Sun Aug 18 10:15:39 EDT 2019 /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06 /usr/local/freesurfer/stable6/bin/recon-all -all -s arap_loom2_7T_sess06 -i /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/arap_loom2_7T_sess06/anat/009/mT1v2.nii -expert /autofs/space/oprah_001/users/jvm27/looming/7T/scripts/Lauri/expertopts/expert.opts -hires -mail zn025 -parallel subjid arap_loom2_7T_sess06 setenv SUBJECTS_DIR /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR FREESURFER_HOME /usr/local/freesurfer/stable6 Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos7_x86_64/stable6 build-stamp.txt: freesurfer-Linux-centos7_x86_64-stable-v6-20161229-80ac5eb Linux bee.nmr.mgh.harvard.edu 3.10.0-957.1.3.el7.x86_64 #1 SMP Thu Nov 29 14:49:43 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 65535 memorylocked 64 kbytes maxproc 772023 maxlocks unlimited maxsignal 772023 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 197833724 18033240 2356176 481984 177444308 178316008 Swap: 62499836 935424 61564412 ######################################## program versions used $Id: recon-all,v 1.580.2.15 2016/12/08 22:02:41 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: 2019/08/18-14:15:39-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 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: 2019/08/18-14:15:39-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 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: 2019/08/18-14:15:39-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/08/18-14:15:39-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/18-14:15:39-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/18-14:15:39-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/08/18-14:15:39-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/08/18-14:15:39-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/08/18-14:15:39-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/08/18-14:15:39-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/08/18-14:15:39-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/08/18-14:15:39-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/18-14:15:39-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/18-14:15:39-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/08/18-14:15:40-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/18-14:15:40-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/18-14:15:40-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/18-14:15:40-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/18-14:15:40-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/18-14:15:40-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/18-14:15:40-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/08/18-14:15:40-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/18-14:15:40-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/18-14:15:40-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/18-14:15:40-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/08/18-14:15:40-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/18-14:15:40-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2019/08/18-14:15:40-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/18-14:15:40-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/18-14:15:40-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/18-14:15:40-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/18-14:15:40-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 $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: 2019/08/18-14:15:40-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 $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: 2019/08/18-14:15:40-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/18-14:15:40-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/18-14:15:40-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/18-14:15:40-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/18-14:15:40-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/18-14:15:40-GMT BuildTimeStamp: Dec 29 2016 04:02:37 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: zn025 Machine: bee.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ####################################### GCADIR /usr/local/freesurfer/stable6/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 /usr/local/freesurfer/stable6/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06 mri_convert /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/arap_loom2_7T_sess06/anat/009/mT1v2.nii /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/mri/orig/001.mgz mri_convert.bin /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/arap_loom2_7T_sess06/anat/009/mT1v2.nii /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/arap_loom2_7T_sess06/anat/009/mT1v2.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (-1, 0, 0) writing to /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Sun Aug 18 10:15:55 EDT 2019 Found 1 runs /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/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 /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/mri/orig/001.mgz /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/mri/rawavg.mgz /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06 mri_convert /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/mri/rawavg.mgz /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/mri/orig.mgz --conform_min mri_convert.bin /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/mri/rawavg.mgz /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/mri/orig.mgz --conform_min $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (-1, 0, 0) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/mri/orig.mgz... mri_add_xform_to_header -c /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/mri/transforms/talairach.xfm /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/mri/orig.mgz /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Sun Aug 18 10:16:19 EDT 2019 /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/mri /usr/local/freesurfer/stable6/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 bee.nmr.mgh.harvard.edu 3.10.0-957.1.3.el7.x86_64 #1 SMP Thu Nov 29 14:49:43 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux Sun Aug 18 10:16:19 EDT 2019 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.31875 /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.31875/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.31875/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.31875/nu0.mnc... -------------------------------------------------------- Iteration 1 Sun Aug 18 10:16:41 EDT 2019 nu_correct -clobber ./tmp.mri_nu_correct.mni.31875/nu0.mnc ./tmp.mri_nu_correct.mni.31875/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.31875/0/ -iterations 1000 -distance 50 [zn025@bee.nmr.mgh.harvard.edu:/autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/mri/] [2019-08-18 10:16:41] running: /usr/local/freesurfer/stable6/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.31875/0/ ./tmp.mri_nu_correct.mni.31875/nu0.mnc ./tmp.mri_nu_correct.mni.31875/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 Number of iterations: 26 CV of field change: 0.000980975 Outputting Volume: ............................................................ mri_convert ./tmp.mri_nu_correct.mni.31875/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.31875/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.31875/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz... Sun Aug 18 10:19:31 EDT 2019 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 Sun Aug 18 10:19:31 EDT 2019 Ended at Sun Aug 18 10:20:30 EDT 2019 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Sun Aug 18 10:20:32 EDT 2019 /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.8008, pval=0.8469 >= threshold=0.0050) awk -f /usr/local/freesurfer/stable6/bin/extract_talairach_avi_QA.awk /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/mri/transforms/talairach_avi.log tal_QC_AZS /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/mri/transforms/talairach_avi.log TalAviQA: 0.97790 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Sun Aug 18 10:20:32 EDT 2019 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --cm --n 2 /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/mri /usr/local/freesurfer/stable6/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --cm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux bee.nmr.mgh.harvard.edu 3.10.0-957.1.3.el7.x86_64 #1 SMP Thu Nov 29 14:49:43 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux Sun Aug 18 10:20:32 EDT 2019 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.32802 /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/mri mri_convert -cm orig.mgz ./tmp.mri_nu_correct.mni.32802/nu0.mnc -odt float mri_convert.bin -cm orig.mgz ./tmp.mri_nu_correct.mni.32802/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.32802/nu0.mnc... -------------------------------------------------------- Iteration 1 Sun Aug 18 10:20:55 EDT 2019 nu_correct -clobber ./tmp.mri_nu_correct.mni.32802/nu0.mnc ./tmp.mri_nu_correct.mni.32802/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.32802/0/ [zn025@bee.nmr.mgh.harvard.edu:/autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/mri/] [2019-08-18 10:20:55] running: /usr/local/freesurfer/stable6/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.32802/0/ ./tmp.mri_nu_correct.mni.32802/nu0.mnc ./tmp.mri_nu_correct.mni.32802/nu1.imp 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: 11 CV of field change: 0.000943369 Outputting Volume: ............................................................ -------------------------------------------------------- Iteration 2 Sun Aug 18 10:22:46 EDT 2019 nu_correct -clobber ./tmp.mri_nu_correct.mni.32802/nu1.mnc ./tmp.mri_nu_correct.mni.32802/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.32802/1/ [zn025@bee.nmr.mgh.harvard.edu:/autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/mri/] [2019-08-18 10:22:46] running: /usr/local/freesurfer/stable6/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.32802/1/ ./tmp.mri_nu_correct.mni.32802/nu1.mnc ./tmp.mri_nu_correct.mni.32802/nu2.imp Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Number of iterations: 6 CV of field change: 0.000960455 Outputting Volume: ............................................................ mri_binarize --i ./tmp.mri_nu_correct.mni.32802/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.32802/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.32802/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.32802/ones.mgz sysname Linux hostname bee.nmr.mgh.harvard.edu machine x86_64 user zn025 input ./tmp.mri_nu_correct.mni.32802/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.32802/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 32768000 values in range Counting number of voxels in first frame Found 32768000 voxels in final mask Count: 32768000 7762391.113281 32768000 100.000000 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.32802/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.32802/sum.junk --avgwf ./tmp.mri_nu_correct.mni.32802/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.32802/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.32802/sum.junk --avgwf ./tmp.mri_nu_correct.mni.32802/input.mean.dat sysname Linux hostname bee.nmr.mgh.harvard.edu machine x86_64 user zn025 UseRobust 0 Loading ./tmp.mri_nu_correct.mni.32802/ones.mgz Loading orig.mgz Voxel Volume is 0.236889 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.32802/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.32802/ones.mgz --i ./tmp.mri_nu_correct.mni.32802/nu2.mnc --sum ./tmp.mri_nu_correct.mni.32802/sum.junk --avgwf ./tmp.mri_nu_correct.mni.32802/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.32802/ones.mgz --i ./tmp.mri_nu_correct.mni.32802/nu2.mnc --sum ./tmp.mri_nu_correct.mni.32802/sum.junk --avgwf ./tmp.mri_nu_correct.mni.32802/output.mean.dat sysname Linux hostname bee.nmr.mgh.harvard.edu machine x86_64 user zn025 UseRobust 0 Loading ./tmp.mri_nu_correct.mni.32802/ones.mgz Loading ./tmp.mri_nu_correct.mni.32802/nu2.mnc Voxel Volume is 0.236889 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.32802/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.32802/nu2.mnc ./tmp.mri_nu_correct.mni.32802/nu2.mnc mul .98718161088348137814 Saving result to './tmp.mri_nu_correct.mni.32802/nu2.mnc' (type = MINC )Outputting Volume: ............................................................ [ ok ] mri_convert ./tmp.mri_nu_correct.mni.32802/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.32802/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.32802/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 13 seconds. mapping (10, 131) to ( 3, 110) Sun Aug 18 10:26:14 EDT 2019 mri_nu_correct.mni done mri_add_xform_to_header -c /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Sun Aug 18 10:26:17 EDT 2019 /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/mri mri_normalize -g 1 -mprage -noconform nu.mgz T1.mgz using max gradient = 1.000 assuming input volume is MGH (Van der Kouwe) MP-RAGE not interpolating and embedding volume to be 256^3... reading from nu.mgz... normalizing image... talairach transform 1.08357 0.07837 -0.03697 -4.91193; -0.05119 1.01126 0.19801 -49.11674; 0.05001 -0.17812 1.15401 9.71591; 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 = 18 Starting OpenSpline(): npoints = 18 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 109 gm peak at 85 (85), valley at 52 (52) csf peak at 43, setting threshold to 71 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 81 (81), valley at 49 (49) csf peak at 41, setting threshold to 67 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 5 minutes and 36 seconds. #-------------------------------------------- #@# Skull Stripping Sun Aug 18 10:31:54 EDT 2019 /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/mri mri_em_register -rusage /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /usr/local/freesurfer/stable6/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 == Number of threads available to mri_em_register for OpenMP = 4 == reading 1 input volumes... logging results to talairach_with_skull.log reading '/usr/local/freesurfer/stable6/average/RB_all_withskull_2016-05-10.vc700.gca'... average std = 22.9 using min determinant for regularization = 52.6 0 singular and 9002 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 8.7 or > 569.1 total sample mean = 77.6 (1399 zeros) ************************************************ spacing=8, using 3243 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3243, passno 0, spacing 8 resetting wm mean[0]: 100 --> 108 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=5.0 skull bounding box = (38, 24, 0) --> (285, 319, 319) using (120, 122, 160) as brain centroid... mean wm in atlas = 108, using box (89,85,120) --> (150, 158,199) to find MRI wm before smoothing, mri peak at 106 robust fit to distribution - 106 +- 5.4 after smoothing, mri peak at 106, scaling input intensities by 1.019 scaling channel 0 by 1.01887 initial log_p = -12647.390 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.464992 @ (27.273, 27.273, 9.091) max log p = -4.442940 @ (4.545, 4.545, -4.545) max log p = -4.408749 @ (-2.273, 2.273, 2.273) max log p = -4.392560 @ (-1.136, 1.136, 1.136) max log p = -4.389555 @ (1.705, -1.705, -0.568) max log p = -4.365757 @ (-0.284, -0.284, -0.284) Found translation: (29.8, 33.2, 7.1): log p = -4.366 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.181, old_max_log_p =-4.366 (thresh=-4.4) 0.70547 -0.09208 -0.01212 25.68014; 0.09984 0.75190 0.09899 -14.08251; 0.00000 -0.08591 0.65256 20.77581; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.177, old_max_log_p =-4.181 (thresh=-4.2) 0.70806 0.02905 -0.07004 13.96735; 0.00663 0.73676 0.19412 -10.83250; 0.07916 -0.19377 0.62705 29.63840; 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=-4.097, old_max_log_p =-4.177 (thresh=-4.2) 0.68464 -0.00572 -0.03206 19.78320; 0.02385 0.74807 0.15173 -11.60324; 0.03354 -0.14941 0.65320 23.69567; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.092, old_max_log_p =-4.097 (thresh=-4.1) 0.69598 -0.00084 -0.05442 21.11271; 0.02340 0.73405 0.14888 -8.19599; 0.05488 -0.14671 0.63958 21.53208; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.076, old_max_log_p =-4.092 (thresh=-4.1) 0.71048 -0.00575 -0.03409 16.66246; 0.02296 0.72028 0.14609 -4.85264; 0.03207 -0.14660 0.64102 25.99721; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.076, old_max_log_p =-4.076 (thresh=-4.1) 0.71048 -0.00575 -0.03409 16.66246; 0.02296 0.72028 0.14609 -4.85264; 0.03207 -0.14660 0.64102 25.99721; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.064, old_max_log_p =-4.076 (thresh=-4.1) 0.70915 -0.01050 -0.04045 18.71717; 0.02846 0.72055 0.14036 -5.31894; 0.03798 -0.14040 0.64039 23.70066; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.063, old_max_log_p =-4.064 (thresh=-4.1) 0.71081 -0.01053 -0.04055 18.39616; 0.02846 0.72055 0.14036 -5.31894; 0.03798 -0.14040 0.64039 23.70066; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3243 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.71081 -0.01053 -0.04055 18.39616; 0.02846 0.72055 0.14036 -5.31894; 0.03798 -0.14040 0.64039 23.70066; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 0.71081 -0.01053 -0.04055 18.39616; 0.02846 0.72055 0.14036 -5.31894; 0.03798 -0.14040 0.64039 23.70066; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.71081 -0.01053 -0.04055 18.39616; 0.02846 0.72055 0.14036 -5.31894; 0.03798 -0.14040 0.64039 23.70066; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -4.063 (old=-12647.390) transform before final EM align: 0.71081 -0.01053 -0.04055 18.39616; 0.02846 0.72055 0.14036 -5.31894; 0.03798 -0.14040 0.64039 23.70066; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 364799 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.71081 -0.01053 -0.04055 18.39616; 0.02846 0.72055 0.14036 -5.31894; 0.03798 -0.14040 0.64039 23.70066; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 0.71081 -0.01053 -0.04055 18.39616; 0.02846 0.72055 0.14036 -5.31894; 0.03798 -0.14040 0.64039 23.70066; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 012: -log(p) = 4.5 tol 0.000000 final transform: 0.71081 -0.01053 -0.04055 18.39616; 0.02846 0.72055 0.14036 -5.31894; 0.03798 -0.14040 0.64039 23.70066; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 1281.427151 mri_em_register stimesec 3.904241 mri_em_register ru_maxrss 766492 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 960590 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 0 mri_em_register ru_oublock 24 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 445 mri_em_register ru_nivcsw 1166 registration took 5 minutes and 59 seconds. mri_watershed -rusage /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/touch/rusage.mri_watershed.dat -T1 -brain_atlas /usr/local/freesurfer/stable6/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz conforming input... updating LTA to account for conformation Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=133 y=109 z=134 r=73 first estimation of the main basin volume: 1682780 voxels Looking for seedpoints 2 found in the cerebellum 16 found in the rest of the brain global maximum in x=150, y=89, z=109, Imax=255 CSF=15, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percent done. Analyze... main basin size=425655585 voxels, voxel volume =1.000 = 425655585 mmm3 = 425655.584 cm3 done. PostAnalyze...Basin Prior 1068 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=129,y=114, z=122, r=9956 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=3, CSF_MAX=17 , nb = 41202 RIGHT_CER CSF_MIN=0, CSF_intensity=3, CSF_MAX=101 , nb = 1926 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=27 , nb = 2052 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=3, CSF_MAX=17 , nb = 19854 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=17 , nb = 17208 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=10 , nb = 162 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 17, 29, 50, 73 after analyzing : 17, 43, 50, 50 RIGHT_CER before analyzing : 101, 64, 54, 82 after analyzing : 39, 64, 64, 68 LEFT_CER before analyzing : 27, 45, 60, 79 after analyzing : 27, 55, 60, 61 RIGHT_BRAIN before analyzing : 17, 26, 46, 73 after analyzing : 17, 39, 46, 47 LEFT_BRAIN before analyzing : 17, 30, 52, 76 after analyzing : 17, 44, 52, 52 OTHER before analyzing : 10, 65, 86, 89 after analyzing : 10, 79, 86, 81 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...64 iterations *********************VALIDATION********************* curvature mean = -0.014, std = 0.010 curvature mean = 69.806, std = 7.382 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 3.24, sigma = 4.64 after rotation: sse = 3.24, sigma = 4.64 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 3.50, its var is 4.42 before Erosion-Dilatation 0.72% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...39 iterations mri_strip_skull: done peeling brain Brain Size = 1627175 voxels, voxel volume = 1.000 mm3 = 1627175 mmm3 = 1627.175 cm3 INFO: MRImask() using MRImaskDifferentGeometry() ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 25.202558 mri_watershed stimesec 0.682206 mri_watershed ru_maxrss 832596 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 371013 mri_watershed ru_majflt 0 mri_watershed ru_nswap 0 mri_watershed ru_inblock 0 mri_watershed ru_oublock 11080 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 4751 mri_watershed ru_nivcsw 39 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Sun Aug 18 10:38:15 EDT 2019 /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/mri mri_em_register -rusage /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /usr/local/freesurfer/stable6/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 = 4 == reading 1 input volumes... logging results to talairach.log reading '/usr/local/freesurfer/stable6/average/RB_all_2016-05-10.vc700.gca'... average std = 7.3 using min determinant for regularization = 5.3 0 singular and 841 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 6.3 or > 503.7 total sample mean = 78.8 (1011 zeros) ************************************************ spacing=8, using 2830 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2830, passno 0, spacing 8 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=20.0 skull bounding box = (57, 38, 23) --> (264, 237, 303) using (126, 104, 163) as brain centroid... mean wm in atlas = 107, using box (100,79,128) --> (151, 128,197) to find MRI wm before smoothing, mri peak at 106 robust fit to distribution - 106 +- 5.0 after smoothing, mri peak at 106, scaling input intensities by 1.009 scaling channel 0 by 1.00943 initial log_p = -13432.274 ************************************************ First Search limited to translation only. ************************************************ max log p = -3.956553 @ (27.273, 27.273, 9.091) max log p = -3.886061 @ (-4.545, 4.545, 4.545) max log p = -3.849436 @ (2.273, 2.273, -2.273) max log p = -3.849436 @ (0.000, 0.000, 0.000) max log p = -3.846629 @ (0.568, -2.841, -2.841) max log p = -3.821471 @ (-0.284, -0.284, 0.284) Found translation: (25.3, 31.0, 8.8): log p = -3.821 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.684, old_max_log_p =-3.821 (thresh=-3.8) 0.65947 0.02247 -0.08386 28.03671; 0.00000 0.64249 0.17216 1.72352; 0.08076 -0.15877 0.59255 25.99420; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.684, old_max_log_p =-3.684 (thresh=-3.7) 0.65947 0.02247 -0.08386 28.03671; 0.00000 0.64249 0.17216 1.72352; 0.08076 -0.15877 0.59255 25.99420; 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=-3.601, old_max_log_p =-3.684 (thresh=-3.7) 0.64983 -0.02731 -0.05189 32.97493; 0.03883 0.66328 0.13229 -1.07188; 0.03659 -0.11543 0.59536 27.36920; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.601, old_max_log_p =-3.601 (thresh=-3.6) 0.64983 -0.02731 -0.05189 32.97493; 0.03883 0.66328 0.13229 -1.07188; 0.03659 -0.11543 0.59536 27.36920; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.566, old_max_log_p =-3.601 (thresh=-3.6) 0.65152 -0.00560 -0.04759 28.99397; 0.01722 0.66397 0.12886 3.16510; 0.03686 -0.11041 0.59853 25.37880; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.566, old_max_log_p =-3.566 (thresh=-3.6) 0.65152 -0.00560 -0.04759 28.99397; 0.01722 0.66397 0.12886 3.16510; 0.03686 -0.11041 0.59853 25.37880; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2830 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.65152 -0.00560 -0.04759 28.99397; 0.01722 0.66397 0.12886 3.16510; 0.03686 -0.11041 0.59853 25.37880; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 0.65152 -0.00560 -0.04759 28.99397; 0.01722 0.66397 0.12886 3.16510; 0.03686 -0.11041 0.59853 25.37880; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.65152 -0.00560 -0.04759 28.99397; 0.01722 0.66397 0.12886 3.16510; 0.03686 -0.11041 0.59853 25.37880; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.566 (old=-13432.274) transform before final EM align: 0.65152 -0.00560 -0.04759 28.99397; 0.01722 0.66397 0.12886 3.16510; 0.03686 -0.11041 0.59853 25.37880; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 315557 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.65152 -0.00560 -0.04759 28.99397; 0.01722 0.66397 0.12886 3.16510; 0.03686 -0.11041 0.59853 25.37880; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 0.65152 -0.00560 -0.04759 28.99397; 0.01722 0.66397 0.12886 3.16510; 0.03686 -0.11041 0.59853 25.37880; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = 4.0 tol 0.000000 final transform: 0.65152 -0.00560 -0.04759 28.99397; 0.01722 0.66397 0.12886 3.16510; 0.03686 -0.11041 0.59853 25.37880; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 988.228947 mri_em_register stimesec 3.723203 mri_em_register ru_maxrss 755832 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 1159491 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 0 mri_em_register ru_oublock 24 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 583 mri_em_register ru_nivcsw 1783 registration took 4 minutes and 35 seconds. #-------------------------------------- #@# CA Normalize Sun Aug 18 10:42:50 EDT 2019 /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/stable6/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 '/usr/local/freesurfer/stable6/average/RB_all_2016-05-10.vc700.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=20.0 skull bounding box = (56, 38, 23) --> (264, 237, 303) using (125, 104, 163) as brain centroid... mean wm in atlas = 107, using box (99,79,128) --> (150, 128,197) to find MRI wm before smoothing, mri peak at 106 robust fit to distribution - 106 +- 5.0 after smoothing, mri peak at 106, scaling input intensities by 1.009 scaling channel 0 by 1.00943 using 246344 sample points... INFO: compute sample coordinates transform 0.65152 -0.00560 -0.04759 28.99397; 0.01722 0.66397 0.12886 3.16510; 0.03686 -0.11041 0.59853 25.37880; 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 (152, 41, 23) --> (263, 213, 294) Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 132.0 0 of 59 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (62, 44, 24) --> (168, 214, 297) Right_Cerebral_White_Matter: limiting intensities to 95.0 --> 132.0 0 of 77 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (160, 179, 66) --> (236, 242, 155) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 8 of 11 (72.7%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (92, 179, 66) --> (159, 240, 160) Right_Cerebellum_White_Matter: limiting intensities to 109.0 --> 132.0 1 of 10 (10.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (137, 158, 127) --> (190, 264, 176) Brain_Stem: limiting intensities to 105.0 --> 132.0 8 of 12 (66.7%) samples deleted using 169 total control points for intensity normalization... bias field = 0.920 +- 0.076 2 of 152 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (152, 41, 23) --> (263, 213, 294) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 138 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (62, 44, 24) --> (168, 214, 297) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 1 of 188 (0.5%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (160, 179, 66) --> (236, 242, 155) Left_Cerebellum_White_Matter: limiting intensities to 89.0 --> 132.0 20 of 32 (62.5%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (92, 179, 66) --> (159, 240, 160) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 35 of 51 (68.6%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (137, 158, 127) --> (190, 264, 176) Brain_Stem: limiting intensities to 88.0 --> 132.0 23 of 50 (46.0%) samples deleted using 459 total control points for intensity normalization... bias field = 1.001 +- 0.071 2 of 378 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (152, 41, 23) --> (263, 213, 294) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 4 of 250 (1.6%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (62, 44, 24) --> (168, 214, 297) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 254 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (160, 179, 66) --> (236, 242, 155) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 35 of 56 (62.5%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (92, 179, 66) --> (159, 240, 160) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 28 of 31 (90.3%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (137, 158, 127) --> (190, 264, 176) Brain_Stem: limiting intensities to 88.0 --> 104.0 88 of 104 (84.6%) samples deleted using 695 total control points for intensity normalization... bias field = 0.999 +- 0.058 3 of 533 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 2 minutes and 17 seconds. #-------------------------------------- #@# CA Reg Sun Aug 18 10:45:07 EDT 2019 /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/mri mri_ca_register -rusage /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer/stable6/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 = 4 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/usr/local/freesurfer/stable6/average/RB_all_2016-05-10.vc700.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 0.27 (predicted orig area = 29.7) 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=0.914, neg=0, invalid=762 0001: dt=517.888000, rms=0.830 (9.123%), neg=0, invalid=762 0002: dt=369.920000, rms=0.805 (3.058%), neg=0, invalid=762 0003: dt=517.888000, rms=0.791 (1.704%), neg=0, invalid=762 0004: dt=295.936000, rms=0.788 (0.456%), neg=0, invalid=762 0005: dt=517.888000, rms=0.785 (0.384%), neg=0, invalid=762 0006: dt=295.936000, rms=0.783 (0.261%), neg=0, invalid=762 0007: dt=517.888000, rms=0.781 (0.220%), neg=0, invalid=762 0008: dt=517.888000, rms=0.780 (0.089%), neg=0, invalid=762 0009: dt=517.888000, rms=0.776 (0.472%), neg=0, invalid=762 0010: dt=517.888000, rms=0.775 (0.218%), neg=0, invalid=762 0011: dt=517.888000, rms=0.773 (0.209%), neg=0, invalid=762 0012: dt=517.888000, rms=0.771 (0.246%), neg=0, invalid=762 0013: dt=517.888000, rms=0.771 (0.065%), neg=0, invalid=762 0014: dt=517.888000, rms=0.770 (0.094%), neg=0, invalid=762 0015: dt=517.888000, rms=0.768 (0.313%), neg=0, invalid=762 0016: dt=517.888000, rms=0.766 (0.157%), neg=0, invalid=762 0017: dt=517.888000, rms=0.766 (-0.003%), neg=0, invalid=762 0018: dt=129.472000, rms=0.766 (0.065%), neg=0, invalid=762 0019: dt=129.472000, rms=0.766 (0.013%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.766, neg=0, invalid=762 0020: dt=129.472000, rms=0.765 (0.110%), neg=0, invalid=762 0021: dt=110.976000, rms=0.765 (0.008%), neg=0, invalid=762 0022: dt=110.976000, rms=0.765 (-0.006%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.776, neg=0, invalid=762 0023: dt=331.776000, rms=0.767 (1.243%), neg=0, invalid=762 0024: dt=145.152000, rms=0.760 (0.889%), neg=0, invalid=762 0025: dt=331.776000, rms=0.756 (0.482%), neg=0, invalid=762 0026: dt=132.535433, rms=0.752 (0.560%), neg=0, invalid=762 0027: dt=124.416000, rms=0.751 (0.187%), neg=0, invalid=762 0028: dt=124.416000, rms=0.749 (0.223%), neg=0, invalid=762 0029: dt=124.416000, rms=0.746 (0.345%), neg=0, invalid=762 0030: dt=124.416000, rms=0.743 (0.418%), neg=0, invalid=762 0031: dt=124.416000, rms=0.740 (0.427%), neg=0, invalid=762 0032: dt=124.416000, rms=0.736 (0.494%), neg=0, invalid=762 0033: dt=124.416000, rms=0.734 (0.383%), neg=0, invalid=762 0034: dt=124.416000, rms=0.731 (0.304%), neg=0, invalid=762 0035: dt=124.416000, rms=0.730 (0.221%), neg=0, invalid=762 0036: dt=124.416000, rms=0.728 (0.224%), neg=0, invalid=762 0037: dt=124.416000, rms=0.726 (0.261%), neg=0, invalid=762 0038: dt=124.416000, rms=0.725 (0.186%), neg=0, invalid=762 0039: dt=124.416000, rms=0.724 (0.145%), neg=0, invalid=762 0040: dt=124.416000, rms=0.723 (0.126%), neg=0, invalid=762 0041: dt=124.416000, rms=0.722 (0.129%), neg=0, invalid=762 0042: dt=124.416000, rms=0.721 (0.157%), neg=0, invalid=762 0043: dt=124.416000, rms=0.720 (0.108%), neg=0, invalid=762 0044: dt=124.416000, rms=0.720 (0.072%), neg=0, invalid=762 0045: dt=124.416000, rms=0.719 (0.020%), neg=0, invalid=762 0046: dt=124.416000, rms=0.719 (0.008%), neg=0, invalid=762 0047: dt=124.416000, rms=0.719 (0.000%), neg=0, invalid=762 0048: dt=124.416000, rms=0.719 (-0.005%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.720, neg=0, invalid=762 0049: dt=36.288000, rms=0.719 (0.118%), neg=0, invalid=762 0050: dt=31.104000, rms=0.719 (0.011%), neg=0, invalid=762 0051: dt=31.104000, rms=0.719 (-0.005%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.765, neg=0, invalid=762 0052: dt=24.222222, rms=0.760 (0.549%), neg=0, invalid=762 0053: dt=24.228571, rms=0.759 (0.153%), neg=0, invalid=762 0054: dt=24.228571, rms=0.759 (0.040%), neg=0, invalid=762 0055: dt=24.228571, rms=0.759 (-0.028%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.760, neg=0, invalid=762 0056: dt=0.000000, rms=0.759 (0.068%), neg=0, invalid=762 0057: dt=0.000000, rms=0.759 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.824, neg=0, invalid=762 0058: dt=7.824176, rms=0.810 (1.700%), neg=0, invalid=762 0059: dt=13.824000, rms=0.803 (0.805%), neg=0, invalid=762 0060: dt=7.000000, rms=0.803 (0.093%), neg=0, invalid=762 0061: dt=7.000000, rms=0.801 (0.171%), neg=0, invalid=762 0062: dt=7.000000, rms=0.800 (0.147%), neg=0, invalid=762 0063: dt=7.000000, rms=0.800 (-0.000%), neg=0, invalid=762 0064: dt=0.000563, rms=0.800 (0.000%), neg=0, invalid=762 0065: dt=0.000000, rms=0.800 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.801, neg=0, invalid=762 0066: dt=0.000000, rms=0.800 (0.053%), neg=0, invalid=762 0067: dt=0.000000, rms=0.800 (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=0.847, neg=0, invalid=762 0068: dt=0.080000, rms=0.847 (0.049%), neg=0, invalid=762 0069: dt=0.028000, rms=0.847 (0.001%), neg=0, invalid=762 0070: dt=0.028000, rms=0.847 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.847, neg=0, invalid=762 0071: dt=0.320000, rms=0.846 (0.078%), neg=0, invalid=762 0072: dt=0.192000, rms=0.846 (0.008%), neg=0, invalid=762 0073: dt=0.192000, rms=0.846 (0.007%), neg=0, invalid=762 0074: dt=0.192000, rms=0.846 (-0.005%), 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=0.775, neg=0, invalid=762 0075: dt=0.640558, rms=0.762 (1.733%), neg=0, invalid=762 0076: dt=0.064000, rms=0.761 (0.056%), neg=0, invalid=762 0077: dt=0.064000, rms=0.761 (-0.055%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.762, neg=0, invalid=762 0078: dt=0.028000, rms=0.761 (0.082%), neg=0, invalid=762 0079: dt=0.016000, rms=0.761 (0.003%), neg=0, invalid=762 0080: dt=0.016000, rms=0.761 (-0.002%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.07482 (41) Left_Lateral_Ventricle (4): linear fit = 2.05 x + 0.0 (9551 voxels, overlap=0.050) Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (9551 voxels, peak = 41), gca=30.0 gca peak = 0.15565 (16) mri peak = 0.10676 (41) Right_Lateral_Ventricle (43): linear fit = 2.68 x + 0.0 (8452 voxels, overlap=0.009) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (8452 voxels, peak = 43), gca=24.0 gca peak = 0.26829 (96) mri peak = 0.05212 (93) Right_Pallidum (52): linear fit = 0.92 x + 0.0 (4817 voxels, overlap=0.685) Right_Pallidum (52): linear fit = 0.92 x + 0.0 (4817 voxels, peak = 88), gca=87.8 gca peak = 0.20183 (93) mri peak = 0.04990 (84) Left_Pallidum (13): linear fit = 0.92 x + 0.0 (4512 voxels, overlap=0.937) Left_Pallidum (13): linear fit = 0.92 x + 0.0 (4512 voxels, peak = 85), gca=85.1 gca peak = 0.21683 (55) mri peak = 0.06178 (68) Right_Hippocampus (53): linear fit = 1.21 x + 0.0 (6365 voxels, overlap=0.143) Right_Hippocampus (53): linear fit = 1.21 x + 0.0 (6365 voxels, peak = 66), gca=66.3 gca peak = 0.30730 (58) mri peak = 0.05694 (69) Left_Hippocampus (17): linear fit = 1.16 x + 0.0 (5181 voxels, overlap=0.285) Left_Hippocampus (17): linear fit = 1.16 x + 0.0 (5181 voxels, peak = 68), gca=67.6 gca peak = 0.11430 (101) mri peak = 0.07657 (104) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (442570 voxels, overlap=0.858) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (442570 voxels, peak = 104), gca=103.5 gca peak = 0.12076 (102) mri peak = 0.07064 (105) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (434392 voxels, overlap=0.828) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (434392 voxels, peak = 106), gca=105.6 gca peak = 0.14995 (59) mri peak = 0.04341 (79) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (231460 voxels, overlap=0.000) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (231460 voxels, peak = 79), gca=79.4 gca peak = 0.15082 (58) mri peak = 0.04220 (78) Right_Cerebral_Cortex (42): linear fit = 1.35 x + 0.0 (252271 voxels, overlap=0.001) Right_Cerebral_Cortex (42): linear fit = 1.35 x + 0.0 (252271 voxels, peak = 78), gca=78.0 gca peak = 0.14161 (67) mri peak = 0.07619 (79) Right_Caudate (50): linear fit = 1.20 x + 0.0 (6797 voxels, overlap=0.038) Right_Caudate (50): linear fit = 1.20 x + 0.0 (6797 voxels, peak = 80), gca=80.1 gca peak = 0.15243 (71) mri peak = 0.07153 (82) Left_Caudate (11): linear fit = 1.12 x + 0.0 (7357 voxels, overlap=0.351) Left_Caudate (11): linear fit = 1.12 x + 0.0 (7357 voxels, peak = 80), gca=79.9 gca peak = 0.13336 (57) mri peak = 0.03207 (69) Left_Cerebellum_Cortex (8): linear fit = 1.29 x + 0.0 (46825 voxels, overlap=0.001) Left_Cerebellum_Cortex (8): linear fit = 1.29 x + 0.0 (46825 voxels, peak = 74), gca=73.8 gca peak = 0.13252 (56) mri peak = 0.03910 (65) Right_Cerebellum_Cortex (47): linear fit = 1.21 x + 0.0 (67056 voxels, overlap=0.093) Right_Cerebellum_Cortex (47): linear fit = 1.21 x + 0.0 (67056 voxels, peak = 67), gca=67.5 gca peak = 0.18181 (84) mri peak = 0.03090 (81) Left_Cerebellum_White_Matter (7): linear fit = 0.98 x + 0.0 (31554 voxels, overlap=0.995) Left_Cerebellum_White_Matter (7): linear fit = 0.98 x + 0.0 (31554 voxels, peak = 82), gca=81.9 gca peak = 0.20573 (83) mri peak = 0.03657 (83) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (35379 voxels, overlap=0.988) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (35379 voxels, peak = 82), gca=81.8 gca peak = 0.21969 (57) mri peak = 0.06276 (69) Left_Amygdala (18): linear fit = 1.18 x + 0.0 (2164 voxels, overlap=0.300) Left_Amygdala (18): linear fit = 1.18 x + 0.0 (2164 voxels, peak = 68), gca=67.5 gca peak = 0.39313 (56) mri peak = 0.05945 (70) Right_Amygdala (54): linear fit = 1.23 x + 0.0 (2790 voxels, overlap=0.162) Right_Amygdala (54): linear fit = 1.23 x + 0.0 (2790 voxels, peak = 69), gca=68.6 gca peak = 0.14181 (85) mri peak = 0.05800 (96) Left_Thalamus_Proper (10): linear fit = 1.09 x + 0.0 (25465 voxels, overlap=0.628) Left_Thalamus_Proper (10): linear fit = 1.09 x + 0.0 (25465 voxels, peak = 92), gca=92.2 gca peak = 0.11978 (83) mri peak = 0.06300 (93) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (24097 voxels, overlap=0.542) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (24097 voxels, peak = 93), gca=92.5 gca peak = 0.13399 (79) mri peak = 0.04843 (87) Left_Putamen (12): linear fit = 1.10 x + 0.0 (13116 voxels, overlap=0.777) Left_Putamen (12): linear fit = 1.10 x + 0.0 (13116 voxels, peak = 87), gca=86.5 gca peak = 0.14159 (79) mri peak = 0.04134 (86) Right_Putamen (51): linear fit = 1.10 x + 0.0 (14172 voxels, overlap=0.766) Right_Putamen (51): linear fit = 1.10 x + 0.0 (14172 voxels, peak = 87), gca=86.5 gca peak = 0.10025 (80) mri peak = 0.14046 (81) Brain_Stem (16): linear fit = 1.07 x + 0.0 (37656 voxels, overlap=0.401) Brain_Stem (16): linear fit = 1.07 x + 0.0 (37656 voxels, peak = 85), gca=85.2 gca peak = 0.13281 (86) mri peak = 0.09391 (82) Right_VentralDC (60): linear fit = 1.03 x + 0.0 (5120 voxels, overlap=0.724) Right_VentralDC (60): linear fit = 1.03 x + 0.0 (5120 voxels, peak = 89), gca=89.0 gca peak = 0.12801 (89) mri peak = 0.10082 (82) Left_VentralDC (28): linear fit = 0.94 x + 0.0 (4857 voxels, overlap=0.832) Left_VentralDC (28): linear fit = 0.94 x + 0.0 (4857 voxels, peak = 84), gca=84.1 gca peak = 0.20494 (23) mri peak = 0.08187 (41) Third_Ventricle (14): linear fit = 1.59 x + 0.0 (438 voxels, overlap=0.107) Third_Ventricle (14): linear fit = 1.59 x + 0.0 (438 voxels, peak = 36), gca=36.5 gca peak = 0.15061 (21) mri peak = 0.06122 (23) Fourth_Ventricle (15): linear fit = 1.22 x + 0.0 (2332 voxels, overlap=0.575) Fourth_Ventricle (15): linear fit = 1.22 x + 0.0 (2332 voxels, peak = 26), gca=25.5 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 1.25 x + 0.0 estimating mean wm scale to be 1.03 x + 0.0 estimating mean csf scale to be 1.41 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=0.743, neg=0, invalid=762 0081: dt=210.073090, rms=0.714 (3.843%), neg=0, invalid=762 0082: dt=517.888000, rms=0.705 (1.266%), neg=0, invalid=762 0083: dt=517.888000, rms=0.702 (0.406%), neg=0, invalid=762 0084: dt=443.904000, rms=0.700 (0.306%), neg=0, invalid=762 0085: dt=129.472000, rms=0.700 (0.079%), neg=0, invalid=762 0086: dt=1183.744000, rms=0.698 (0.180%), neg=0, invalid=762 0087: dt=221.952000, rms=0.697 (0.252%), neg=0, invalid=762 0088: dt=129.472000, rms=0.696 (0.027%), neg=0, invalid=762 0089: dt=129.472000, rms=0.696 (0.021%), neg=0, invalid=762 0090: dt=129.472000, rms=0.696 (0.043%), neg=0, invalid=762 0091: dt=129.472000, rms=0.696 (0.057%), neg=0, invalid=762 0092: dt=129.472000, rms=0.695 (0.068%), neg=0, invalid=762 0093: dt=129.472000, rms=0.695 (0.072%), neg=0, invalid=762 0094: dt=129.472000, rms=0.694 (0.085%), neg=0, invalid=762 0095: dt=129.472000, rms=0.693 (0.084%), neg=0, invalid=762 0096: dt=129.472000, rms=0.693 (0.086%), neg=0, invalid=762 0097: dt=129.472000, rms=0.692 (0.088%), neg=0, invalid=762 0098: dt=129.472000, rms=0.692 (0.092%), neg=0, invalid=762 0099: dt=129.472000, rms=0.691 (0.086%), neg=0, invalid=762 0100: dt=129.472000, rms=0.690 (0.084%), neg=0, invalid=762 0101: dt=129.472000, rms=0.690 (0.079%), neg=0, invalid=762 0102: dt=129.472000, rms=0.689 (0.065%), neg=0, invalid=762 0103: dt=129.472000, rms=0.689 (0.058%), neg=0, invalid=762 0104: dt=129.472000, rms=0.689 (0.065%), neg=0, invalid=762 0105: dt=129.472000, rms=0.688 (0.070%), neg=0, invalid=762 0106: dt=129.472000, rms=0.688 (0.072%), neg=0, invalid=762 0107: dt=129.472000, rms=0.687 (0.060%), neg=0, invalid=762 0108: dt=129.472000, rms=0.687 (0.054%), neg=0, invalid=762 0109: dt=129.472000, rms=0.686 (0.051%), neg=0, invalid=762 0110: dt=129.472000, rms=0.686 (0.049%), neg=0, invalid=762 0111: dt=129.472000, rms=0.686 (0.040%), neg=0, invalid=762 0112: dt=129.472000, rms=0.686 (0.037%), neg=0, invalid=762 0113: dt=129.472000, rms=0.685 (0.037%), neg=0, invalid=762 0114: dt=129.472000, rms=0.685 (0.040%), neg=0, invalid=762 0115: dt=129.472000, rms=0.685 (0.039%), neg=0, invalid=762 0116: dt=129.472000, rms=0.685 (0.039%), neg=0, invalid=762 0117: dt=129.472000, rms=0.684 (0.040%), neg=0, invalid=762 0118: dt=129.472000, rms=0.684 (0.040%), neg=0, invalid=762 0119: dt=129.472000, rms=0.684 (0.042%), neg=0, invalid=762 0120: dt=129.472000, rms=0.683 (0.048%), neg=0, invalid=762 0121: dt=129.472000, rms=0.683 (0.044%), neg=0, invalid=762 0122: dt=129.472000, rms=0.683 (0.046%), neg=0, invalid=762 0123: dt=129.472000, rms=0.682 (0.044%), neg=0, invalid=762 0124: dt=129.472000, rms=0.682 (0.044%), neg=0, invalid=762 0125: dt=129.472000, rms=0.682 (0.039%), neg=0, invalid=762 0126: dt=129.472000, rms=0.682 (0.032%), neg=0, invalid=762 0127: dt=129.472000, rms=0.681 (0.027%), neg=0, invalid=762 0128: dt=129.472000, rms=0.681 (0.023%), neg=0, invalid=762 0129: dt=129.472000, rms=0.681 (0.017%), neg=0, invalid=762 0130: dt=517.888000, rms=0.681 (0.006%), neg=0, invalid=762 0131: dt=517.888000, rms=0.681 (0.002%), neg=0, invalid=762 0132: dt=517.888000, rms=0.681 (0.019%), neg=0, invalid=762 0133: dt=517.888000, rms=0.681 (0.012%), neg=0, invalid=762 0134: dt=517.888000, rms=0.681 (0.015%), neg=0, invalid=762 0135: dt=517.888000, rms=0.681 (0.047%), neg=0, invalid=762 0136: dt=517.888000, rms=0.680 (0.035%), neg=0, invalid=762 0137: dt=517.888000, rms=0.680 (0.042%), neg=0, invalid=762 0138: dt=517.888000, rms=0.680 (0.068%), neg=0, invalid=762 0139: dt=517.888000, rms=0.679 (0.048%), neg=0, invalid=762 0140: dt=517.888000, rms=0.679 (0.031%), neg=0, invalid=762 0141: dt=517.888000, rms=0.679 (0.073%), neg=0, invalid=762 0142: dt=517.888000, rms=0.678 (0.043%), neg=0, invalid=762 0143: dt=517.888000, rms=0.678 (0.036%), neg=0, invalid=762 0144: dt=517.888000, rms=0.678 (0.054%), neg=0, invalid=762 0145: dt=517.888000, rms=0.677 (0.046%), neg=0, invalid=762 0146: dt=517.888000, rms=0.677 (0.043%), neg=0, invalid=762 0147: dt=517.888000, rms=0.677 (0.035%), neg=0, invalid=762 0148: dt=517.888000, rms=0.676 (0.050%), neg=0, invalid=762 0149: dt=517.888000, rms=0.676 (0.059%), neg=0, invalid=762 0150: dt=517.888000, rms=0.676 (0.031%), neg=0, invalid=762 0151: dt=517.888000, rms=0.676 (0.045%), neg=0, invalid=762 0152: dt=517.888000, rms=0.675 (0.039%), neg=0, invalid=762 0153: dt=517.888000, rms=0.675 (0.033%), neg=0, invalid=762 0154: dt=517.888000, rms=0.675 (0.038%), neg=0, invalid=762 0155: dt=517.888000, rms=0.675 (0.033%), neg=0, invalid=762 0156: dt=517.888000, rms=0.674 (0.035%), neg=0, invalid=762 0157: dt=517.888000, rms=0.674 (0.026%), neg=0, invalid=762 0158: dt=517.888000, rms=0.674 (0.027%), neg=0, invalid=762 0159: dt=517.888000, rms=0.674 (0.043%), neg=0, invalid=762 0160: dt=517.888000, rms=0.674 (0.015%), neg=0, invalid=762 0161: dt=517.888000, rms=0.673 (0.028%), neg=0, invalid=762 0162: dt=517.888000, rms=0.673 (0.025%), neg=0, invalid=762 0163: dt=517.888000, rms=0.673 (0.020%), neg=0, invalid=762 0164: dt=517.888000, rms=0.673 (0.035%), neg=0, invalid=762 0165: dt=517.888000, rms=0.673 (0.028%), neg=0, invalid=762 0166: dt=517.888000, rms=0.672 (0.022%), neg=0, invalid=762 0167: dt=517.888000, rms=0.672 (0.025%), neg=0, invalid=762 0168: dt=517.888000, rms=0.672 (0.017%), neg=0, invalid=762 0169: dt=1183.744000, rms=0.672 (0.009%), neg=0, invalid=762 0170: dt=1183.744000, rms=0.672 (-0.764%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.673, neg=0, invalid=762 0171: dt=-0.006250, rms=0.672 (0.052%), neg=0, invalid=762 0172: dt=0.000000, rms=0.672 (0.000%), neg=0, invalid=762 0173: dt=0.850000, rms=0.672 (-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=0.675, neg=0, invalid=762 0174: dt=414.720000, rms=0.670 (0.717%), neg=0, invalid=762 0175: dt=125.848739, rms=0.667 (0.578%), neg=0, invalid=762 0176: dt=145.152000, rms=0.665 (0.201%), neg=0, invalid=762 0177: dt=145.152000, rms=0.663 (0.273%), neg=0, invalid=762 0178: dt=145.152000, rms=0.662 (0.157%), neg=0, invalid=762 0179: dt=145.152000, rms=0.661 (0.229%), neg=0, invalid=762 0180: dt=145.152000, rms=0.660 (0.141%), neg=0, invalid=762 0181: dt=248.832000, rms=0.658 (0.256%), neg=0, invalid=762 0182: dt=103.680000, rms=0.657 (0.122%), neg=0, invalid=762 0183: dt=580.608000, rms=0.654 (0.452%), neg=0, invalid=762 0184: dt=87.229630, rms=0.654 (0.145%), neg=0, invalid=762 0185: dt=580.608000, rms=0.652 (0.307%), neg=0, invalid=762 0186: dt=145.152000, rms=0.650 (0.182%), neg=0, invalid=762 0187: dt=145.152000, rms=0.649 (0.179%), neg=0, invalid=762 0188: dt=124.416000, rms=0.649 (0.036%), neg=0, invalid=762 0189: dt=124.416000, rms=0.648 (0.111%), neg=0, invalid=762 0190: dt=124.416000, rms=0.647 (0.152%), neg=0, invalid=762 0191: dt=124.416000, rms=0.646 (0.187%), neg=0, invalid=762 0192: dt=124.416000, rms=0.645 (0.221%), neg=0, invalid=762 0193: dt=124.416000, rms=0.643 (0.306%), neg=0, invalid=762 0194: dt=124.416000, rms=0.641 (0.280%), neg=0, invalid=762 0195: dt=124.416000, rms=0.639 (0.228%), neg=0, invalid=762 0196: dt=124.416000, rms=0.638 (0.172%), neg=0, invalid=762 0197: dt=124.416000, rms=0.637 (0.228%), neg=0, invalid=762 0198: dt=124.416000, rms=0.636 (0.203%), neg=0, invalid=762 0199: dt=124.416000, rms=0.634 (0.187%), neg=0, invalid=762 0200: dt=124.416000, rms=0.633 (0.176%), neg=0, invalid=762 0201: dt=124.416000, rms=0.632 (0.202%), neg=0, invalid=762 0202: dt=124.416000, rms=0.630 (0.241%), neg=0, invalid=762 0203: dt=124.416000, rms=0.629 (0.188%), neg=0, invalid=762 0204: dt=124.416000, rms=0.628 (0.138%), neg=0, invalid=762 0205: dt=124.416000, rms=0.628 (0.122%), neg=0, invalid=762 0206: dt=124.416000, rms=0.627 (0.144%), neg=0, invalid=762 0207: dt=124.416000, rms=0.626 (0.120%), neg=0, invalid=762 0208: dt=124.416000, rms=0.625 (0.116%), neg=0, invalid=762 0209: dt=124.416000, rms=0.624 (0.130%), neg=0, invalid=762 0210: dt=124.416000, rms=0.624 (0.080%), neg=0, invalid=762 0211: dt=124.416000, rms=0.623 (0.122%), neg=0, invalid=762 0212: dt=124.416000, rms=0.622 (0.119%), neg=0, invalid=762 0213: dt=124.416000, rms=0.622 (0.110%), neg=0, invalid=762 0214: dt=124.416000, rms=0.621 (0.074%), neg=0, invalid=762 0215: dt=124.416000, rms=0.621 (0.046%), neg=0, invalid=762 0216: dt=124.416000, rms=0.621 (0.076%), neg=0, invalid=762 0217: dt=124.416000, rms=0.620 (0.053%), neg=0, invalid=762 0218: dt=124.416000, rms=0.620 (0.036%), neg=0, invalid=762 0219: dt=124.416000, rms=0.620 (0.027%), neg=0, invalid=762 0220: dt=124.416000, rms=0.620 (0.041%), neg=0, invalid=762 0221: dt=124.416000, rms=0.619 (0.081%), neg=0, invalid=762 0222: dt=124.416000, rms=0.619 (0.058%), neg=0, invalid=762 0223: dt=124.416000, rms=0.618 (0.039%), neg=0, invalid=762 0224: dt=124.416000, rms=0.618 (0.040%), neg=0, invalid=762 0225: dt=124.416000, rms=0.618 (0.067%), neg=0, invalid=762 0226: dt=124.416000, rms=0.617 (0.053%), neg=0, invalid=762 0227: dt=124.416000, rms=0.617 (0.043%), neg=0, invalid=762 0228: dt=124.416000, rms=0.617 (0.048%), neg=0, invalid=762 0229: dt=124.416000, rms=0.617 (0.037%), neg=0, invalid=762 0230: dt=124.416000, rms=0.617 (0.019%), neg=0, invalid=762 0231: dt=124.416000, rms=0.616 (0.038%), neg=0, invalid=762 0232: dt=124.416000, rms=0.616 (0.042%), neg=0, invalid=762 0233: dt=124.416000, rms=0.616 (0.032%), neg=0, invalid=762 0234: dt=124.416000, rms=0.616 (0.021%), neg=0, invalid=762 0235: dt=124.416000, rms=0.615 (0.042%), neg=0, invalid=762 0236: dt=124.416000, rms=0.615 (0.044%), neg=0, invalid=762 0237: dt=124.416000, rms=0.615 (0.035%), neg=0, invalid=762 0238: dt=124.416000, rms=0.615 (0.038%), neg=0, invalid=762 0239: dt=124.416000, rms=0.614 (0.042%), neg=0, invalid=762 0240: dt=124.416000, rms=0.614 (0.051%), neg=0, invalid=762 0241: dt=124.416000, rms=0.614 (0.039%), neg=0, invalid=762 0242: dt=124.416000, rms=0.614 (0.013%), neg=0, invalid=762 0243: dt=124.416000, rms=0.614 (0.025%), neg=0, invalid=762 0244: dt=124.416000, rms=0.614 (0.027%), neg=0, invalid=762 0245: dt=124.416000, rms=0.613 (0.052%), neg=0, invalid=762 0246: dt=124.416000, rms=0.613 (0.027%), neg=0, invalid=762 0247: dt=124.416000, rms=0.613 (0.042%), neg=0, invalid=762 0248: dt=124.416000, rms=0.613 (0.008%), neg=0, invalid=762 0249: dt=124.416000, rms=0.612 (0.047%), neg=0, invalid=762 0250: dt=124.416000, rms=0.612 (0.032%), neg=0, invalid=762 0251: dt=124.416000, rms=0.612 (0.003%), neg=0, invalid=762 0252: dt=124.416000, rms=0.612 (0.021%), neg=0, invalid=762 0253: dt=124.416000, rms=0.612 (0.034%), neg=0, invalid=762 0254: dt=124.416000, rms=0.612 (0.047%), neg=0, invalid=762 0255: dt=124.416000, rms=0.611 (0.020%), neg=0, invalid=762 0256: dt=124.416000, rms=0.611 (0.031%), neg=0, invalid=762 0257: dt=124.416000, rms=0.611 (0.027%), neg=0, invalid=762 0258: dt=124.416000, rms=0.611 (0.017%), neg=0, invalid=762 0259: dt=124.416000, rms=0.611 (0.007%), neg=0, invalid=762 0260: dt=103.680000, rms=0.611 (0.041%), neg=0, invalid=762 0261: dt=36.288000, rms=0.611 (0.007%), neg=0, invalid=762 0262: dt=36.288000, rms=0.611 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.611, neg=0, invalid=762 0263: dt=82.944000, rms=0.610 (0.143%), neg=0, invalid=762 0264: dt=103.680000, rms=0.610 (0.028%), neg=0, invalid=762 0265: dt=103.680000, rms=0.610 (0.002%), neg=0, invalid=762 0266: dt=103.680000, rms=0.610 (-0.023%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.631, neg=0, invalid=762 0267: dt=44.800000, rms=0.628 (0.356%), neg=0, invalid=762 0268: dt=94.439024, rms=0.626 (0.333%), neg=0, invalid=762 0269: dt=44.800000, rms=0.625 (0.191%), neg=0, invalid=762 0270: dt=179.200000, rms=0.622 (0.464%), neg=0, invalid=762 0271: dt=32.000000, rms=0.621 (0.192%), neg=0, invalid=762 0272: dt=409.600000, rms=0.617 (0.690%), neg=0, invalid=762 0273: dt=38.400000, rms=0.614 (0.364%), neg=0, invalid=762 0274: dt=44.800000, rms=0.613 (0.253%), neg=0, invalid=762 0275: dt=44.800000, rms=0.612 (0.137%), neg=0, invalid=762 0276: dt=102.400000, rms=0.611 (0.195%), neg=0, invalid=762 0277: dt=32.000000, rms=0.610 (0.061%), neg=0, invalid=762 0278: dt=179.200000, rms=0.609 (0.296%), neg=0, invalid=762 0279: dt=25.600000, rms=0.608 (0.030%), neg=0, invalid=762 0280: dt=25.600000, rms=0.608 (0.062%), neg=0, invalid=762 0281: dt=25.600000, rms=0.608 (0.056%), neg=0, invalid=762 0282: dt=25.600000, rms=0.607 (0.082%), neg=0, invalid=762 0283: dt=25.600000, rms=0.607 (0.112%), neg=0, invalid=762 0284: dt=25.600000, rms=0.606 (0.115%), neg=0, invalid=762 0285: dt=25.600000, rms=0.605 (0.124%), neg=0, invalid=762 0286: dt=25.600000, rms=0.604 (0.117%), neg=0, invalid=762 0287: dt=25.600000, rms=0.604 (0.133%), neg=0, invalid=762 0288: dt=25.600000, rms=0.603 (0.137%), neg=0, invalid=762 0289: dt=25.600000, rms=0.602 (0.136%), neg=0, invalid=762 0290: dt=25.600000, rms=0.601 (0.128%), neg=0, invalid=762 0291: dt=25.600000, rms=0.601 (0.118%), neg=0, invalid=762 0292: dt=25.600000, rms=0.600 (0.120%), neg=0, invalid=762 0293: dt=25.600000, rms=0.599 (0.108%), neg=0, invalid=762 0294: dt=25.600000, rms=0.599 (0.095%), neg=0, invalid=762 0295: dt=25.600000, rms=0.598 (0.089%), neg=0, invalid=762 0296: dt=25.600000, rms=0.598 (0.081%), neg=0, invalid=762 0297: dt=25.600000, rms=0.597 (0.085%), neg=0, invalid=762 0298: dt=25.600000, rms=0.597 (0.065%), neg=0, invalid=762 0299: dt=25.600000, rms=0.596 (0.049%), neg=0, invalid=762 0300: dt=25.600000, rms=0.596 (0.051%), neg=0, invalid=762 0301: dt=25.600000, rms=0.596 (0.056%), neg=0, invalid=762 0302: dt=25.600000, rms=0.595 (0.055%), neg=0, invalid=762 0303: dt=25.600000, rms=0.595 (0.065%), neg=0, invalid=762 0304: dt=25.600000, rms=0.595 (0.067%), neg=0, invalid=762 0305: dt=25.600000, rms=0.594 (0.074%), neg=0, invalid=762 0306: dt=25.600000, rms=0.594 (0.067%), neg=0, invalid=762 0307: dt=25.600000, rms=0.593 (0.058%), neg=0, invalid=762 0308: dt=25.600000, rms=0.593 (0.052%), neg=0, invalid=762 0309: dt=25.600000, rms=0.593 (0.048%), neg=0, invalid=762 0310: dt=25.600000, rms=0.593 (0.035%), neg=0, invalid=762 0311: dt=25.600000, rms=0.593 (0.021%), neg=0, invalid=762 0312: dt=25.600000, rms=0.592 (0.021%), neg=0, invalid=762 0313: dt=44.800000, rms=0.592 (0.011%), neg=0, invalid=762 0314: dt=44.800000, rms=0.592 (-0.019%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.593, neg=0, invalid=762 0315: dt=25.600000, rms=0.592 (0.130%), neg=0, invalid=762 0316: dt=11.200000, rms=0.592 (0.009%), neg=0, invalid=762 0317: dt=11.200000, rms=0.592 (-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=0.624, neg=0, invalid=762 0318: dt=0.000000, rms=0.624 (0.073%), neg=0, invalid=762 0319: dt=0.000000, rms=0.624 (0.000%), neg=0, invalid=762 0320: dt=0.150000, rms=0.624 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.624, neg=0, invalid=762 0321: dt=1.787234, rms=0.624 (0.107%), neg=0, invalid=762 0322: dt=0.576000, rms=0.624 (0.003%), neg=0, invalid=762 0323: dt=0.576000, rms=0.624 (-0.003%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.682, neg=0, invalid=762 0324: dt=3.448598, rms=0.665 (2.493%), neg=0, invalid=762 0325: dt=3.532308, rms=0.661 (0.638%), neg=0, invalid=762 0326: dt=5.120000, rms=0.658 (0.352%), neg=0, invalid=762 0327: dt=5.120000, rms=0.656 (0.312%), neg=0, invalid=762 0328: dt=7.636364, rms=0.655 (0.242%), neg=0, invalid=762 0329: dt=7.168000, rms=0.653 (0.194%), neg=0, invalid=762 0330: dt=5.120000, rms=0.653 (0.092%), neg=0, invalid=762 0331: dt=5.120000, rms=0.652 (0.085%), neg=0, invalid=762 0332: dt=1.792000, rms=0.652 (0.029%), neg=0, invalid=762 0333: dt=1.792000, rms=0.652 (0.013%), neg=0, invalid=762 0334: dt=1.792000, rms=0.652 (0.028%), neg=0, invalid=762 0335: dt=1.792000, rms=0.652 (0.035%), neg=0, invalid=762 0336: dt=1.792000, rms=0.651 (0.041%), neg=0, invalid=762 0337: dt=1.792000, rms=0.651 (0.048%), neg=0, invalid=762 0338: dt=1.792000, rms=0.651 (0.043%), neg=0, invalid=762 0339: dt=1.792000, rms=0.650 (0.027%), neg=0, invalid=762 0340: dt=1.792000, rms=0.650 (0.016%), neg=0, invalid=762 0341: dt=1.792000, rms=0.650 (0.010%), neg=0, invalid=762 0342: dt=0.000050, rms=0.650 (-0.003%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.651, neg=0, invalid=762 0343: dt=5.120000, rms=0.648 (0.477%), neg=0, invalid=762 0344: dt=8.918919, rms=0.644 (0.580%), neg=0, invalid=762 0345: dt=1.792000, rms=0.643 (0.116%), neg=0, invalid=762 0346: dt=4.096000, rms=0.643 (0.071%), neg=0, invalid=762 0347: dt=7.200000, rms=0.641 (0.207%), neg=0, invalid=762 0348: dt=3.072000, rms=0.641 (0.055%), neg=0, invalid=762 0349: dt=7.168000, rms=0.640 (0.122%), neg=0, invalid=762 0350: dt=5.120000, rms=0.640 (0.072%), neg=0, invalid=762 0351: dt=4.096000, rms=0.639 (0.049%), neg=0, invalid=762 0352: dt=4.096000, rms=0.639 (0.056%), neg=0, invalid=762 0353: dt=4.096000, rms=0.639 (0.087%), neg=0, invalid=762 0354: dt=4.096000, rms=0.638 (0.106%), neg=0, invalid=762 0355: dt=4.096000, rms=0.637 (0.134%), neg=0, invalid=762 0356: dt=4.096000, rms=0.636 (0.135%), neg=0, invalid=762 0357: dt=4.096000, rms=0.635 (0.108%), neg=0, invalid=762 0358: dt=4.096000, rms=0.635 (0.081%), neg=0, invalid=762 0359: dt=4.096000, rms=0.634 (0.079%), neg=0, invalid=762 0360: dt=4.096000, rms=0.634 (0.057%), neg=0, invalid=762 0361: dt=4.096000, rms=0.634 (0.032%), neg=0, invalid=762 0362: dt=4.096000, rms=0.634 (0.019%), neg=0, invalid=762 0363: dt=4.096000, rms=0.634 (0.021%), neg=0, invalid=762 0364: dt=4.096000, rms=0.634 (0.015%), neg=0, invalid=762 0365: dt=1.280000, rms=0.633 (0.001%), neg=0, invalid=762 0366: dt=1.280000, rms=0.633 (0.000%), neg=0, invalid=762 0367: dt=1.280000, rms=0.633 (-0.004%), 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=0.625, neg=0, invalid=762 0368: dt=1.536000, rms=0.582 (6.867%), neg=0, invalid=762 0369: dt=0.000000, rms=0.582 (0.007%), neg=0, invalid=762 0370: dt=0.050000, rms=0.582 (-0.105%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.582, neg=0, invalid=762 0371: dt=0.001750, rms=0.582 (0.084%), neg=0, invalid=762 0372: dt=0.000750, rms=0.582 (0.000%), neg=0, invalid=762 0373: dt=0.000750, rms=0.582 (-0.000%), 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=0.569, neg=0, invalid=762 0374: dt=32.368000, rms=0.568 (0.145%), neg=0, invalid=762 0375: dt=8.092000, rms=0.568 (0.004%), neg=0, invalid=762 0376: dt=8.092000, rms=0.568 (0.001%), neg=0, invalid=762 0377: dt=8.092000, rms=0.568 (-0.006%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.569, neg=0, invalid=762 0378: dt=27.744000, rms=0.568 (0.092%), neg=0, invalid=762 0379: dt=18.496000, rms=0.568 (0.002%), neg=0, invalid=762 0380: dt=18.496000, rms=0.568 (-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=0.569, neg=0, invalid=762 0381: dt=31.104000, rms=0.567 (0.252%), neg=0, invalid=762 0382: dt=17.454545, rms=0.567 (0.025%), neg=0, invalid=762 0383: dt=17.454545, rms=0.567 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.568, neg=0, invalid=762 0384: dt=81.582418, rms=0.566 (0.324%), neg=0, invalid=762 0385: dt=36.288000, rms=0.566 (0.051%), neg=0, invalid=762 0386: dt=36.288000, rms=0.565 (0.038%), neg=0, invalid=762 0387: dt=36.288000, rms=0.565 (0.049%), neg=0, invalid=762 0388: dt=36.288000, rms=0.565 (0.050%), neg=0, invalid=762 0389: dt=36.288000, rms=0.565 (0.038%), neg=0, invalid=762 0390: dt=36.288000, rms=0.564 (0.025%), neg=0, invalid=762 0391: dt=580.608000, rms=0.563 (0.285%), neg=0, invalid=762 0392: dt=20.736000, rms=0.563 (0.009%), neg=0, invalid=762 0393: dt=20.736000, rms=0.563 (0.002%), neg=0, invalid=762 0394: dt=20.736000, rms=0.563 (-0.006%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.564, neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0395: dt=21.949458, rms=0.562 (0.316%), neg=0, invalid=762 0396: dt=11.200000, rms=0.562 (0.034%), neg=0, invalid=762 0397: dt=11.200000, rms=0.562 (0.008%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0398: dt=11.200000, rms=0.562 (-0.039%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.563, neg=0, invalid=762 0399: dt=74.666667, rms=0.557 (1.069%), neg=0, invalid=762 0400: dt=38.400000, rms=0.554 (0.519%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0401: dt=32.000000, rms=0.553 (0.176%), neg=0, invalid=762 0402: dt=32.000000, rms=0.552 (0.196%), neg=0, invalid=762 0403: dt=32.000000, rms=0.550 (0.281%), neg=0, invalid=762 0404: dt=32.000000, rms=0.548 (0.295%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0405: dt=32.000000, rms=0.547 (0.345%), neg=0, invalid=762 0406: dt=32.000000, rms=0.545 (0.336%), neg=0, invalid=762 0407: dt=32.000000, rms=0.543 (0.316%), neg=0, invalid=762 0408: dt=32.000000, rms=0.542 (0.234%), neg=0, invalid=762 0409: dt=32.000000, rms=0.540 (0.234%), neg=0, invalid=762 0410: dt=32.000000, rms=0.539 (0.199%), neg=0, invalid=762 0411: dt=32.000000, rms=0.539 (0.157%), neg=0, invalid=762 0412: dt=32.000000, rms=0.538 (0.179%), neg=0, invalid=762 0413: dt=32.000000, rms=0.537 (0.141%), neg=0, invalid=762 0414: dt=32.000000, rms=0.536 (0.114%), neg=0, invalid=762 0415: dt=32.000000, rms=0.536 (0.084%), neg=0, invalid=762 0416: dt=11.200000, rms=0.536 (0.011%), neg=0, invalid=762 0417: dt=11.200000, rms=0.536 (0.023%), neg=0, invalid=762 0418: dt=11.200000, rms=0.536 (0.013%), neg=0, invalid=762 0419: dt=11.200000, rms=0.535 (0.015%), neg=0, invalid=762 0420: dt=11.200000, rms=0.535 (0.012%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.546, neg=0, invalid=762 0421: dt=1.008000, rms=0.545 (0.097%), neg=0, invalid=762 0422: dt=0.576000, rms=0.545 (0.001%), neg=0, invalid=762 0423: dt=0.576000, rms=0.545 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.546, neg=0, invalid=762 0424: dt=4.000000, rms=0.545 (0.139%), neg=0, invalid=762 0425: dt=1.008000, rms=0.545 (0.003%), neg=0, invalid=762 0426: dt=1.008000, rms=0.545 (0.001%), neg=0, invalid=762 0427: dt=1.008000, rms=0.545 (-0.004%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.562, neg=0, invalid=762 0428: dt=0.112000, rms=0.562 (0.081%), neg=0, invalid=762 0429: dt=0.028000, rms=0.562 (0.000%), neg=0, invalid=762 0430: dt=0.028000, rms=0.562 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.562, neg=0, invalid=762 0431: dt=1.280000, rms=0.561 (0.264%), neg=0, invalid=762 0432: dt=0.448000, rms=0.561 (0.018%), neg=0, invalid=762 0433: dt=0.448000, rms=0.561 (-0.003%), 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=0.541, neg=0, invalid=762 iter 0, gcam->neg = 43 after 1 iterations, nbhd size=0, neg = 0 0434: dt=1.888889, rms=0.515 (4.785%), neg=0, invalid=762 0435: dt=0.080000, rms=0.515 (0.038%), neg=0, invalid=762 0436: dt=0.080000, rms=0.515 (-0.036%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.516, neg=0, invalid=762 0437: dt=0.112000, rms=0.515 (0.212%), neg=0, invalid=762 0438: dt=0.048000, rms=0.514 (0.013%), neg=0, invalid=762 0439: dt=0.048000, rms=0.514 (-0.002%), 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=0.503, neg=0, invalid=762 0440: dt=0.000000, rms=0.503 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.503, neg=0, invalid=762 0441: dt=0.000000, rms=0.503 (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=0.504, neg=0, invalid=762 0442: dt=0.000000, rms=0.504 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.504, neg=0, invalid=762 0443: dt=20.736000, rms=0.504 (0.007%), neg=0, invalid=762 0444: dt=9.072000, rms=0.504 (0.001%), neg=0, invalid=762 0445: dt=9.072000, rms=0.504 (0.001%), neg=0, invalid=762 0446: dt=9.072000, rms=0.504 (0.000%), neg=0, invalid=762 0447: dt=9.072000, rms=0.504 (-0.003%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.504, neg=0, invalid=762 0448: dt=8.000000, rms=0.504 (0.039%), neg=0, invalid=762 0449: dt=1.200000, rms=0.504 (0.001%), neg=0, invalid=762 0450: dt=1.200000, rms=0.504 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.504, neg=0, invalid=762 0451: dt=70.956522, rms=0.502 (0.406%), neg=0, invalid=762 0452: dt=44.800000, rms=0.500 (0.284%), neg=0, invalid=762 0453: dt=38.400000, rms=0.500 (0.142%), neg=0, invalid=762 0454: dt=38.400000, rms=0.499 (0.100%), neg=0, invalid=762 0455: dt=38.400000, rms=0.498 (0.152%), neg=0, invalid=762 0456: dt=38.400000, rms=0.497 (0.191%), neg=0, invalid=762 0457: dt=38.400000, rms=0.497 (0.161%), neg=0, invalid=762 0458: dt=38.400000, rms=0.496 (0.169%), neg=0, invalid=762 0459: dt=38.400000, rms=0.495 (0.148%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0460: dt=38.400000, rms=0.494 (0.146%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0461: dt=38.400000, rms=0.494 (0.122%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0462: dt=38.400000, rms=0.493 (0.119%), neg=0, invalid=762 0463: dt=44.800000, rms=0.493 (0.028%), neg=0, invalid=762 0464: dt=44.800000, rms=0.493 (0.010%), neg=0, invalid=762 0465: dt=44.800000, rms=0.493 (0.024%), neg=0, invalid=762 0466: dt=44.800000, rms=0.493 (0.025%), neg=0, invalid=762 0467: dt=44.800000, rms=0.493 (0.018%), neg=0, invalid=762 0468: dt=44.800000, rms=0.493 (0.013%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.497, neg=0, invalid=762 0469: dt=0.576000, rms=0.497 (0.002%), neg=0, invalid=762 0470: dt=0.054000, rms=0.497 (0.000%), neg=0, invalid=762 0471: dt=0.054000, rms=0.497 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.497, neg=0, invalid=762 0472: dt=9.866667, rms=0.496 (0.140%), neg=0, invalid=762 0473: dt=14.545455, rms=0.496 (0.078%), neg=0, invalid=762 0474: dt=14.545455, rms=0.495 (0.122%), neg=0, invalid=762 0475: dt=14.545455, rms=0.495 (0.184%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0476: dt=14.545455, rms=0.493 (0.224%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0477: dt=14.545455, rms=0.492 (0.277%), neg=0, invalid=762 0478: dt=14.545455, rms=0.491 (0.291%), neg=0, invalid=762 0479: dt=14.545455, rms=0.490 (0.220%), neg=0, invalid=762 0480: dt=14.545455, rms=0.489 (0.101%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0481: dt=14.545455, rms=0.489 (-0.002%), neg=0, invalid=762 0482: dt=0.000000, rms=0.489 (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=0.496, neg=0, invalid=762 0483: dt=0.000000, rms=0.496 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.496, neg=0, invalid=762 0484: dt=0.000000, rms=0.496 (0.000%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.484, neg=0, invalid=762 iter 0, gcam->neg = 22 after 2 iterations, nbhd size=0, neg = 0 0485: dt=1.536000, rms=0.471 (2.750%), neg=0, invalid=762 0486: dt=0.000023, rms=0.471 (0.000%), neg=0, invalid=762 0487: dt=0.000023, rms=0.471 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.471, neg=0, invalid=762 0488: dt=0.112000, rms=0.470 (0.136%), neg=0, invalid=762 0489: dt=0.112000, rms=0.470 (0.042%), neg=0, invalid=762 0490: dt=0.112000, rms=0.470 (-0.006%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 1 hours, 34 minutes and 1 seconds. mri_ca_register utimesec 6881.833566 mri_ca_register stimesec 44.564352 mri_ca_register ru_maxrss 1704728 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 48469009 mri_ca_register ru_majflt 0 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 0 mri_ca_register ru_oublock 63784 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 151616 mri_ca_register ru_nivcsw 9107 FSRUNTIME@ mri_ca_register 1.5669 hours 4 threads #-------------------------------------- #@# SubCort Seg Sun Aug 18 12:19:08 EDT 2019 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/stable6/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz sysname Linux hostname bee.nmr.mgh.harvard.edu machine x86_64 setenv SUBJECTS_DIR /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR cd /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/stable6/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz == Number of threads available to mri_ca_label for OpenMP = 4 == 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 /usr/local/freesurfer/stable6/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 29.69 Atlas used for the 3D morph was /usr/local/freesurfer/stable6/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 = 0.08282 (41) Left_Lateral_Ventricle (4): linear fit = 2.06 x + 0.0 (7412 voxels, overlap=0.010) Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (7412 voxels, peak = 41), gca=30.0 gca peak = 0.17677 (13) mri peak = 0.09954 (41) Right_Lateral_Ventricle (43): linear fit = 3.11 x + 0.0 (6601 voxels, overlap=0.010) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (6601 voxels, peak = 40), gca=19.5 gca peak = 0.28129 (95) mri peak = 0.08578 (93) Right_Pallidum (52): linear fit = 0.98 x + 0.0 (3722 voxels, overlap=1.015) Right_Pallidum (52): linear fit = 0.98 x + 0.0 (3722 voxels, peak = 93), gca=92.6 gca peak = 0.16930 (96) mri peak = 0.08237 (94) Left_Pallidum (13): linear fit = 0.99 x + 0.0 (3626 voxels, overlap=1.011) Left_Pallidum (13): linear fit = 0.99 x + 0.0 (3626 voxels, peak = 95), gca=94.6 gca peak = 0.24553 (55) mri peak = 0.06750 (70) Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (5771 voxels, overlap=0.211) Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (5771 voxels, peak = 67), gca=67.4 gca peak = 0.30264 (59) mri peak = 0.07005 (69) Left_Hippocampus (17): linear fit = 1.20 x + 0.0 (4900 voxels, overlap=0.138) Left_Hippocampus (17): linear fit = 1.20 x + 0.0 (4900 voxels, peak = 71), gca=70.5 gca peak = 0.07580 (103) mri peak = 0.07901 (104) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (356499 voxels, overlap=0.781) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (356499 voxels, peak = 105), gca=104.5 gca peak = 0.07714 (104) mri peak = 0.07483 (105) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (359907 voxels, overlap=0.750) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (359907 voxels, peak = 106), gca=105.6 gca peak = 0.09712 (58) mri peak = 0.04829 (79) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (246131 voxels, overlap=0.000) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (246131 voxels, peak = 78), gca=78.0 gca peak = 0.11620 (58) mri peak = 0.04379 (78) Right_Cerebral_Cortex (42): linear fit = 1.33 x + 0.0 (257306 voxels, overlap=0.001) Right_Cerebral_Cortex (42): linear fit = 1.33 x + 0.0 (257306 voxels, peak = 77), gca=76.9 gca peak = 0.30970 (66) mri peak = 0.08960 (82) Right_Caudate (50): linear fit = 1.21 x + 0.0 (6617 voxels, overlap=0.024) Right_Caudate (50): linear fit = 1.21 x + 0.0 (6617 voxels, peak = 80), gca=79.5 gca peak = 0.15280 (69) mri peak = 0.08371 (82) Left_Caudate (11): linear fit = 1.12 x + 0.0 (7768 voxels, overlap=0.432) Left_Caudate (11): linear fit = 1.12 x + 0.0 (7768 voxels, peak = 78), gca=77.6 gca peak = 0.13902 (56) mri peak = 0.04550 (68) Left_Cerebellum_Cortex (8): linear fit = 1.26 x + 0.0 (58579 voxels, overlap=0.036) Left_Cerebellum_Cortex (8): linear fit = 1.26 x + 0.0 (58579 voxels, peak = 71), gca=70.8 gca peak = 0.14777 (55) mri peak = 0.04904 (65) Right_Cerebellum_Cortex (47): linear fit = 1.17 x + 0.0 (82347 voxels, overlap=0.439) Right_Cerebellum_Cortex (47): linear fit = 1.17 x + 0.0 (82347 voxels, peak = 65), gca=64.6 gca peak = 0.16765 (84) mri peak = 0.04917 (85) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (20971 voxels, overlap=0.976) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (20971 voxels, peak = 86), gca=86.1 gca peak = 0.18739 (84) mri peak = 0.06852 (83) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (23156 voxels, overlap=0.994) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (23156 voxels, peak = 83), gca=82.7 gca peak = 0.29869 (57) mri peak = 0.07225 (69) Left_Amygdala (18): linear fit = 1.18 x + 0.0 (1748 voxels, overlap=0.512) Left_Amygdala (18): linear fit = 1.18 x + 0.0 (1748 voxels, peak = 68), gca=67.5 gca peak = 0.33601 (57) mri peak = 0.07768 (70) Right_Amygdala (54): linear fit = 1.21 x + 0.0 (2149 voxels, overlap=0.071) Right_Amygdala (54): linear fit = 1.21 x + 0.0 (2149 voxels, peak = 69), gca=68.7 gca peak = 0.11131 (90) mri peak = 0.05423 (94) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (21166 voxels, overlap=0.835) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (21166 voxels, peak = 96), gca=95.9 gca peak = 0.11793 (83) mri peak = 0.05846 (93) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (20943 voxels, overlap=0.609) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (20943 voxels, peak = 93), gca=92.5 gca peak = 0.08324 (81) mri peak = 0.04720 (81) Left_Putamen (12): linear fit = 1.12 x + 0.0 (10203 voxels, overlap=0.713) Left_Putamen (12): linear fit = 1.12 x + 0.0 (10203 voxels, peak = 90), gca=90.3 gca peak = 0.10360 (77) mri peak = 0.04548 (78) Right_Putamen (51): linear fit = 1.09 x + 0.0 (10912 voxels, overlap=0.741) Right_Putamen (51): linear fit = 1.09 x + 0.0 (10912 voxels, peak = 84), gca=83.5 gca peak = 0.08424 (78) mri peak = 0.13875 (81) Brain_Stem (16): linear fit = 1.03 x + 0.0 (36676 voxels, overlap=0.476) Brain_Stem (16): linear fit = 1.03 x + 0.0 (36676 voxels, peak = 81), gca=80.7 gca peak = 0.12631 (89) mri peak = 0.07400 (88) Right_VentralDC (60): linear fit = 0.99 x + 0.0 (6564 voxels, overlap=0.823) Right_VentralDC (60): linear fit = 0.99 x + 0.0 (6564 voxels, peak = 88), gca=87.7 gca peak = 0.14500 (87) mri peak = 0.07834 (88) Left_VentralDC (28): linear fit = 0.96 x + 0.0 (5701 voxels, overlap=0.916) Left_VentralDC (28): linear fit = 0.96 x + 0.0 (5701 voxels, peak = 84), gca=84.0 gca peak = 0.14975 (24) mri peak = 0.08633 (38) Third_Ventricle (14): linear fit = 1.52 x + 0.0 (328 voxels, overlap=0.074) Third_Ventricle (14): linear fit = 1.52 x + 0.0 (328 voxels, peak = 37), gca=36.6 gca peak = 0.19357 (14) mri peak = 0.08988 (23) Fourth_Ventricle (15): linear fit = 1.39 x + 0.0 (1642 voxels, overlap=0.928) Fourth_Ventricle (15): linear fit = 1.39 x + 0.0 (1642 voxels, peak = 20), gca=19.5 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 1.00000 (94) gca peak Third_Ventricle = 0.14975 (24) gca peak 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 1.25 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 1.47 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.12544 (31) mri peak = 0.08282 (41) Left_Lateral_Ventricle (4): linear fit = 1.34 x + 0.0 (7412 voxels, overlap=0.254) Left_Lateral_Ventricle (4): linear fit = 1.34 x + 0.0 (7412 voxels, peak = 41), gca=41.4 gca peak = 0.13981 (19) mri peak = 0.09954 (41) Right_Lateral_Ventricle (43): linear fit = 1.98 x + 0.0 (6601 voxels, overlap=0.170) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (6601 voxels, peak = 38), gca=28.5 gca peak = 0.24581 (92) mri peak = 0.08578 (93) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (3722 voxels, overlap=1.004) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (3722 voxels, peak = 92), gca=91.5 gca peak = 0.20438 (95) mri peak = 0.08237 (94) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (3626 voxels, overlap=1.009) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (3626 voxels, peak = 96), gca=96.4 gca peak = 0.24059 (68) mri peak = 0.06750 (70) Right_Hippocampus (53): linear fit = 0.98 x + 0.0 (5771 voxels, overlap=1.002) Right_Hippocampus (53): linear fit = 0.98 x + 0.0 (5771 voxels, peak = 66), gca=66.3 gca peak = 0.28258 (67) mri peak = 0.07005 (69) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (4900 voxels, overlap=1.004) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (4900 voxels, peak = 67), gca=67.0 gca peak = 0.07771 (104) mri peak = 0.07901 (104) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (356499 voxels, overlap=0.816) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (356499 voxels, peak = 103), gca=103.5 gca peak = 0.07820 (106) mri peak = 0.07483 (105) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (359907 voxels, overlap=0.802) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (359907 voxels, peak = 105), gca=105.5 gca peak = 0.07291 (78) mri peak = 0.04829 (79) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (246131 voxels, overlap=0.929) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (246131 voxels, peak = 78), gca=78.0 gca peak = 0.09012 (77) mri peak = 0.04379 (78) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (257306 voxels, overlap=0.941) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (257306 voxels, peak = 76), gca=75.8 gca peak = 0.21545 (80) mri peak = 0.08960 (82) Right_Caudate (50): linear fit = 1.00 x + 0.0 (6617 voxels, overlap=1.005) Right_Caudate (50): linear fit = 1.00 x + 0.0 (6617 voxels, peak = 80), gca=80.0 gca peak = 0.16640 (87) mri peak = 0.08371 (82) Left_Caudate (11): linear fit = 0.99 x + 0.0 (7768 voxels, overlap=1.000) Left_Caudate (11): linear fit = 0.99 x + 0.0 (7768 voxels, peak = 86), gca=85.7 gca peak = 0.11310 (70) mri peak = 0.04550 (68) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (58579 voxels, overlap=0.986) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (58579 voxels, peak = 69), gca=69.0 gca peak = 0.12967 (64) mri peak = 0.04904 (65) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (82347 voxels, overlap=0.995) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (82347 voxels, peak = 64), gca=63.7 gca peak = 0.15768 (86) mri peak = 0.04917 (85) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (20971 voxels, overlap=0.990) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (20971 voxels, peak = 86), gca=85.6 gca peak = 0.17315 (83) mri peak = 0.06852 (83) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (23156 voxels, overlap=0.989) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (23156 voxels, peak = 83), gca=82.6 gca peak = 0.29963 (69) mri peak = 0.07225 (69) Left_Amygdala (18): linear fit = 0.99 x + 0.0 (1748 voxels, overlap=1.008) Left_Amygdala (18): linear fit = 0.99 x + 0.0 (1748 voxels, peak = 68), gca=68.0 gca peak = 0.29097 (69) mri peak = 0.07768 (70) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (2149 voxels, overlap=1.012) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (2149 voxels, peak = 69), gca=69.0 gca peak = 0.11504 (94) mri peak = 0.05423 (94) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (21166 voxels, overlap=0.993) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (21166 voxels, peak = 94), gca=93.5 gca peak = 0.09127 (90) mri peak = 0.05846 (93) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (20943 voxels, overlap=0.994) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (20943 voxels, peak = 90), gca=90.4 gca peak = 0.07907 (84) mri peak = 0.04720 (81) Left_Putamen (12): linear fit = 1.00 x + 0.0 (10203 voxels, overlap=0.993) Left_Putamen (12): linear fit = 1.00 x + 0.0 (10203 voxels, peak = 84), gca=83.6 gca peak = 0.08958 (85) mri peak = 0.04548 (78) Right_Putamen (51): linear fit = 1.00 x + 0.0 (10912 voxels, overlap=0.986) Right_Putamen (51): linear fit = 1.00 x + 0.0 (10912 voxels, peak = 85), gca=84.6 gca peak = 0.08492 (81) mri peak = 0.13875 (81) Brain_Stem: unreasonable value (79.8/81.0), not in range [80, 110] - rejecting gca peak = 0.12602 (84) mri peak = 0.07400 (88) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (6564 voxels, overlap=0.800) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (6564 voxels, peak = 84), gca=83.6 gca peak = 0.16091 (84) mri peak = 0.07834 (88) Left_VentralDC (28): linear fit = 1.01 x + 0.0 (5701 voxels, overlap=0.864) Left_VentralDC (28): linear fit = 1.01 x + 0.0 (5701 voxels, peak = 85), gca=85.3 gca peak = 0.14011 (35) mri peak = 0.08633 (38) Third_Ventricle (14): linear fit = 1.10 x + 0.0 (328 voxels, overlap=0.817) Third_Ventricle (14): linear fit = 1.10 x + 0.0 (328 voxels, peak = 38), gca=38.3 gca peak = 0.14735 (21) mri peak = 0.08988 (23) Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (1642 voxels, overlap=0.803) Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (1642 voxels, peak = 22), gca=21.5 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.13617 (32) gca peak Left_Thalamus = 0.36646 (104) gca peak Brain_Stem = 0.08492 (81) gca peak CSF = 0.17073 (53) gca peak Left_Accumbens_area = 0.59892 (70) gca peak Left_undetermined = 0.95280 (34) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.12303 (35) gca peak Right_Inf_Lat_Vent = 0.20093 (28) gca peak Right_Accumbens_area = 0.39494 (78) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14504 (37) gca peak Fifth_Ventricle = 0.51669 (45) gca peak WM_hypointensities = 0.07818 (78) gca peak non_WM_hypointensities = 0.09187 (44) gca peak Optic_Chiasm = 0.69230 (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 1.24 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 533979 voxels changed in iteration 0 of unlikely voxel relabeling 2509 voxels changed in iteration 1 of unlikely voxel relabeling 57 voxels changed in iteration 2 of unlikely voxel relabeling 1 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 445178 gm and wm labels changed (%39 to gray, %61 to white out of all changed labels) 1776 hippocampal voxels changed. 4 amygdala voxels changed. pass 1: 361861 changed. image ll: -2.637, PF=0.500 pass 2: 135082 changed. image ll: -2.628, PF=0.500 pass 3: 46731 changed. pass 4: 20248 changed. pass 5: 10074 changed. pass 6: 5668 changed. pass 7: 3217 changed. 446715 voxels changed in iteration 0 of unlikely voxel relabeling 3710 voxels changed in iteration 1 of unlikely voxel relabeling 285 voxels changed in iteration 2 of unlikely voxel relabeling 195 voxels changed in iteration 3 of unlikely voxel relabeling 67 voxels changed in iteration 4 of unlikely voxel relabeling 32098 voxels changed in iteration 0 of unlikely voxel relabeling 517 voxels changed in iteration 1 of unlikely voxel relabeling 97 voxels changed in iteration 2 of unlikely voxel relabeling 13 voxels changed in iteration 3 of unlikely voxel relabeling 9 voxels changed in iteration 4 of unlikely voxel relabeling 29843 voxels changed in iteration 0 of unlikely voxel relabeling 267 voxels changed in iteration 1 of unlikely voxel relabeling 44 voxels changed in iteration 2 of unlikely voxel relabeling 3 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 25919 voxels changed in iteration 0 of unlikely voxel relabeling 108 voxels changed in iteration 1 of unlikely voxel relabeling 6 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling MRItoUCHAR: min=0, max=85 MRItoUCHAR: converting to UCHAR writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 9568.530500 mri_ca_label stimesec 25.449639 mri_ca_label ru_maxrss 3484388 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 34876062 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 0 mri_ca_label ru_oublock 1232 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 945 mri_ca_label ru_nivcsw 11093 auto-labeling took 158 minutes and 14 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/mri/transforms/cc_up.lta arap_loom2_7T_sess06 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/mri/transforms/cc_up.lta reading aseg from /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/mri/aseg.auto_noCCseg.mgz reading norm from /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/mri/norm.mgz 294018 voxels in left wm, 358492 in right wm, xrange [147, 173] searching rotation angles z=[-5 9], y=[-12 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 searching scale 1 Z rot 6.3 searching scale 1 Z rot 6.5 searching scale 1 Z rot 6.8 searching scale 1 Z rot 7.0 searching scale 1 Z rot 7.3 searching scale 1 Z rot 7.5 searching scale 1 Z rot 7.8 searching scale 1 Z rot 8.0 searching scale 1 Z rot 8.3 searching scale 1 Z rot 8.5 searching scale 1 Z rot 8.8 searching scale 1 Z rot 9.0 global minimum found at slice 161.0, rotations (-4.35, 2.28) final transformation (x=161.0, yr=-4.352, zr=2.277): 0.99633 -0.03973 -0.07582 -16.05225; 0.03962 0.99921 -0.00301 8.18215; 0.07588 0.00000 0.99712 -39.76661; 0.00000 0.00000 0.00000 1.00000; updating x range to be [122, 132] in xformed coordinates best xformed slice 128 cc center is found at 128 114 156 eigenvectors: 0.00052 -0.00057 1.00000; 0.02309 -0.99973 -0.00058; 0.99973 0.02309 -0.00051; writing aseg with callosum to /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/mri/aseg.auto.mgz... corpus callosum segmentation took 5.9 minutes #-------------------------------------- #@# Merge ASeg Sun Aug 18 15:03:18 EDT 2019 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Sun Aug 18 15:03:18 EDT 2019 /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/mri mri_normalize -mprage -noconform -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz assuming input volume is MGH (Van der Kouwe) MP-RAGE not interpolating and embedding volume to be 256^3... using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.presurf.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 4650 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 89 gm peak at 67 (67), valley at 23 (23) csf peak at 34, setting threshold to 56 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 109 gm peak at 81 (81), valley at 22 (22) csf peak at 41, setting threshold to 67 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 5 minutes and 58 seconds. #-------------------------------------------- #@# Mask BFS Sun Aug 18 15:09:19 EDT 2019 /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 6612047 voxels in mask (pct= 20.18) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Sun Aug 18 15:09:21 EDT 2019 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): 103.9 +- 7.5 [79.0 --> 125.0] GM (72.0) : 69.7 +- 12.3 [30.0 --> 95.0] setting bottom of white matter range to 81.9 setting top of gray matter range to 94.2 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... thickening thin strands.... 20 segments, 8703 filled 46925 bright non-wm voxels segmented. 47423 diagonally connected voxels added... white matter segmentation took 4.9 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 1.44 minutes reading wm segmentation from wm.seg.mgz... 1771 voxels added to wm to prevent paths from MTL structures to cortex 18265 additional wm voxels added 0 additional wm voxels added SEG EDIT: 178423 voxels turned on, 144423 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 110 new 110 115,126,128 old 110 new 110 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 210 found - 210 modified | TOTAL: 210 pass 2 (xy+): 0 found - 210 modified | TOTAL: 210 pass 1 (xy-): 228 found - 228 modified | TOTAL: 438 pass 2 (xy-): 0 found - 228 modified | TOTAL: 438 pass 1 (yz+): 261 found - 261 modified | TOTAL: 699 pass 2 (yz+): 0 found - 261 modified | TOTAL: 699 pass 1 (yz-): 317 found - 317 modified | TOTAL: 1016 pass 2 (yz-): 0 found - 317 modified | TOTAL: 1016 pass 1 (xz+): 242 found - 242 modified | TOTAL: 1258 pass 2 (xz+): 0 found - 242 modified | TOTAL: 1258 pass 1 (xz-): 260 found - 260 modified | TOTAL: 1518 pass 2 (xz-): 0 found - 260 modified | TOTAL: 1518 Iteration Number : 1 pass 1 (+++): 496 found - 496 modified | TOTAL: 496 pass 2 (+++): 0 found - 496 modified | TOTAL: 496 pass 1 (+++): 595 found - 595 modified | TOTAL: 1091 pass 2 (+++): 2 found - 597 modified | TOTAL: 1093 pass 3 (+++): 0 found - 597 modified | TOTAL: 1093 pass 1 (+++): 539 found - 539 modified | TOTAL: 1632 pass 2 (+++): 0 found - 539 modified | TOTAL: 1632 pass 1 (+++): 701 found - 701 modified | TOTAL: 2333 pass 2 (+++): 0 found - 701 modified | TOTAL: 2333 Iteration Number : 1 pass 1 (++): 966 found - 966 modified | TOTAL: 966 pass 2 (++): 1 found - 967 modified | TOTAL: 967 pass 3 (++): 0 found - 967 modified | TOTAL: 967 pass 1 (+-): 980 found - 980 modified | TOTAL: 1947 pass 2 (+-): 3 found - 983 modified | TOTAL: 1950 pass 3 (+-): 0 found - 983 modified | TOTAL: 1950 pass 1 (--): 906 found - 906 modified | TOTAL: 2856 pass 2 (--): 6 found - 912 modified | TOTAL: 2862 pass 3 (--): 0 found - 912 modified | TOTAL: 2862 pass 1 (-+): 969 found - 969 modified | TOTAL: 3831 pass 2 (-+): 0 found - 969 modified | TOTAL: 3831 Iteration Number : 2 pass 1 (xy+): 216 found - 216 modified | TOTAL: 216 pass 2 (xy+): 0 found - 216 modified | TOTAL: 216 pass 1 (xy-): 201 found - 201 modified | TOTAL: 417 pass 2 (xy-): 0 found - 201 modified | TOTAL: 417 pass 1 (yz+): 198 found - 198 modified | TOTAL: 615 pass 2 (yz+): 0 found - 198 modified | TOTAL: 615 pass 1 (yz-): 236 found - 236 modified | TOTAL: 851 pass 2 (yz-): 0 found - 236 modified | TOTAL: 851 pass 1 (xz+): 218 found - 218 modified | TOTAL: 1069 pass 2 (xz+): 0 found - 218 modified | TOTAL: 1069 pass 1 (xz-): 195 found - 195 modified | TOTAL: 1264 pass 2 (xz-): 0 found - 195 modified | TOTAL: 1264 Iteration Number : 2 pass 1 (+++): 42 found - 42 modified | TOTAL: 42 pass 2 (+++): 0 found - 42 modified | TOTAL: 42 pass 1 (+++): 59 found - 59 modified | TOTAL: 101 pass 2 (+++): 0 found - 59 modified | TOTAL: 101 pass 1 (+++): 46 found - 46 modified | TOTAL: 147 pass 2 (+++): 0 found - 46 modified | TOTAL: 147 pass 1 (+++): 53 found - 53 modified | TOTAL: 200 pass 2 (+++): 0 found - 53 modified | TOTAL: 200 Iteration Number : 2 pass 1 (++): 106 found - 106 modified | TOTAL: 106 pass 2 (++): 0 found - 106 modified | TOTAL: 106 pass 1 (+-): 137 found - 137 modified | TOTAL: 243 pass 2 (+-): 2 found - 139 modified | TOTAL: 245 pass 3 (+-): 0 found - 139 modified | TOTAL: 245 pass 1 (--): 124 found - 124 modified | TOTAL: 369 pass 2 (--): 1 found - 125 modified | TOTAL: 370 pass 3 (--): 0 found - 125 modified | TOTAL: 370 pass 1 (-+): 102 found - 102 modified | TOTAL: 472 pass 2 (-+): 0 found - 102 modified | TOTAL: 472 Iteration Number : 3 pass 1 (xy+): 34 found - 34 modified | TOTAL: 34 pass 2 (xy+): 0 found - 34 modified | TOTAL: 34 pass 1 (xy-): 27 found - 27 modified | TOTAL: 61 pass 2 (xy-): 0 found - 27 modified | TOTAL: 61 pass 1 (yz+): 31 found - 31 modified | TOTAL: 92 pass 2 (yz+): 0 found - 31 modified | TOTAL: 92 pass 1 (yz-): 22 found - 22 modified | TOTAL: 114 pass 2 (yz-): 0 found - 22 modified | TOTAL: 114 pass 1 (xz+): 11 found - 11 modified | TOTAL: 125 pass 2 (xz+): 0 found - 11 modified | TOTAL: 125 pass 1 (xz-): 19 found - 19 modified | TOTAL: 144 pass 2 (xz-): 0 found - 19 modified | TOTAL: 144 Iteration Number : 3 pass 1 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 pass 1 (+++): 6 found - 6 modified | TOTAL: 10 pass 2 (+++): 0 found - 6 modified | TOTAL: 10 pass 1 (+++): 8 found - 8 modified | TOTAL: 18 pass 2 (+++): 0 found - 8 modified | TOTAL: 18 pass 1 (+++): 5 found - 5 modified | TOTAL: 23 pass 2 (+++): 0 found - 5 modified | TOTAL: 23 Iteration Number : 3 pass 1 (++): 11 found - 11 modified | TOTAL: 11 pass 2 (++): 0 found - 11 modified | TOTAL: 11 pass 1 (+-): 16 found - 16 modified | TOTAL: 27 pass 2 (+-): 0 found - 16 modified | TOTAL: 27 pass 1 (--): 8 found - 8 modified | TOTAL: 35 pass 2 (--): 0 found - 8 modified | TOTAL: 35 pass 1 (-+): 11 found - 11 modified | TOTAL: 46 pass 2 (-+): 0 found - 11 modified | TOTAL: 46 Iteration Number : 4 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 3 found - 3 modified | TOTAL: 6 pass 2 (xy-): 0 found - 3 modified | TOTAL: 6 pass 1 (yz+): 1 found - 1 modified | TOTAL: 7 pass 2 (yz+): 0 found - 1 modified | TOTAL: 7 pass 1 (yz-): 3 found - 3 modified | TOTAL: 10 pass 2 (yz-): 0 found - 3 modified | TOTAL: 10 pass 1 (xz+): 3 found - 3 modified | TOTAL: 13 pass 2 (xz+): 0 found - 3 modified | TOTAL: 13 pass 1 (xz-): 2 found - 2 modified | TOTAL: 15 pass 2 (xz-): 0 found - 2 modified | TOTAL: 15 Iteration Number : 4 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 pass 1 (+++): 2 found - 2 modified | TOTAL: 6 pass 2 (+++): 0 found - 2 modified | TOTAL: 6 pass 1 (+++): 0 found - 0 modified | TOTAL: 6 Iteration Number : 4 pass 1 (++): 3 found - 3 modified | TOTAL: 3 pass 2 (++): 0 found - 3 modified | TOTAL: 3 pass 1 (+-): 2 found - 2 modified | TOTAL: 5 pass 2 (+-): 0 found - 2 modified | TOTAL: 5 pass 1 (--): 2 found - 2 modified | TOTAL: 7 pass 2 (--): 0 found - 2 modified | TOTAL: 7 pass 1 (-+): 3 found - 3 modified | TOTAL: 10 pass 2 (-+): 0 found - 3 modified | TOTAL: 10 Iteration Number : 5 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 1 found - 1 modified | TOTAL: 2 pass 2 (yz+): 0 found - 1 modified | TOTAL: 2 pass 1 (yz-): 0 found - 0 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 Iteration Number : 5 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 5 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 2 found - 2 modified | TOTAL: 2 pass 2 (+-): 1 found - 3 modified | TOTAL: 3 pass 3 (+-): 0 found - 3 modified | TOTAL: 3 pass 1 (--): 0 found - 0 modified | TOTAL: 3 pass 1 (-+): 0 found - 0 modified | TOTAL: 3 Iteration Number : 6 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 0 found - 0 modified | TOTAL: 2 pass 1 (yz+): 0 found - 0 modified | TOTAL: 2 pass 1 (yz-): 0 found - 0 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 Iteration Number : 6 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 6 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 7 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 : 7 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 : 7 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 = 9869 (out of 2303916: 0.428358) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Sun Aug 18 15:15:52 EDT 2019 /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/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 1.05296 -0.00905 -0.07691 -0.00975; 0.02784 1.07308 0.20826 -41.75337; 0.05957 -0.17843 0.96732 -5.85243; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.05296 -0.00905 -0.07691 -0.00975; 0.02784 1.07308 0.20826 -41.75337; 0.05957 -0.17843 0.96732 -5.85243; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (914, 3657) area[0] = 2630 (min = 914, max = 3657), aspect = 0.45 (min = 0.10, max = 0.75) no need to search using seed (158, 139, 101), TAL = (1.2, -36.5, 13.0) talairach voxel to voxel transform 0.94517 0.01976 0.07089 1.24922; -0.01276 0.89942 -0.19466 36.41463; -0.06056 0.16469 0.99351 12.69029; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (158, 139, 101) --> (1.2, -36.5, 13.0) done. writing output to filled.mgz... filling took 0.9 minutes talairach cc position changed to (1.24, -36.51, 12.99) Erasing brainstem...done. seed_search_size = 15, min_neighbors = 5 search rh wm seed point around talairach space:(19.24, -36.51, 12.99) SRC: (133.00, 140.13, 128.12) search lh wm seed point around talairach space (-16.76, -36.51, 12.99), SRC: (187.99, 139.39, 124.60) 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 ... #-------------------------------------------- #@# Tessellate lh Sun Aug 18 15:16:46 EDT 2019 /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 10 found - 10 modified | TOTAL: 10 pass 2 (xy+): 0 found - 10 modified | TOTAL: 10 pass 1 (xy-): 5 found - 5 modified | TOTAL: 15 pass 2 (xy-): 0 found - 5 modified | TOTAL: 15 pass 1 (yz+): 21 found - 21 modified | TOTAL: 36 pass 2 (yz+): 0 found - 21 modified | TOTAL: 36 pass 1 (yz-): 11 found - 11 modified | TOTAL: 47 pass 2 (yz-): 0 found - 11 modified | TOTAL: 47 pass 1 (xz+): 10 found - 10 modified | TOTAL: 57 pass 2 (xz+): 0 found - 10 modified | TOTAL: 57 pass 1 (xz-): 3 found - 3 modified | TOTAL: 60 pass 2 (xz-): 0 found - 3 modified | TOTAL: 60 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 3 found - 3 modified | TOTAL: 3 pass 2 (+++): 0 found - 3 modified | TOTAL: 3 pass 1 (+++): 2 found - 2 modified | TOTAL: 5 pass 2 (+++): 0 found - 2 modified | TOTAL: 5 Iteration Number : 1 pass 1 (++): 2 found - 2 modified | TOTAL: 2 pass 2 (++): 0 found - 2 modified | TOTAL: 2 pass 1 (+-): 7 found - 7 modified | TOTAL: 9 pass 2 (+-): 0 found - 7 modified | TOTAL: 9 pass 1 (--): 2 found - 2 modified | TOTAL: 11 pass 2 (--): 0 found - 2 modified | TOTAL: 11 pass 1 (-+): 3 found - 3 modified | TOTAL: 14 pass 2 (-+): 0 found - 3 modified | TOTAL: 14 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 2 found - 2 modified | TOTAL: 3 pass 2 (yz+): 0 found - 2 modified | TOTAL: 3 pass 1 (yz-): 0 found - 0 modified | TOTAL: 3 pass 1 (xz+): 0 found - 0 modified | TOTAL: 3 pass 1 (xz-): 1 found - 1 modified | TOTAL: 4 pass 2 (xz-): 0 found - 1 modified | TOTAL: 4 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 1 found - 1 modified | TOTAL: 1 pass 2 (-+): 0 found - 1 modified | TOTAL: 1 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 84 (out of 1163999: 0.007217) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 30: 2638 vertices, 2835 faces slice 40: 12366 vertices, 12874 faces slice 50: 28840 vertices, 29578 faces slice 60: 49812 vertices, 50861 faces slice 70: 74441 vertices, 75677 faces slice 80: 100123 vertices, 101408 faces slice 90: 125869 vertices, 127228 faces slice 100: 150652 vertices, 152034 faces slice 110: 175924 vertices, 177405 faces slice 120: 202131 vertices, 203760 faces slice 130: 227829 vertices, 229551 faces slice 140: 254232 vertices, 256185 faces slice 150: 281005 vertices, 283072 faces slice 160: 305416 vertices, 307573 faces slice 170: 330369 vertices, 332759 faces slice 180: 356420 vertices, 359012 faces slice 190: 384034 vertices, 386745 faces slice 200: 407026 vertices, 409938 faces slice 210: 427598 vertices, 430611 faces slice 220: 448396 vertices, 451493 faces slice 230: 468487 vertices, 471641 faces slice 240: 484273 vertices, 487415 faces slice 250: 499653 vertices, 502858 faces slice 260: 514069 vertices, 517309 faces slice 270: 528522 vertices, 531790 faces slice 280: 541115 vertices, 544472 faces slice 290: 550208 vertices, 553438 faces slice 300: 552694 vertices, 555742 faces slice 310: 552694 vertices, 555742 faces slice 320: 552694 vertices, 555742 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -0.61875 0.00000 0.00000 99.00000; 0.00000 0.00000 0.61875 -99.00000; 0.00000 -0.61875 0.00000 99.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 552678 voxel in cpt #1: X=-3052 [v=552678,e=1667190,f=1111460] located at (-26.992332, -5.866978, 19.938362) 8 voxel in cpt #2: X=2 [v=8,e=18,f=12] located at (-4.949993, 24.131245, 26.606251) 8 voxel in cpt #3: X=2 [v=8,e=18,f=12] located at (-5.568745, 25.368748, 24.750004) For the whole surface: X=-3048 [v=552694,e=1667226,f=1111484] 3 components have been found keeping component #1 with 552678 vertices done #-------------------------------------------- #@# Tessellate rh Sun Aug 18 15:17:04 EDT 2019 /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 8 found - 8 modified | TOTAL: 8 pass 2 (xy+): 0 found - 8 modified | TOTAL: 8 pass 1 (xy-): 5 found - 5 modified | TOTAL: 13 pass 2 (xy-): 0 found - 5 modified | TOTAL: 13 pass 1 (yz+): 14 found - 14 modified | TOTAL: 27 pass 2 (yz+): 0 found - 14 modified | TOTAL: 27 pass 1 (yz-): 19 found - 19 modified | TOTAL: 46 pass 2 (yz-): 0 found - 19 modified | TOTAL: 46 pass 1 (xz+): 13 found - 13 modified | TOTAL: 59 pass 2 (xz+): 0 found - 13 modified | TOTAL: 59 pass 1 (xz-): 4 found - 4 modified | TOTAL: 63 pass 2 (xz-): 0 found - 4 modified | TOTAL: 63 Iteration Number : 1 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 1 pass 1 (++): 2 found - 2 modified | TOTAL: 2 pass 2 (++): 0 found - 2 modified | TOTAL: 2 pass 1 (+-): 7 found - 7 modified | TOTAL: 9 pass 2 (+-): 0 found - 7 modified | TOTAL: 9 pass 1 (--): 6 found - 6 modified | TOTAL: 15 pass 2 (--): 0 found - 6 modified | TOTAL: 15 pass 1 (-+): 2 found - 2 modified | TOTAL: 17 pass 2 (-+): 0 found - 2 modified | TOTAL: 17 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 2 found - 2 modified | TOTAL: 2 pass 2 (xy-): 0 found - 2 modified | TOTAL: 2 pass 1 (yz+): 0 found - 0 modified | TOTAL: 2 pass 1 (yz-): 1 found - 1 modified | TOTAL: 3 pass 2 (yz-): 0 found - 1 modified | TOTAL: 3 pass 1 (xz+): 1 found - 1 modified | TOTAL: 4 pass 2 (xz+): 0 found - 1 modified | TOTAL: 4 pass 1 (xz-): 0 found - 0 modified | TOTAL: 4 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 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-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 90 (out of 1099996: 0.008182) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 30: 207 vertices, 241 faces slice 40: 4689 vertices, 4945 faces slice 50: 15485 vertices, 15917 faces slice 60: 31730 vertices, 32405 faces slice 70: 50954 vertices, 51840 faces slice 80: 74340 vertices, 75407 faces slice 90: 98765 vertices, 99917 faces slice 100: 121828 vertices, 122955 faces slice 110: 146674 vertices, 148024 faces slice 120: 170510 vertices, 171869 faces slice 130: 195011 vertices, 196442 faces slice 140: 219220 vertices, 220728 faces slice 150: 243735 vertices, 245395 faces slice 160: 266840 vertices, 268502 faces slice 170: 289168 vertices, 291017 faces slice 180: 313687 vertices, 315635 faces slice 190: 338815 vertices, 340903 faces slice 200: 361278 vertices, 363300 faces slice 210: 381908 vertices, 383908 faces slice 220: 400638 vertices, 402784 faces slice 230: 418544 vertices, 420625 faces slice 240: 433286 vertices, 435304 faces slice 250: 446941 vertices, 448996 faces slice 260: 460233 vertices, 462322 faces slice 270: 472872 vertices, 474978 faces slice 280: 483530 vertices, 485568 faces slice 290: 491254 vertices, 493213 faces slice 300: 494518 vertices, 496254 faces slice 310: 494518 vertices, 496254 faces slice 320: 494518 vertices, 496254 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -0.61875 0.00000 0.00000 99.00000; 0.00000 0.00000 0.61875 -99.00000; 0.00000 -0.61875 0.00000 99.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 494478 voxel in cpt #1: X=-1744 [v=494478,e=1488666,f=992444] located at (25.006008, -3.817875, 17.664394) 8 voxel in cpt #2: X=2 [v=8,e=18,f=12] located at (-3.093746, 32.174995, 18.562504) 16 voxel in cpt #3: X=2 [v=16,e=42,f=28] located at (-3.093746, 35.036713, 12.607037) 8 voxel in cpt #4: X=2 [v=8,e=18,f=12] located at (-3.712498, 37.743744, 14.231251) 8 voxel in cpt #5: X=2 [v=8,e=18,f=12] located at (-3.712498, 40.218742, 13.612503) For the whole surface: X=-1736 [v=494518,e=1488762,f=992508] 5 components have been found keeping component #1 with 494478 vertices done #-------------------------------------------- #@# Smooth1 lh Sun Aug 18 15:17:22 EDT 2019 /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix #-------------------------------------------- #@# Smooth1 rh Sun Aug 18 15:17:22 EDT 2019 /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix Waiting for PID 15006 of (15006 15009) to complete... Waiting for PID 15009 of (15006 15009) to complete... mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... PIDs (15006 15009) completed and logs appended. #-------------------------------------------- #@# Inflation1 lh Sun Aug 18 15:17:43 EDT 2019 /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/scripts mris_inflate -no-save-sulc -n 15 -w 10 ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix #-------------------------------------------- #@# Inflation1 rh Sun Aug 18 15:17:43 EDT 2019 /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/scripts mris_inflate -no-save-sulc -n 15 -w 10 ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Waiting for PID 15086 of (15086 15089) to complete... Waiting for PID 15089 of (15086 15089) to complete... mris_inflate -no-save-sulc -n 15 -w 10 ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix niterations = 15 write iterations = 10 Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 48.5 mm, total surface area = 103845 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 2.8 minutes step 000: RMS=0.203 (target=0.015) step 005: RMS=0.161 (target=0.015) step 010: RMS=0.143 (target=0.015) step 015: RMS=0.133 (target=0.015) step 020: RMS=0.126 (target=0.015) step 025: RMS=0.121 (target=0.015) step 030: RMS=0.117 (target=0.015) step 035: RMS=0.115 (target=0.015) step 040: RMS=0.113 (target=0.015) step 045: RMS=0.111 (target=0.015) step 050: RMS=0.109 (target=0.015) step 055: RMS=0.108 (target=0.015) step 060: RMS=0.107 (target=0.015) step 065: RMS=0.106 (target=0.015) step 070: RMS=0.105 (target=0.015) step 075: RMS=0.105 (target=0.015) step 080: RMS=0.105 (target=0.015) step 085: RMS=0.106 (target=0.015) step 090: RMS=0.106 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 363.838423 mris_inflate stimesec 18.224405 mris_inflate ru_maxrss 859128 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 14446420 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 429136 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 335107 mris_inflate ru_nivcsw 512 mris_inflate -no-save-sulc -n 15 -w 10 ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix niterations = 15 write iterations = 10 Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 47.3 mm, total surface area = 97319 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 2.3 minutes step 000: RMS=0.182 (target=0.015) step 005: RMS=0.144 (target=0.015) step 010: RMS=0.125 (target=0.015) step 015: RMS=0.114 (target=0.015) step 020: RMS=0.107 (target=0.015) step 025: RMS=0.102 (target=0.015) step 030: RMS=0.097 (target=0.015) step 035: RMS=0.094 (target=0.015) step 040: RMS=0.091 (target=0.015) step 045: RMS=0.089 (target=0.015) step 050: RMS=0.088 (target=0.015) step 055: RMS=0.087 (target=0.015) step 060: RMS=0.086 (target=0.015) step 065: RMS=0.085 (target=0.015) step 070: RMS=0.084 (target=0.015) step 075: RMS=0.083 (target=0.015) step 080: RMS=0.084 (target=0.015) step 085: RMS=0.085 (target=0.015) step 090: RMS=0.084 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 289.098246 mris_inflate stimesec 6.949298 mris_inflate ru_maxrss 763748 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 6308886 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 383464 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 188287 mris_inflate ru_nivcsw 2245 PIDs (15086 15089) completed and logs appended. #-------------------------------------------- #@# QSphere lh Sun Aug 18 15:20:33 EDT 2019 /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix #-------------------------------------------- #@# QSphere rh Sun Aug 18 15:20:33 EDT 2019 /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix Waiting for PID 15428 of (15428 15431) to complete... Waiting for PID 15431 of (15428 15431) to complete... mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.50 +- 0.41 (0.00-->9.30) (max @ vno 314426 --> 314427) face area 0.01 +- 0.01 (-0.18-->0.37) == Number of threads available to mris_sphere for OpenMP = 4 == scaling brain by 0.266... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.452, avgs=0 005/300: dt: 0.9000, rms radial error=177.191, avgs=0 010/300: dt: 0.9000, rms radial error=176.631, avgs=0 015/300: dt: 0.9000, rms radial error=175.895, avgs=0 020/300: dt: 0.9000, rms radial error=175.057, avgs=0 025/300: dt: 0.9000, rms radial error=174.158, avgs=0 030/300: dt: 0.9000, rms radial error=173.229, avgs=0 035/300: dt: 0.9000, rms radial error=172.283, avgs=0 040/300: dt: 0.9000, rms radial error=171.329, avgs=0 045/300: dt: 0.9000, rms radial error=170.372, avgs=0 050/300: dt: 0.9000, rms radial error=169.417, avgs=0 055/300: dt: 0.9000, rms radial error=168.465, avgs=0 060/300: dt: 0.9000, rms radial error=167.516, avgs=0 065/300: dt: 0.9000, rms radial error=166.572, avgs=0 070/300: dt: 0.9000, rms radial error=165.633, avgs=0 075/300: dt: 0.9000, rms radial error=164.698, avgs=0 080/300: dt: 0.9000, rms radial error=163.768, avgs=0 085/300: dt: 0.9000, rms radial error=162.843, avgs=0 090/300: dt: 0.9000, rms radial error=161.922, avgs=0 095/300: dt: 0.9000, rms radial error=161.007, avgs=0 100/300: dt: 0.9000, rms radial error=160.097, avgs=0 105/300: dt: 0.9000, rms radial error=159.194, avgs=0 110/300: dt: 0.9000, rms radial error=158.295, avgs=0 115/300: dt: 0.9000, rms radial error=157.402, avgs=0 120/300: dt: 0.9000, rms radial error=156.513, avgs=0 125/300: dt: 0.9000, rms radial error=155.630, avgs=0 130/300: dt: 0.9000, rms radial error=154.752, avgs=0 135/300: dt: 0.9000, rms radial error=153.878, avgs=0 140/300: dt: 0.9000, rms radial error=153.010, avgs=0 145/300: dt: 0.9000, rms radial error=152.146, avgs=0 150/300: dt: 0.9000, rms radial error=151.287, avgs=0 155/300: dt: 0.9000, rms radial error=150.434, avgs=0 160/300: dt: 0.9000, rms radial error=149.585, avgs=0 165/300: dt: 0.9000, rms radial error=148.740, avgs=0 170/300: dt: 0.9000, rms radial error=147.901, avgs=0 175/300: dt: 0.9000, rms radial error=147.066, avgs=0 180/300: dt: 0.9000, rms radial error=146.235, avgs=0 185/300: dt: 0.9000, rms radial error=145.410, avgs=0 190/300: dt: 0.9000, rms radial error=144.589, avgs=0 195/300: dt: 0.9000, rms radial error=143.772, avgs=0 200/300: dt: 0.9000, rms radial error=142.961, avgs=0 205/300: dt: 0.9000, rms radial error=142.153, avgs=0 210/300: dt: 0.9000, rms radial error=141.351, avgs=0 215/300: dt: 0.9000, rms radial error=140.553, avgs=0 220/300: dt: 0.9000, rms radial error=139.759, avgs=0 225/300: dt: 0.9000, rms radial error=138.970, avgs=0 230/300: dt: 0.9000, rms radial error=138.185, avgs=0 235/300: dt: 0.9000, rms radial error=137.405, avgs=0 240/300: dt: 0.9000, rms radial error=136.629, avgs=0 245/300: dt: 0.9000, rms radial error=135.857, avgs=0 250/300: dt: 0.9000, rms radial error=135.090, avgs=0 255/300: dt: 0.9000, rms radial error=134.328, avgs=0 260/300: dt: 0.9000, rms radial error=133.569, avgs=0 265/300: dt: 0.9000, rms radial error=132.815, avgs=0 270/300: dt: 0.9000, rms radial error=132.065, avgs=0 275/300: dt: 0.9000, rms radial error=131.319, avgs=0 280/300: dt: 0.9000, rms radial error=130.577, avgs=0 285/300: dt: 0.9000, rms radial error=129.840, avgs=0 290/300: dt: 0.9000, rms radial error=129.106, avgs=0 295/300: dt: 0.9000, rms radial error=128.377, avgs=0 300/300: dt: 0.9000, rms radial error=127.651, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 73683.49 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00004 epoch 2 (K=40.0), pass 1, starting sse = 16542.65 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00003 epoch 3 (K=160.0), pass 1, starting sse = 3248.77 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00047 epoch 4 (K=640.0), pass 1, starting sse = 648.49 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.03/10 = 0.00302 final distance error %36.49 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.15 hours mris_sphere utimesec 1227.485028 mris_sphere stimesec 23.668575 mris_sphere ru_maxrss 859356 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 21135584 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 39048 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 336637 mris_sphere ru_nivcsw 1249 FSRUNTIME@ mris_sphere 0.1538 hours 1 threads mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.52 +- 0.40 (0.00-->7.55) (max @ vno 366805 --> 366806) face area 0.01 +- 0.01 (-0.10-->0.35) == Number of threads available to mris_sphere for OpenMP = 4 == scaling brain by 0.276... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.218, avgs=0 005/300: dt: 0.9000, rms radial error=176.957, avgs=0 010/300: dt: 0.9000, rms radial error=176.394, avgs=0 015/300: dt: 0.9000, rms radial error=175.657, avgs=0 020/300: dt: 0.9000, rms radial error=174.817, avgs=0 025/300: dt: 0.9000, rms radial error=173.919, avgs=0 030/300: dt: 0.9000, rms radial error=172.988, avgs=0 035/300: dt: 0.9000, rms radial error=172.040, avgs=0 040/300: dt: 0.9000, rms radial error=171.085, avgs=0 045/300: dt: 0.9000, rms radial error=170.128, avgs=0 050/300: dt: 0.9000, rms radial error=169.171, avgs=0 055/300: dt: 0.9000, rms radial error=168.218, avgs=0 060/300: dt: 0.9000, rms radial error=167.269, avgs=0 065/300: dt: 0.9000, rms radial error=166.324, avgs=0 070/300: dt: 0.9000, rms radial error=165.386, avgs=0 075/300: dt: 0.9000, rms radial error=164.453, avgs=0 080/300: dt: 0.9000, rms radial error=163.525, avgs=0 085/300: dt: 0.9000, rms radial error=162.603, avgs=0 090/300: dt: 0.9000, rms radial error=161.686, avgs=0 095/300: dt: 0.9000, rms radial error=160.775, avgs=0 100/300: dt: 0.9000, rms radial error=159.868, avgs=0 105/300: dt: 0.9000, rms radial error=158.967, avgs=0 110/300: dt: 0.9000, rms radial error=158.071, avgs=0 115/300: dt: 0.9000, rms radial error=157.180, avgs=0 120/300: dt: 0.9000, rms radial error=156.294, avgs=0 125/300: dt: 0.9000, rms radial error=155.413, avgs=0 130/300: dt: 0.9000, rms radial error=154.537, avgs=0 135/300: dt: 0.9000, rms radial error=153.666, avgs=0 140/300: dt: 0.9000, rms radial error=152.799, avgs=0 145/300: dt: 0.9000, rms radial error=151.938, avgs=0 150/300: dt: 0.9000, rms radial error=151.082, avgs=0 155/300: dt: 0.9000, rms radial error=150.230, avgs=0 160/300: dt: 0.9000, rms radial error=149.383, avgs=0 165/300: dt: 0.9000, rms radial error=148.541, avgs=0 170/300: dt: 0.9000, rms radial error=147.704, avgs=0 175/300: dt: 0.9000, rms radial error=146.871, avgs=0 180/300: dt: 0.9000, rms radial error=146.043, avgs=0 185/300: dt: 0.9000, rms radial error=145.220, avgs=0 190/300: dt: 0.9000, rms radial error=144.401, avgs=0 195/300: dt: 0.9000, rms radial error=143.587, avgs=0 200/300: dt: 0.9000, rms radial error=142.778, avgs=0 205/300: dt: 0.9000, rms radial error=141.973, avgs=0 210/300: dt: 0.9000, rms radial error=141.173, avgs=0 215/300: dt: 0.9000, rms radial error=140.377, avgs=0 220/300: dt: 0.9000, rms radial error=139.586, avgs=0 225/300: dt: 0.9000, rms radial error=138.799, avgs=0 230/300: dt: 0.9000, rms radial error=138.017, avgs=0 235/300: dt: 0.9000, rms radial error=137.239, avgs=0 240/300: dt: 0.9000, rms radial error=136.465, avgs=0 245/300: dt: 0.9000, rms radial error=135.696, avgs=0 250/300: dt: 0.9000, rms radial error=134.931, avgs=0 255/300: dt: 0.9000, rms radial error=134.170, avgs=0 260/300: dt: 0.9000, rms radial error=133.414, avgs=0 265/300: dt: 0.9000, rms radial error=132.661, avgs=0 270/300: dt: 0.9000, rms radial error=131.913, avgs=0 275/300: dt: 0.9000, rms radial error=131.170, avgs=0 280/300: dt: 0.9000, rms radial error=130.430, avgs=0 285/300: dt: 0.9000, rms radial error=129.694, avgs=0 290/300: dt: 0.9000, rms radial error=128.963, avgs=0 295/300: dt: 0.9000, rms radial error=128.236, avgs=0 300/300: dt: 0.9000, rms radial error=127.512, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 65373.41 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00006 epoch 2 (K=40.0), pass 1, starting sse = 14355.05 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00001 epoch 3 (K=160.0), pass 1, starting sse = 2599.30 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/10 = 0.00056 epoch 4 (K=640.0), pass 1, starting sse = 404.03 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.04/10 = 0.00366 final distance error %34.81 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.12 hours mris_sphere utimesec 992.037959 mris_sphere stimesec 18.908469 mris_sphere ru_maxrss 763992 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 22601942 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 34896 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 158129 mris_sphere ru_nivcsw 905 FSRUNTIME@ mris_sphere 0.1243 hours 1 threads PIDs (15428 15431) completed and logs appended. #-------------------------------------------- #@# Fix Topology Copy lh Sun Aug 18 15:29:47 EDT 2019 /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Sun Aug 18 15:29:51 EDT 2019 /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Sun Aug 18 15:29:54 EDT 2019 mris_fix_topology -rusage /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 arap_loom2_7T_sess06 lh #@# Fix Topology rh Sun Aug 18 15:29:54 EDT 2019 mris_fix_topology -rusage /autofs/space/oprah_001/users/jvm27/looming/7T/SUBJECTS_DIR/arap_loom2_7T_sess06/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 arap_loom2_7T_sess06 rh Waiting for PID 16283 of (16283 16286) to complete...