rms=0.452 (0.108%), neg=0, invalid=762 0323: dt=0.666667, rms=0.452 (0.002%), neg=0, invalid=762 0324: dt=0.666667, rms=0.452 (-0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.452, neg=0, invalid=762 0325: dt=3.456000, rms=0.452 (0.150%), neg=0, invalid=762 0326: dt=1.728000, rms=0.452 (0.012%), neg=0, invalid=762 0327: dt=1.728000, rms=0.452 (-0.001%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.466, neg=0, invalid=762 0328: dt=1.280000, rms=0.464 (0.386%), neg=0, invalid=762 0329: dt=0.448000, rms=0.464 (0.025%), neg=0, invalid=762 0330: dt=0.448000, rms=0.464 (0.004%), neg=0, invalid=762 0331: dt=0.448000, rms=0.464 (-0.054%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.465, neg=0, invalid=762 0332: dt=1.792000, rms=0.463 (0.281%), neg=0, invalid=762 0333: dt=1.024000, rms=0.463 (0.026%), neg=0, invalid=762 0334: dt=1.024000, rms=0.463 (0.000%), neg=0, invalid=762 0335: dt=1.024000, rms=0.463 (-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=0.455, neg=0, invalid=762 iter 0, gcam->neg = 564 after 14 iterations, nbhd size=1, neg = 0 0336: dt=2.313364, rms=0.426 (6.503%), neg=0, invalid=762 0337: dt=0.096000, rms=0.425 (0.096%), neg=0, invalid=762 0338: dt=0.096000, rms=0.425 (-0.065%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.426, neg=0, invalid=762 0339: dt=0.064000, rms=0.425 (0.153%), neg=0, invalid=762 0340: dt=0.000000, rms=0.425 (0.003%), neg=0, invalid=762 0341: dt=0.050000, rms=0.425 (-0.017%), 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=0.410, neg=0, invalid=762 0342: dt=0.000000, rms=0.410 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.410, neg=0, invalid=762 0343: dt=32.368000, rms=0.410 (0.002%), neg=0, invalid=762 0344: dt=1.734000, rms=0.410 (0.000%), neg=0, invalid=762 0345: dt=1.734000, rms=0.410 (-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=0.410, neg=0, invalid=762 0346: dt=0.000000, rms=0.410 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.410, neg=0, invalid=762 0347: dt=82.944000, rms=0.410 (0.056%), neg=0, invalid=762 0348: dt=145.152000, rms=0.409 (0.098%), neg=0, invalid=762 0349: dt=36.288000, rms=0.409 (0.032%), neg=0, invalid=762 0350: dt=36.288000, rms=0.409 (0.012%), neg=0, invalid=762 0351: dt=36.288000, rms=0.409 (0.022%), neg=0, invalid=762 0352: dt=36.288000, rms=0.409 (0.029%), neg=0, invalid=762 0353: dt=36.288000, rms=0.409 (0.034%), neg=0, invalid=762 0354: dt=36.288000, rms=0.409 (0.034%), neg=0, invalid=762 0355: dt=36.288000, rms=0.409 (0.029%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.409, neg=0, invalid=762 0356: dt=11.200000, rms=0.409 (0.112%), neg=0, invalid=762 0357: dt=11.200000, rms=0.409 (0.063%), neg=0, invalid=762 0358: dt=11.200000, rms=0.409 (0.050%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 7 iterations, nbhd size=1, neg = 0 0359: dt=11.200000, rms=0.408 (0.023%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 8 iterations, nbhd size=1, neg = 0 0360: dt=11.200000, rms=0.408 (-0.038%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.408, neg=0, invalid=762 iter 0, gcam->neg = 1 after 7 iterations, nbhd size=1, neg = 0 0361: dt=44.800000, rms=0.405 (0.729%), neg=0, invalid=762 0362: dt=30.295858, rms=0.404 (0.265%), neg=0, invalid=762 0363: dt=44.800000, rms=0.404 (0.206%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0364: dt=44.800000, rms=0.403 (0.086%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 7 iterations, nbhd size=1, neg = 0 0365: dt=44.800000, rms=0.402 (0.406%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 0366: dt=44.800000, rms=0.401 (0.184%), neg=0, invalid=762 iter 0, gcam->neg = 13 after 2 iterations, nbhd size=0, neg = 0 0367: dt=44.800000, rms=0.399 (0.349%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 11 iterations, nbhd size=1, neg = 0 0368: dt=44.800000, rms=0.399 (0.193%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0369: dt=44.800000, rms=0.398 (0.195%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 8 iterations, nbhd size=1, neg = 0 0370: dt=44.800000, rms=0.397 (0.194%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0371: dt=44.800000, rms=0.397 (0.087%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0372: dt=44.800000, rms=0.396 (0.157%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0373: dt=44.800000, rms=0.396 (0.061%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0374: dt=44.800000, rms=0.396 (0.050%), neg=0, invalid=762 0375: dt=19.200000, rms=0.395 (0.061%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0376: dt=102.400000, rms=0.395 (0.025%), neg=0, invalid=762 0377: dt=102.400000, rms=0.395 (-0.082%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.401, neg=0, invalid=762 0378: dt=0.000244, rms=0.401 (0.000%), neg=0, invalid=762 0379: dt=0.000000, rms=0.401 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.401, neg=0, invalid=762 0380: dt=1.008000, rms=0.401 (0.005%), neg=0, invalid=762 0381: dt=0.720000, rms=0.401 (0.002%), neg=0, invalid=762 0382: dt=0.720000, rms=0.401 (-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=0.413, neg=0, invalid=762 0383: dt=0.000000, rms=0.413 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.413, neg=0, invalid=762 0384: dt=0.448000, rms=0.412 (0.031%), neg=0, invalid=762 0385: dt=0.028000, rms=0.412 (0.000%), neg=0, invalid=762 0386: dt=0.028000, rms=0.412 (0.000%), neg=0, invalid=762 0387: dt=0.028000, rms=0.412 (-0.001%), 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=0.395, neg=0, invalid=762 iter 0, gcam->neg = 419 after 15 iterations, nbhd size=1, neg = 0 0388: dt=1.280000, rms=0.386 (2.248%), neg=0, invalid=762 0389: dt=0.000020, rms=0.386 (0.000%), neg=0, invalid=762 0390: dt=0.000020, rms=0.386 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.386, neg=0, invalid=762 0391: dt=0.080000, rms=0.386 (0.029%), neg=0, invalid=762 0392: dt=0.028000, rms=0.386 (0.004%), neg=0, invalid=762 0393: dt=0.028000, rms=0.386 (0.002%), neg=0, invalid=762 0394: dt=0.028000, rms=0.386 (-0.007%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 0 hours, 50 minutes and 36 seconds. mri_ca_register utimesec 4211.695884 mri_ca_register stimesec 3.351764 mri_ca_register ru_maxrss 1330560 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 4560305 mri_ca_register ru_majflt 12 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 2144 mri_ca_register ru_oublock 63112 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 16836 mri_ca_register ru_nivcsw 12694 FSRUNTIME@ mri_ca_register 0.8432 hours 8 threads #-------------------------------------- #@# SubCort Seg Mon Mar 29 23:28:39 UTC 2021 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 83ec93b3099f machine x86_64 setenv SUBJECTS_DIR /out/out/freesurfer cd /out/out/freesurfer/sub-05/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 = 8 == 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 7.07 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 = 0.12797 (24) Left_Lateral_Ventricle (4): linear fit = 1.12 x + 0.0 (1208 voxels, overlap=0.820) Left_Lateral_Ventricle (4): linear fit = 1.12 x + 0.0 (1208 voxels, peak = 22), gca=22.5 gca peak = 0.17677 (13) mri peak = 0.15100 (24) Right_Lateral_Ventricle (43): linear fit = 1.74 x + 0.0 (363 voxels, overlap=0.368) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (363 voxels, peak = 23), gca=19.5 gca peak = 0.28129 (95) mri peak = 0.19380 (100) Right_Pallidum (52): linear fit = 1.04 x + 0.0 (772 voxels, overlap=0.737) Right_Pallidum (52): linear fit = 1.04 x + 0.0 (772 voxels, peak = 99), gca=99.3 gca peak = 0.16930 (96) mri peak = 0.15561 (100) Left_Pallidum (13): linear fit = 1.03 x + 0.0 (826 voxels, overlap=0.743) Left_Pallidum (13): linear fit = 1.03 x + 0.0 (826 voxels, peak = 99), gca=99.4 gca peak = 0.24553 (55) mri peak = 0.10187 (69) Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (1067 voxels, overlap=0.020) Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (1067 voxels, peak = 67), gca=67.4 gca peak = 0.30264 (59) mri peak = 0.09367 (70) Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (975 voxels, overlap=0.018) Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (975 voxels, peak = 72), gca=72.3 gca peak = 0.07580 (103) mri peak = 0.21873 (106) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (40295 voxels, overlap=0.545) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (40295 voxels, peak = 105), gca=104.5 gca peak = 0.07714 (104) mri peak = 0.13546 (106) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (42754 voxels, overlap=0.566) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (42754 voxels, peak = 105), gca=104.5 gca peak = 0.09712 (58) mri peak = 0.05194 (66) Left_Cerebral_Cortex (3): linear fit = 1.12 x + 0.0 (46181 voxels, overlap=0.722) Left_Cerebral_Cortex (3): linear fit = 1.12 x + 0.0 (46181 voxels, peak = 65), gca=64.7 gca peak = 0.11620 (58) mri peak = 0.04642 (63) Right_Cerebral_Cortex (42): linear fit = 1.12 x + 0.0 (44553 voxels, overlap=0.656) Right_Cerebral_Cortex (42): linear fit = 1.12 x + 0.0 (44553 voxels, peak = 65), gca=64.7 gca peak = 0.30970 (66) mri peak = 0.13263 (79) Right_Caudate (50): linear fit = 1.17 x + 0.0 (1047 voxels, overlap=0.015) Right_Caudate (50): linear fit = 1.17 x + 0.0 (1047 voxels, peak = 78), gca=77.5 gca peak = 0.15280 (69) mri peak = 0.14535 (79) Left_Caudate (11): linear fit = 1.07 x + 0.0 (1082 voxels, overlap=0.503) Left_Caudate (11): linear fit = 1.07 x + 0.0 (1082 voxels, peak = 73), gca=73.5 gca peak = 0.13902 (56) mri peak = 0.05713 (70) Left_Cerebellum_Cortex (8): linear fit = 1.23 x + 0.0 (28773 voxels, overlap=0.132) Left_Cerebellum_Cortex (8): linear fit = 1.23 x + 0.0 (28773 voxels, peak = 69), gca=68.6 gca peak = 0.14777 (55) mri peak = 0.06437 (68) Right_Cerebellum_Cortex (47): linear fit = 1.23 x + 0.0 (29371 voxels, overlap=0.148) Right_Cerebellum_Cortex (47): linear fit = 1.23 x + 0.0 (29371 voxels, peak = 67), gca=67.4 gca peak = 0.16765 (84) mri peak = 0.15277 (89) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (6436 voxels, overlap=0.404) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (6436 voxels, peak = 89), gca=89.5 gca peak = 0.18739 (84) mri peak = 0.14357 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (6307 voxels, overlap=0.466) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (6307 voxels, peak = 89), gca=89.5 gca peak = 0.29869 (57) mri peak = 0.10231 (70) Left_Amygdala (18): linear fit = 1.18 x + 0.0 (582 voxels, overlap=0.061) Left_Amygdala (18): linear fit = 1.18 x + 0.0 (582 voxels, peak = 68), gca=67.5 gca peak = 0.33601 (57) mri peak = 0.09153 (66) Right_Amygdala (54): linear fit = 1.18 x + 0.0 (590 voxels, overlap=0.053) Right_Amygdala (54): linear fit = 1.18 x + 0.0 (590 voxels, peak = 68), gca=67.5 gca peak = 0.11131 (90) mri peak = 0.07443 (92) Left_Thalamus_Proper (10): linear fit = 1.05 x + 0.0 (5211 voxels, overlap=0.788) Left_Thalamus_Proper (10): linear fit = 1.05 x + 0.0 (5211 voxels, peak = 95), gca=94.9 gca peak = 0.11793 (83) mri peak = 0.08258 (92) Right_Thalamus_Proper (49): linear fit = 1.11 x + 0.0 (5322 voxels, overlap=0.498) Right_Thalamus_Proper (49): linear fit = 1.11 x + 0.0 (5322 voxels, peak = 92), gca=91.7 gca peak = 0.08324 (81) mri peak = 0.07696 (84) Left_Putamen (12): linear fit = 1.07 x + 0.0 (2040 voxels, overlap=0.633) Left_Putamen (12): linear fit = 1.07 x + 0.0 (2040 voxels, peak = 86), gca=86.3 gca peak = 0.10360 (77) mri peak = 0.07982 (85) Right_Putamen (51): linear fit = 1.09 x + 0.0 (2200 voxels, overlap=0.752) Right_Putamen (51): linear fit = 1.09 x + 0.0 (2200 voxels, peak = 84), gca=83.5 gca peak = 0.08424 (78) mri peak = 0.09576 (90) Brain_Stem (16): linear fit = 1.11 x + 0.0 (12914 voxels, overlap=0.359) Brain_Stem (16): linear fit = 1.11 x + 0.0 (12914 voxels, peak = 86), gca=86.2 gca peak = 0.12631 (89) mri peak = 0.11053 (97) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1759 voxels, overlap=0.490) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1759 voxels, peak = 97), gca=97.5 gca peak = 0.14500 (87) mri peak = 0.10033 (97) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1846 voxels, overlap=0.474) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1846 voxels, peak = 94), gca=93.5 gca peak = 0.14975 (24) mri peak = 0.17241 (26) gca peak = 0.19357 (14) mri peak = 0.13400 (27) Fourth_Ventricle (15): linear fit = 1.62 x + 0.0 (296 voxels, overlap=0.227) Fourth_Ventricle (15): linear fit = 1.62 x + 0.0 (296 voxels, peak = 23), gca=22.8 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 1.17 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 1.31 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.13944 (23) mri peak = 0.12797 (24) Left_Lateral_Ventricle (4): linear fit = 1.07 x + 0.0 (1208 voxels, overlap=0.888) Left_Lateral_Ventricle (4): linear fit = 1.07 x + 0.0 (1208 voxels, peak = 24), gca=24.5 gca peak = 0.13422 (19) mri peak = 0.15100 (24) Right_Lateral_Ventricle (43): linear fit = 1.13 x + 0.0 (363 voxels, overlap=0.630) Right_Lateral_Ventricle (43): linear fit = 1.13 x + 0.0 (363 voxels, peak = 22), gca=21.6 gca peak = 0.28968 (100) mri peak = 0.19380 (100) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (772 voxels, overlap=1.004) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (772 voxels, peak = 100), gca=100.0 gca peak = 0.15778 (100) mri peak = 0.15561 (100) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (826 voxels, overlap=1.000) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (826 voxels, peak = 100), gca=100.0 gca peak = 0.25345 (68) mri peak = 0.10187 (69) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (1067 voxels, overlap=0.978) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (1067 voxels, peak = 67), gca=67.0 gca peak = 0.28383 (69) mri peak = 0.09367 (70) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (975 voxels, overlap=1.001) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (975 voxels, peak = 68), gca=68.0 gca peak = 0.07767 (104) mri peak = 0.21873 (106) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (40295 voxels, overlap=0.598) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (40295 voxels, peak = 105), gca=104.5 gca peak = 0.07908 (105) mri peak = 0.13546 (106) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (42754 voxels, overlap=0.589) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (42754 voxels, peak = 106), gca=105.5 gca peak = 0.08782 (64) mri peak = 0.05194 (66) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (46181 voxels, overlap=0.973) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (46181 voxels, peak = 64), gca=64.0 gca peak = 0.10507 (65) mri peak = 0.04642 (63) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (44553 voxels, overlap=0.958) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (44553 voxels, peak = 65), gca=65.0 gca peak = 0.23103 (78) mri peak = 0.13263 (79) Right_Caudate (50): linear fit = 0.99 x + 0.0 (1047 voxels, overlap=0.998) Right_Caudate (50): linear fit = 0.99 x + 0.0 (1047 voxels, peak = 77), gca=76.8 gca peak = 0.12679 (73) mri peak = 0.14535 (79) Left_Caudate (11): linear fit = 1.00 x + 0.0 (1082 voxels, overlap=0.835) Left_Caudate (11): linear fit = 1.00 x + 0.0 (1082 voxels, peak = 73), gca=73.0 gca peak = 0.11770 (68) mri peak = 0.05713 (70) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (28773 voxels, overlap=0.989) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (28773 voxels, peak = 68), gca=68.0 gca peak = 0.12396 (67) mri peak = 0.06437 (68) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (29371 voxels, overlap=0.982) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (29371 voxels, peak = 67), gca=67.0 gca peak = 0.15888 (90) mri peak = 0.15277 (89) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6436 voxels, overlap=0.865) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6436 voxels, peak = 90), gca=89.6 gca peak = 0.15222 (90) mri peak = 0.14357 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6307 voxels, overlap=0.868) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6307 voxels, peak = 90), gca=89.6 gca peak = 0.29337 (69) mri peak = 0.10231 (70) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (582 voxels, overlap=1.016) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (582 voxels, peak = 69), gca=69.0 gca peak = 0.31336 (68) mri peak = 0.09153 (66) Right_Amygdala (54): linear fit = 0.99 x + 0.0 (590 voxels, overlap=1.011) Right_Amygdala (54): linear fit = 0.99 x + 0.0 (590 voxels, peak = 67), gca=67.0 gca peak = 0.10636 (95) mri peak = 0.07443 (92) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5211 voxels, overlap=0.947) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5211 voxels, peak = 95), gca=94.5 gca peak = 0.09657 (89) mri peak = 0.08258 (92) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (5322 voxels, overlap=0.948) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (5322 voxels, peak = 89), gca=88.6 gca peak = 0.08912 (80) mri peak = 0.07696 (84) Left_Putamen (12): linear fit = 1.01 x + 0.0 (2040 voxels, overlap=0.867) Left_Putamen (12): linear fit = 1.01 x + 0.0 (2040 voxels, peak = 81), gca=81.2 gca peak = 0.08619 (85) mri peak = 0.07982 (85) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2200 voxels, overlap=0.989) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2200 voxels, peak = 85), gca=85.0 gca peak = 0.07357 (86) mri peak = 0.09576 (90) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12914 voxels, overlap=0.722) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12914 voxels, peak = 86), gca=85.6 gca peak = 0.12269 (92) mri peak = 0.11053 (97) Right_VentralDC (60): linear fit = 0.99 x + 0.0 (1759 voxels, overlap=0.826) Right_VentralDC (60): linear fit = 0.99 x + 0.0 (1759 voxels, peak = 91), gca=90.6 gca peak = 0.16820 (92) mri peak = 0.10033 (97) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1846 voxels, overlap=0.877) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1846 voxels, peak = 91), gca=90.6 gca peak = 0.12662 (36) mri peak = 0.17241 (26) gca peak = 0.16542 (21) mri peak = 0.13400 (27) Fourth_Ventricle (15): linear fit = 1.25 x + 0.0 (296 voxels, overlap=0.592) Fourth_Ventricle (15): linear fit = 1.25 x + 0.0 (296 voxels, peak = 26), gca=26.4 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 = 0.12662 (36) gca peak CSF = 0.17638 (48) gca peak Left_Accumbens_area = 0.62352 (66) gca peak Left_undetermined = 0.96707 (27) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.11914 (35) gca peak Right_Inf_Lat_Vent = 0.20093 (28) gca peak Right_Accumbens_area = 0.29837 (76) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14509 (37) gca peak Fifth_Ventricle = 0.75707 (41) gca peak WM_hypointensities = 0.08123 (77) gca peak non_WM_hypointensities = 0.12165 (55) gca peak Optic_Chiasm = 0.70845 (75) not using caudate to estimate GM means estimating mean gm scale to be 0.99 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.15 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 51695 voxels changed in iteration 0 of unlikely voxel relabeling 170 voxels changed in iteration 1 of unlikely voxel relabeling 3 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 40718 gm and wm labels changed (%32 to gray, %68 to white out of all changed labels) 346 hippocampal voxels changed. 1 amygdala voxels changed. pass 1: 59098 changed. image ll: -2.094, PF=0.500 pass 2: 14974 changed. image ll: -2.093, PF=0.500 pass 3: 4350 changed. 34513 voxels changed in iteration 0 of unlikely voxel relabeling 340 voxels changed in iteration 1 of unlikely voxel relabeling 12 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 6786 voxels changed in iteration 0 of unlikely voxel relabeling 116 voxels changed in iteration 1 of unlikely voxel relabeling 10 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 5762 voxels changed in iteration 0 of unlikely voxel relabeling 62 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 4743 voxels changed in iteration 0 of unlikely voxel relabeling 49 voxels changed in iteration 1 of unlikely voxel relabeling 8 voxels changed in iteration 2 of unlikely voxel relabeling 2 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 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 1403.226387 mri_ca_label stimesec 0.675994 mri_ca_label ru_maxrss 2120388 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 909790 mri_ca_label ru_majflt 1 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 152 mri_ca_label ru_oublock 472 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 519 mri_ca_label ru_nivcsw 5988 auto-labeling took 22 minutes and 49 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /out/out/freesurfer/sub-05/mri/transforms/cc_up.lta sub-05 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /out/out/freesurfer/sub-05/mri/transforms/cc_up.lta reading aseg from /out/out/freesurfer/sub-05/mri/aseg.auto_noCCseg.mgz reading norm from /out/out/freesurfer/sub-05/mri/norm.mgz 20178 voxels in left wm, 49891 in right wm, xrange [123, 130] searching rotation angles z=[-8 6], y=[-8 6] searching scale 1 Z rot -7.7 searching scale 1 Z rot -7.5 searching scale 1 Z rot -7.2 searching scale 1 Z rot -7.0 searching scale 1 Z rot -6.7 searching scale 1 Z rot -6.5 searching scale 1 Z rot -6.2 searching scale 1 Z rot -6.0 searching scale 1 Z rot -5.7 searching scale 1 Z rot -5.5 searching scale 1 Z rot -5.2 searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.7 searching scale 1 Z rot -4.5 searching scale 1 Z rot -4.2 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.2 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.2 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.2 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.0 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.8 searching scale 1 Z rot 4.0 searching scale 1 Z rot 4.3 searching scale 1 Z rot 4.5 searching scale 1 Z rot 4.8 searching scale 1 Z rot 5.0 searching scale 1 Z rot 5.3 searching scale 1 Z rot 5.5 searching scale 1 Z rot 5.8 searching scale 1 Z rot 6.0 global minimum found at slice 127.4, rotations (-1.16, -0.73) final transformation (x=127.4, yr=-1.161, zr=-0.727): 0.99971 0.01269 -0.02026 1.55643; -0.01268 0.99992 0.00026 33.59650; 0.02026 0.00000 0.99979 18.43970; 0.00000 0.00000 0.00000 1.00000; updating x range to be [125, 130] in xformed coordinates best xformed slice 127 cc center is found at 127 96 107 eigenvectors: -0.00058 -0.00422 0.99999; -0.06590 -0.99782 -0.00425; 0.99783 -0.06590 0.00030; writing aseg with callosum to /out/out/freesurfer/sub-05/mri/aseg.auto.mgz... corpus callosum segmentation took 0.3 minutes #-------------------------------------- #@# Merge ASeg Mon Mar 29 23:51:45 UTC 2021 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Mon Mar 29 23:51:45 UTC 2021 /out/out/freesurfer/sub-05/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... INFO: MRImask() using MRImaskDifferentGeometry() Reading aseg aseg.presurf.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 733 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 75 (75), valley at 0 (-1) csf peak at 37, setting threshold to 62 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 72 (72), valley at 0 (-1) csf peak at 36, setting threshold to 60 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 1 minutes and 15 seconds. #-------------------------------------------- #@# Mask BFS Mon Mar 29 23:53:02 UTC 2021 /out/out/freesurfer/sub-05/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1566199 voxels in mask (pct= 9.34) INFO: MRImask() using MRImaskDifferentGeometry() Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Mon Mar 29 23:53:04 UTC 2021 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 (103.0): 103.0 +- 6.6 [79.0 --> 125.0] GM (74.0) : 73.5 +- 9.3 [30.0 --> 95.0] setting bottom of white matter range to 82.8 setting top of gray matter range to 92.2 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... 4507 sparsely connected voxels removed... thickening thin strands.... 20 segments, 2581 filled 25 bright non-wm voxels segmented. 3571 diagonally connected voxels added... white matter segmentation took 0.8 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 0.20 minutes reading wm segmentation from wm.seg.mgz... 164 voxels added to wm to prevent paths from MTL structures to cortex 3109 additional wm voxels added 0 additional wm voxels added SEG EDIT: 36850 voxels turned on, 63531 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 0 new 0 115,126,128 old 0 new 0 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 17 found - 17 modified | TOTAL: 17 pass 2 (xy+): 0 found - 17 modified | TOTAL: 17 pass 1 (xy-): 18 found - 18 modified | TOTAL: 35 pass 2 (xy-): 0 found - 18 modified | TOTAL: 35 pass 1 (yz+): 16 found - 16 modified | TOTAL: 51 pass 2 (yz+): 0 found - 16 modified | TOTAL: 51 pass 1 (yz-): 17 found - 17 modified | TOTAL: 68 pass 2 (yz-): 0 found - 17 modified | TOTAL: 68 pass 1 (xz+): 7 found - 7 modified | TOTAL: 75 pass 2 (xz+): 0 found - 7 modified | TOTAL: 75 pass 1 (xz-): 16 found - 16 modified | TOTAL: 91 pass 2 (xz-): 0 found - 16 modified | TOTAL: 91 Iteration Number : 1 pass 1 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 pass 1 (+++): 10 found - 10 modified | TOTAL: 14 pass 2 (+++): 0 found - 10 modified | TOTAL: 14 pass 1 (+++): 2 found - 2 modified | TOTAL: 16 pass 2 (+++): 0 found - 2 modified | TOTAL: 16 pass 1 (+++): 10 found - 10 modified | TOTAL: 26 pass 2 (+++): 0 found - 10 modified | TOTAL: 26 Iteration Number : 1 pass 1 (++): 88 found - 88 modified | TOTAL: 88 pass 2 (++): 0 found - 88 modified | TOTAL: 88 pass 1 (+-): 70 found - 70 modified | TOTAL: 158 pass 2 (+-): 1 found - 71 modified | TOTAL: 159 pass 3 (+-): 0 found - 71 modified | TOTAL: 159 pass 1 (--): 93 found - 93 modified | TOTAL: 252 pass 2 (--): 0 found - 93 modified | TOTAL: 252 pass 1 (-+): 69 found - 69 modified | TOTAL: 321 pass 2 (-+): 0 found - 69 modified | TOTAL: 321 Iteration Number : 2 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 2 found - 2 modified | TOTAL: 3 pass 2 (xy-): 0 found - 2 modified | TOTAL: 3 pass 1 (yz+): 1 found - 1 modified | TOTAL: 4 pass 2 (yz+): 0 found - 1 modified | TOTAL: 4 pass 1 (yz-): 2 found - 2 modified | TOTAL: 6 pass 2 (yz-): 0 found - 2 modified | TOTAL: 6 pass 1 (xz+): 3 found - 3 modified | TOTAL: 9 pass 2 (xz+): 0 found - 3 modified | TOTAL: 9 pass 1 (xz-): 0 found - 0 modified | TOTAL: 9 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 4 pass 2 (+++): 0 found - 2 modified | TOTAL: 4 Iteration Number : 2 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 2 found - 2 modified | TOTAL: 3 pass 2 (+-): 0 found - 2 modified | TOTAL: 3 pass 1 (--): 1 found - 1 modified | TOTAL: 4 pass 2 (--): 0 found - 1 modified | TOTAL: 4 pass 1 (-+): 0 found - 0 modified | TOTAL: 4 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-): 1 found - 1 modified | TOTAL: 1 pass 2 (yz-): 0 found - 1 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 1 found - 1 modified | TOTAL: 2 pass 2 (xz-): 0 found - 1 modified | TOTAL: 2 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 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 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 458 (out of 559189: 0.081904) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Mon Mar 29 23:54:04 UTC 2021 /out/out/freesurfer/sub-05/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.07226 0.01721 -0.01208 -11.48413; -0.01620 1.08259 0.16184 -15.78963; 0.01624 -0.15521 0.95104 15.49117; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.07226 0.01721 -0.01208 -11.48413; -0.01620 1.08259 0.16184 -15.78963; 0.01624 -0.15521 0.95104 15.49117; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 962 (min = 350, max = 1400), aspect = 0.46 (min = 0.10, max = 0.75) no need to search using seed (126, 118, 147), TAL = (2.0, 19.0, 10.0) talairach voxel to voxel transform 0.93221 -0.01281 0.01402 10.28617; 0.01594 0.90150 -0.15321 16.79061; -0.01332 0.14734 1.02624 -13.72415; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (126, 118, 147) --> (2.0, 19.0, 10.0) done. writing output to filled.mgz... filling took 0.3 minutes talairach cc position changed to (2.00, 19.00, 10.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, 19.00, 10.00) SRC: (111.51, 102.37, 153.08) search lh wm seed point around talairach space (-16.00, 19.00, 10.00), SRC: (145.07, 102.94, 152.60) 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 ... Started at Mon Mar 29 22:35:31 UTC 2021 Ended at Mon Mar 29 23:54:20 UTC 2021 #@#%# recon-all-run-time-hours 1.314 recon-all -s sub-05 finished without error at Mon Mar 29 23:54:20 UTC 2021