Wed Feb 20 15:05:08 EST 2019 /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T /usr/local/freesurfer/stable6/bin/recon-all -all -s inul_loom2_7T -i /autofs/space/oprah_001/users/jvm27/looming/7T/inul_loom2_7T/anat/016/mT1v2.nii -expert /autofs/space/oprah_001/users/jvm27/looming/7T/scripts/Lauri/expertopts/expert.opts -hires -mail zn025 -parallel subjid inul_loom2_7T setenv SUBJECTS_DIR /autofs/space/oprah_001/users/jvm27/looming/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 17200724 5205140 445328 175427860 179209212 Swap: 62499836 529408 61970428 ######################################## 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: 2019/02/20-20:05:09-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: 2019/02/20-20:05:09-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: 2019/02/20-20:05:09-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: 2019/02/20-20:05:09-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: 2019/02/20-20:05:09-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: 2019/02/20-20:05:09-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: 2019/02/20-20:05:09-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: 2019/02/20-20:05:09-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: 2019/02/20-20:05:10-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: 2019/02/20-20:05:10-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: 2019/02/20-20:05:10-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: 2019/02/20-20:05:10-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: 2019/02/20-20:05:10-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: 2019/02/20-20:05:10-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: 2019/02/20-20:05:10-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: 2019/02/20-20:05:10-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: 2019/02/20-20:05:10-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: 2019/02/20-20:05:10-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: 2019/02/20-20:05:10-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: 2019/02/20-20:05:10-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: 2019/02/20-20:05:10-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: 2019/02/20-20:05:11-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: 2019/02/20-20:05:11-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: 2019/02/20-20:05:11-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: 2019/02/20-20:05:11-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: 2019/02/20-20:05:11-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: 2019/02/20-20:05:11-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: 2019/02/20-20:05:11-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: 2019/02/20-20:05:11-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: 2019/02/20-20:05:11-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: 2019/02/20-20:05:11-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: 2019/02/20-20:05:11-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: 2019/02/20-20:05:11-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: 2019/02/20-20:05:12-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: 2019/02/20-20:05:12-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: 2019/02/20-20:05:12-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: 2019/02/20-20:05:12-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: 2019/02/20-20:05:12-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: 2019/02/20-20:05:12-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/SUBJECTS_DIR/inul_loom2_7T mri_convert /autofs/space/oprah_001/users/jvm27/looming/7T/inul_loom2_7T/anat/016/mT1v2.nii /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/mri/orig/001.mgz mri_convert.bin /autofs/space/oprah_001/users/jvm27/looming/7T/inul_loom2_7T/anat/016/mT1v2.nii /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/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/inul_loom2_7T/anat/016/mT1v2.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.00267468, -0.968786, -0.247884) j_ras = (-0.084721, 0.246774, -0.965363) k_ras = (-0.996401, -0.023583, 0.0814164) writing to /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Wed Feb 20 15:05:25 EST 2019 Found 1 runs /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/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/SUBJECTS_DIR/inul_loom2_7T/mri/orig/001.mgz /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/mri/rawavg.mgz /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T mri_convert /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/mri/rawavg.mgz /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/mri/orig.mgz --conform_min mri_convert.bin /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/mri/rawavg.mgz /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/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/SUBJECTS_DIR/inul_loom2_7T/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.00267468, -0.968786, -0.247884) j_ras = (-0.084721, 0.246774, -0.965363) k_ras = (-0.996401, -0.023583, 0.0814164) 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/SUBJECTS_DIR/inul_loom2_7T/mri/orig.mgz... mri_add_xform_to_header -c /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/mri/transforms/talairach.xfm /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/mri/orig.mgz /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Wed Feb 20 15:05:47 EST 2019 /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/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/SUBJECTS_DIR/inul_loom2_7T/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 Wed Feb 20 15:05:47 EST 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.24614 /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.24614/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.24614/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, 4.96705e-09, -1.49012e-08) j_ras = (9.93411e-09, 2.111e-08, -1) k_ras = (-2.48353e-09, 1, -1.98682e-08) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.24614/nu0.mnc... -------------------------------------------------------- Iteration 1 Wed Feb 20 15:06:11 EST 2019 nu_correct -clobber ./tmp.mri_nu_correct.mni.24614/nu0.mnc ./tmp.mri_nu_correct.mni.24614/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.24614/0/ -iterations 1000 -distance 50 [zn025@bee.nmr.mgh.harvard.edu:/autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/mri/] [2019-02-20 15:06:11] 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.24614/0/ ./tmp.mri_nu_correct.mni.24614/nu0.mnc ./tmp.mri_nu_correct.mni.24614/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 Number of iterations: 24 CV of field change: 0.000985173 mri_convert ./tmp.mri_nu_correct.mni.24614/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.24614/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.24614/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 4.96705e-09, -1.49012e-08) j_ras = (9.93411e-09, 2.111e-08, -1) k_ras = (-2.48353e-09, 1, -1.98682e-08) 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... Wed Feb 20 15:08:46 EST 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 Wed Feb 20 15:08:46 EST 2019 Ended at Wed Feb 20 15:09:46 EST 2019 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Wed Feb 20 15:09:48 EST 2019 /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.5644, pval=0.2115 >= threshold=0.0050) awk -f /usr/local/freesurfer/stable6/bin/extract_talairach_avi_QA.awk /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/mri/transforms/talairach_avi.log tal_QC_AZS /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/mri/transforms/talairach_avi.log TalAviQA: 0.97294 z-score: -1 #-------------------------------------------- #@# Nu Intensity Correction Wed Feb 20 15:09:49 EST 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/SUBJECTS_DIR/inul_loom2_7T/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 Wed Feb 20 15:09:49 EST 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.33725 /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/mri mri_convert -cm orig.mgz ./tmp.mri_nu_correct.mni.33725/nu0.mnc -odt float mri_convert.bin -cm orig.mgz ./tmp.mri_nu_correct.mni.33725/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, 4.96705e-09, -1.49012e-08) j_ras = (9.93411e-09, 2.111e-08, -1) k_ras = (-2.48353e-09, 1, -1.98682e-08) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.33725/nu0.mnc... Outputting Volume: ............................................................ -------------------------------------------------------- Iteration 1 Wed Feb 20 15:10:20 EST 2019 nu_correct -clobber ./tmp.mri_nu_correct.mni.33725/nu0.mnc ./tmp.mri_nu_correct.mni.33725/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.33725/0/ [zn025@bee.nmr.mgh.harvard.edu:/autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/mri/] [2019-02-20 15:10:20] 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.33725/0/ ./tmp.mri_nu_correct.mni.33725/nu0.mnc ./tmp.mri_nu_correct.mni.33725/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 Number of iterations: 17 CV of field change: 0.000982066 Outputting Volume: ............................................................ -------------------------------------------------------- Iteration 2 Wed Feb 20 15:12:31 EST 2019 nu_correct -clobber ./tmp.mri_nu_correct.mni.33725/nu1.mnc ./tmp.mri_nu_correct.mni.33725/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.33725/1/ [zn025@bee.nmr.mgh.harvard.edu:/autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/mri/] [2019-02-20 15:12:31] 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.33725/1/ ./tmp.mri_nu_correct.mni.33725/nu1.mnc ./tmp.mri_nu_correct.mni.33725/nu2.imp Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Processing:.................................................................................Done Number of iterations: 8 CV of field change: 0.000975774 mri_binarize --i ./tmp.mri_nu_correct.mni.33725/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.33725/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/SUBJECTS_DIR/inul_loom2_7T/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.33725/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.33725/ones.mgz sysname Linux hostname bee.nmr.mgh.harvard.edu machine x86_64 user zn025 input ./tmp.mri_nu_correct.mni.33725/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.33725/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 13824000.000000 32768000 100.000000 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.33725/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.33725/sum.junk --avgwf ./tmp.mri_nu_correct.mni.33725/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.33725/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.33725/sum.junk --avgwf ./tmp.mri_nu_correct.mni.33725/input.mean.dat sysname Linux hostname bee.nmr.mgh.harvard.edu machine x86_64 user zn025 UseRobust 0 Loading ./tmp.mri_nu_correct.mni.33725/ones.mgz Loading orig.mgz Voxel Volume is 0.421875 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.33725/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.33725/ones.mgz --i ./tmp.mri_nu_correct.mni.33725/nu2.mnc --sum ./tmp.mri_nu_correct.mni.33725/sum.junk --avgwf ./tmp.mri_nu_correct.mni.33725/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.33725/ones.mgz --i ./tmp.mri_nu_correct.mni.33725/nu2.mnc --sum ./tmp.mri_nu_correct.mni.33725/sum.junk --avgwf ./tmp.mri_nu_correct.mni.33725/output.mean.dat sysname Linux hostname bee.nmr.mgh.harvard.edu machine x86_64 user zn025 UseRobust 0 Loading ./tmp.mri_nu_correct.mni.33725/ones.mgz Loading ./tmp.mri_nu_correct.mni.33725/nu2.mnc Voxel Volume is 0.421875 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.33725/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.33725/nu2.mnc ./tmp.mri_nu_correct.mni.33725/nu2.mnc mul .96645327585795405519 Saving result to './tmp.mri_nu_correct.mni.33725/nu2.mnc' (type = MINC )Outputting Volume: ............................................................ [ ok ] mri_convert ./tmp.mri_nu_correct.mni.33725/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.33725/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.33725/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 4.96705e-09, -1.49012e-08) j_ras = (9.93411e-09, 2.111e-08, -1) k_ras = (-2.48353e-09, 1, -1.98682e-08) 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 ( 8, 142) to ( 3, 110) Wed Feb 20 15:16:00 EST 2019 mri_nu_correct.mni done mri_add_xform_to_header -c /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Wed Feb 20 15:16:03 EST 2019 /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/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 1.08225 -0.00338 -0.08163 -15.38412; 0.01875 0.89691 0.39365 -45.51677; 0.07147 -0.36202 1.01986 28.67577; 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 = 23 Starting OpenSpline(): npoints = 23 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 84 (84), valley at 39 (39) csf peak at 42, setting threshold to 70 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 82 (82), valley at 36 (36) csf peak at 41, setting threshold to 68 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 4 minutes and 23 seconds. #-------------------------------------------- #@# Skull Stripping Wed Feb 20 15:20:28 EST 2019 /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/mri mri_em_register -rusage /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/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=8.0 skull bounding box = (53, 19, 0) --> (260, 254, 298) using (122, 97, 149) as brain centroid... mean wm in atlas = 108, using box (96,68,112) --> (147, 126,185) to find MRI wm before smoothing, mri peak at 106 robust fit to distribution - 107 +- 3.9 after smoothing, mri peak at 107, scaling input intensities by 1.009 scaling channel 0 by 1.00935 initial log_p = -4.633 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.472024 @ (9.091, 27.273, -9.091) max log p = -4.427106 @ (4.545, 4.545, -4.545) max log p = -4.403322 @ (-6.818, 2.273, 2.273) max log p = -4.397553 @ (1.136, -1.136, 3.409) max log p = -4.378651 @ (-0.568, 0.568, -1.705) max log p = -4.368399 @ (-0.284, -0.284, 0.852) Found translation: (7.1, 33.2, -8.8): log p = -4.368 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.265, old_max_log_p =-4.368 (thresh=-4.4) 0.85132 -0.10978 -0.06338 14.91607; 0.08371 0.64725 0.37369 -20.06638; 0.00000 -0.39891 0.69093 71.50525; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.265, old_max_log_p =-4.265 (thresh=-4.3) 0.85132 -0.10978 -0.06338 14.91607; 0.08371 0.64725 0.37369 -20.06638; 0.00000 -0.39891 0.69093 71.50525; 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=-4.211, old_max_log_p =-4.265 (thresh=-4.3) 0.83770 -0.08568 -0.05047 11.16665; 0.06001 0.70083 0.37278 -25.90996; 0.00279 -0.38433 0.71547 65.66640; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.211, old_max_log_p =-4.211 (thresh=-4.2) 0.83770 -0.08568 -0.05047 11.16665; 0.06001 0.70083 0.37278 -25.90996; 0.00279 -0.38433 0.71547 65.66640; 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=-4.187, old_max_log_p =-4.211 (thresh=-4.2) 0.83699 -0.08931 -0.02977 9.35987; 0.05320 0.70007 0.37977 -25.75783; -0.01831 -0.38920 0.71592 69.25599; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.184, old_max_log_p =-4.187 (thresh=-4.2) 0.83503 -0.08910 -0.02970 9.70433; 0.05308 0.69842 0.37888 -25.28354; -0.01835 -0.39011 0.71760 69.09501; 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 0.83503 -0.08910 -0.02970 9.70433; 0.05308 0.69842 0.37888 -25.28354; -0.01835 -0.39011 0.71760 69.09501; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 0.83503 -0.08910 -0.02970 9.70433; 0.05308 0.69842 0.37888 -25.28354; -0.01835 -0.39011 0.71760 69.09501; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.83503 -0.08910 -0.02970 9.70433; 0.05308 0.69842 0.37888 -25.28354; -0.01835 -0.39011 0.71760 69.09501; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -4.184 (old=-4.633) transform before final EM align: 0.83503 -0.08910 -0.02970 9.70433; 0.05308 0.69842 0.37888 -25.28354; -0.01835 -0.39011 0.71760 69.09501; 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 0.83503 -0.08910 -0.02970 9.70433; 0.05308 0.69842 0.37888 -25.28354; -0.01835 -0.39011 0.71760 69.09501; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 0.83503 -0.08910 -0.02970 9.70433; 0.05308 0.69842 0.37888 -25.28354; -0.01835 -0.39011 0.71760 69.09501; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = 4.6 tol 0.000000 final transform: 0.83503 -0.08910 -0.02970 9.70433; 0.05308 0.69842 0.37888 -25.28354; -0.01835 -0.39011 0.71760 69.09501; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 1027.816413 mri_em_register stimesec 3.839188 mri_em_register ru_maxrss 766320 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 1254637 mri_em_register ru_majflt 1 mri_em_register ru_nswap 0 mri_em_register ru_inblock 149760 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 731 mri_em_register ru_nivcsw 1330 registration took 4 minutes and 57 seconds. mri_watershed -rusage /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/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=125 y=98 z=99 r=79 first estimation of the main basin volume: 2111836 voxels Looking for seedpoints 2 found in the cerebellum 15 found in the rest of the brain global maximum in x=103, y=92, z=67, Imax=255 CSF=13, 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=707675056 voxels, voxel volume =1.000 = 707675056 mmm3 = 707675.072 cm3 done. PostAnalyze...Basin Prior 479 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=124,y=103, z=103, r=10365 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=9, CSF_MAX=27 , nb = 39024 RIGHT_CER CSF_MIN=3, CSF_intensity=20, CSF_MAX=82 , nb = 1224 LEFT_CER CSF_MIN=4, CSF_intensity=16, CSF_MAX=98 , nb = 576 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=23 , nb = 18072 LEFT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=27 , nb = 16470 OTHER CSF_MIN=4, CSF_intensity=13, CSF_MAX=32 , nb = 2682 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 27, 32, 45, 82 after analyzing : 27, 40, 45, 50 RIGHT_CER before analyzing : 82, 66, 59, 88 after analyzing : 52, 66, 66, 71 LEFT_CER before analyzing : 98, 66, 58, 81 after analyzing : 52, 66, 66, 69 RIGHT_BRAIN before analyzing : 23, 29, 44, 77 after analyzing : 23, 39, 44, 48 LEFT_BRAIN before analyzing : 27, 34, 48, 80 after analyzing : 27, 43, 48, 52 OTHER before analyzing : 32, 44, 64, 93 after analyzing : 32, 57, 64, 66 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...68 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.009 curvature mean = 71.723, std = 9.113 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 4.56, sigma = 8.92 after rotation: sse = 4.56, sigma = 8.92 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 5.24, its var is 8.86 before Erosion-Dilatation 2.73% of inacurate vertices after Erosion-Dilatation 3.66% 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...35 iterations mri_strip_skull: done peeling brain Brain Size = 1793350 voxels, voxel volume = 1.000 mm3 = 1793350 mmm3 = 1793.350 cm3 INFO: MRImask() using MRImaskDifferentGeometry() ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 26.511176 mri_watershed stimesec 0.667004 mri_watershed ru_maxrss 848136 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 389974 mri_watershed ru_majflt 1 mri_watershed ru_nswap 0 mri_watershed ru_inblock 9224 mri_watershed ru_oublock 6608 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 5060 mri_watershed ru_nivcsw 38 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Wed Feb 20 15:25:48 EST 2019 /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/mri mri_em_register -rusage /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/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=23.0 skull bounding box = (70, 38, 23) --> (244, 233, 257) using (128, 103, 140) as brain centroid... mean wm in atlas = 107, using box (107,79,111) --> (149, 127,168) to find MRI wm before smoothing, mri peak at 106 robust fit to distribution - 107 +- 3.6 after smoothing, mri peak at 107, scaling input intensities by 1.000 scaling channel 0 by 1 initial log_p = -4.568 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.068945 @ (9.091, 27.273, 9.091) max log p = -4.068945 @ (0.000, 0.000, 0.000) max log p = -3.944411 @ (2.273, 2.273, -6.818) max log p = -3.944411 @ (0.000, 0.000, 0.000) max log p = -3.936241 @ (-0.568, 0.568, 0.568) max log p = -3.922362 @ (-0.284, 0.284, 0.284) Found translation: (10.5, 30.4, 3.1): log p = -3.922 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.712, old_max_log_p =-3.922 (thresh=-3.9) 0.80625 0.00000 0.00000 -0.61175; 0.00000 0.69291 0.28701 -9.29667; 0.00000 -0.26549 0.64094 56.07635; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.712, old_max_log_p =-3.712 (thresh=-3.7) 0.80625 0.00000 0.00000 -0.61175; 0.00000 0.69291 0.28701 -9.29667; 0.00000 -0.26549 0.64094 56.07635; 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=-3.695, old_max_log_p =-3.712 (thresh=-3.7) 0.79071 -0.02225 -0.00921 7.53977; 0.02638 0.69254 0.28686 -14.42842; 0.00000 -0.27046 0.65296 54.68243; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.687, old_max_log_p =-3.695 (thresh=-3.7) 0.77587 0.00865 -0.02176 7.97483; 0.00050 0.71425 0.27120 -9.83776; 0.02724 -0.25291 0.67374 44.73679; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.687, old_max_log_p =-3.687 (thresh=-3.7) 0.77587 0.00865 -0.02176 7.97483; 0.00050 0.71425 0.27120 -9.83776; 0.02724 -0.25291 0.67374 44.73679; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.669, old_max_log_p =-3.687 (thresh=-3.7) 0.77868 -0.00519 -0.02101 9.43010; 0.01391 0.71038 0.28824 -13.50306; 0.02066 -0.26941 0.66472 49.71139; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.663, old_max_log_p =-3.669 (thresh=-3.7) 0.78142 -0.00521 -0.02109 8.90449; 0.01393 0.71121 0.28858 -13.69335; 0.02066 -0.26941 0.66472 49.71139; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.652, old_max_log_p =-3.663 (thresh=-3.7) 0.78214 -0.00301 -0.02654 9.39335; 0.01391 0.71037 0.28824 -13.50283; 0.02697 -0.26849 0.66219 48.77256; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 8 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.652, old_max_log_p =-3.652 (thresh=-3.6) 0.78214 -0.00301 -0.02654 9.39335; 0.01391 0.71037 0.28824 -13.50283; 0.02697 -0.26849 0.66219 48.77256; 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 0.78214 -0.00301 -0.02654 9.39335; 0.01391 0.71037 0.28824 -13.50283; 0.02697 -0.26849 0.66219 48.77256; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 0.78214 -0.00301 -0.02654 9.39335; 0.01391 0.71037 0.28824 -13.50283; 0.02697 -0.26849 0.66219 48.77256; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.78214 -0.00301 -0.02654 9.39335; 0.01391 0.71037 0.28824 -13.50283; 0.02697 -0.26849 0.66219 48.77256; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.652 (old=-4.568) transform before final EM align: 0.78214 -0.00301 -0.02654 9.39335; 0.01391 0.71037 0.28824 -13.50283; 0.02697 -0.26849 0.66219 48.77256; 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 0.78214 -0.00301 -0.02654 9.39335; 0.01391 0.71037 0.28824 -13.50283; 0.02697 -0.26849 0.66219 48.77256; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 0.78214 -0.00301 -0.02654 9.39335; 0.01391 0.71037 0.28824 -13.50283; 0.02697 -0.26849 0.66219 48.77256; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 013: -log(p) = 4.1 tol 0.000000 final transform: 0.78214 -0.00301 -0.02654 9.39335; 0.01391 0.71037 0.28824 -13.50283; 0.02697 -0.26849 0.66219 48.77256; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 1107.540842 mri_em_register stimesec 4.561102 mri_em_register ru_maxrss 755592 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 1238554 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 140152 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 929 mri_em_register ru_nivcsw 1300 registration took 5 minutes and 5 seconds. #-------------------------------------- #@# CA Normalize Wed Feb 20 15:30:54 EST 2019 /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/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=23.0 skull bounding box = (70, 38, 23) --> (244, 233, 257) using (128, 103, 140) as brain centroid... mean wm in atlas = 107, using box (107,79,111) --> (149, 127,168) to find MRI wm before smoothing, mri peak at 106 robust fit to distribution - 107 +- 3.6 after smoothing, mri peak at 107, scaling input intensities by 1.000 scaling channel 0 by 1 using 246344 sample points... INFO: compute sample coordinates transform 0.78214 -0.00301 -0.02654 9.39335; 0.01391 0.71037 0.28824 -13.50283; 0.02697 -0.26849 0.66219 48.77256; 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 (151, 42, 29) --> (239, 208, 255) Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0 3 of 2299 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (72, 41, 30) --> (158, 197, 256) Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0 8 of 3392 (0.2%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (156, 169, 76) --> (218, 226, 151) Left_Cerebellum_White_Matter: limiting intensities to 115.0 --> 132.0 5 of 7 (71.4%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (98, 169, 74) --> (154, 224, 152) Right_Cerebellum_White_Matter: limiting intensities to 97.0 --> 132.0 0 of 9 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (134, 145, 121) --> (178, 236, 166) Brain_Stem: limiting intensities to 94.0 --> 132.0 0 of 44 (0.0%) samples deleted using 5751 total control points for intensity normalization... bias field = 0.982 +- 0.045 43 of 5735 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (151, 42, 29) --> (239, 208, 255) Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 132.0 5 of 2624 (0.2%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (72, 41, 30) --> (158, 197, 256) Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 6 of 3841 (0.2%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (156, 169, 76) --> (218, 226, 151) Left_Cerebellum_White_Matter: limiting intensities to 103.0 --> 132.0 14 of 19 (73.7%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (98, 169, 74) --> (154, 224, 152) Right_Cerebellum_White_Matter: limiting intensities to 93.0 --> 132.0 7 of 24 (29.2%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (134, 145, 121) --> (178, 236, 166) Brain_Stem: limiting intensities to 88.0 --> 132.0 0 of 63 (0.0%) samples deleted using 6571 total control points for intensity normalization... bias field = 1.023 +- 0.043 47 of 6506 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (151, 42, 29) --> (239, 208, 255) Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 115.0 5 of 2613 (0.2%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (72, 41, 30) --> (158, 197, 256) Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0 2 of 3833 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (156, 169, 76) --> (218, 226, 151) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 12 of 23 (52.2%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (98, 169, 74) --> (154, 224, 152) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 18 of 41 (43.9%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (134, 145, 121) --> (178, 236, 166) Brain_Stem: limiting intensities to 88.0 --> 106.0 12 of 168 (7.1%) samples deleted using 6678 total control points for intensity normalization... bias field = 1.019 +- 0.044 52 of 6554 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 2 minutes and 23 seconds. #-------------------------------------- #@# CA Reg Wed Feb 20 15:33:17 EST 2019 /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/mri mri_ca_register -rusage /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/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) = 0.43 (predicted orig area = 18.6) 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=1.019, neg=0, invalid=762 0001: dt=598.586741, rms=0.925 (9.253%), neg=0, invalid=762 0002: dt=367.981630, rms=0.898 (2.890%), neg=0, invalid=762 0003: dt=517.888000, rms=0.885 (1.468%), neg=0, invalid=762 0004: dt=295.936000, rms=0.878 (0.782%), neg=0, invalid=762 0005: dt=443.904000, rms=0.874 (0.449%), neg=0, invalid=762 0006: dt=369.920000, rms=0.871 (0.379%), neg=0, invalid=762 0007: dt=369.920000, rms=0.869 (0.281%), neg=0, invalid=762 0008: dt=295.936000, rms=0.866 (0.258%), neg=0, invalid=762 0009: dt=517.888000, rms=0.864 (0.256%), neg=0, invalid=762 0010: dt=295.936000, rms=0.863 (0.177%), neg=0, invalid=762 0011: dt=295.936000, rms=0.861 (0.141%), neg=0, invalid=762 0012: dt=295.936000, rms=0.860 (0.195%), neg=0, invalid=762 0013: dt=295.936000, rms=0.857 (0.311%), neg=0, invalid=762 0014: dt=295.936000, rms=0.855 (0.250%), neg=0, invalid=762 0015: dt=295.936000, rms=0.852 (0.378%), neg=0, invalid=762 0016: dt=295.936000, rms=0.850 (0.216%), neg=0, invalid=762 0017: dt=295.936000, rms=0.848 (0.233%), neg=0, invalid=762 0018: dt=295.936000, rms=0.846 (0.177%), neg=0, invalid=762 0019: dt=295.936000, rms=0.845 (0.193%), neg=0, invalid=762 0020: dt=295.936000, rms=0.843 (0.222%), neg=0, invalid=762 0021: dt=295.936000, rms=0.841 (0.185%), neg=0, invalid=762 0022: dt=295.936000, rms=0.840 (0.100%), neg=0, invalid=762 0023: dt=295.936000, rms=0.839 (0.202%), neg=0, invalid=762 0024: dt=295.936000, rms=0.837 (0.182%), neg=0, invalid=762 0025: dt=295.936000, rms=0.836 (0.138%), neg=0, invalid=762 0026: dt=295.936000, rms=0.835 (0.124%), neg=0, invalid=762 0027: dt=295.936000, rms=0.834 (0.100%), neg=0, invalid=762 0028: dt=129.472000, rms=0.834 (0.018%), neg=0, invalid=762 0029: dt=129.472000, rms=0.834 (0.016%), neg=0, invalid=762 0030: dt=129.472000, rms=0.834 (0.032%), neg=0, invalid=762 0031: dt=129.472000, rms=0.833 (0.016%), neg=0, invalid=762 0032: dt=129.472000, rms=0.833 (0.043%), neg=0, invalid=762 0033: dt=129.472000, rms=0.833 (0.032%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.833, neg=0, invalid=762 0034: dt=129.472000, rms=0.832 (0.165%), neg=0, invalid=762 0035: dt=73.984000, rms=0.832 (0.009%), neg=0, invalid=762 0036: dt=73.984000, rms=0.832 (0.000%), neg=0, invalid=762 0037: dt=73.984000, rms=0.832 (-0.007%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.853, neg=0, invalid=762 0038: dt=144.963855, rms=0.845 (0.843%), neg=0, invalid=762 0039: dt=103.680000, rms=0.839 (0.821%), neg=0, invalid=762 0040: dt=36.288000, rms=0.836 (0.254%), neg=0, invalid=762 0041: dt=414.720000, rms=0.829 (0.895%), neg=0, invalid=762 0042: dt=70.068966, rms=0.821 (0.956%), neg=0, invalid=762 0043: dt=31.104000, rms=0.820 (0.118%), neg=0, invalid=762 0044: dt=31.104000, rms=0.819 (0.073%), neg=0, invalid=762 0045: dt=31.104000, rms=0.818 (0.129%), neg=0, invalid=762 0046: dt=31.104000, rms=0.817 (0.213%), neg=0, invalid=762 0047: dt=31.104000, rms=0.814 (0.287%), neg=0, invalid=762 0048: dt=31.104000, rms=0.812 (0.324%), neg=0, invalid=762 0049: dt=31.104000, rms=0.809 (0.344%), neg=0, invalid=762 0050: dt=31.104000, rms=0.806 (0.318%), neg=0, invalid=762 0051: dt=31.104000, rms=0.804 (0.271%), neg=0, invalid=762 0052: dt=31.104000, rms=0.802 (0.267%), neg=0, invalid=762 0053: dt=31.104000, rms=0.800 (0.272%), neg=0, invalid=762 0054: dt=31.104000, rms=0.798 (0.264%), neg=0, invalid=762 0055: dt=31.104000, rms=0.797 (0.021%), neg=0, invalid=762 0056: dt=31.104000, rms=0.797 (0.033%), neg=0, invalid=762 0057: dt=31.104000, rms=0.797 (0.048%), neg=0, invalid=762 0058: dt=31.104000, rms=0.796 (0.072%), neg=0, invalid=762 0059: dt=31.104000, rms=0.796 (0.075%), neg=0, invalid=762 0060: dt=31.104000, rms=0.795 (0.082%), neg=0, invalid=762 0061: dt=31.104000, rms=0.794 (0.080%), neg=0, invalid=762 0062: dt=580.608000, rms=0.792 (0.258%), neg=0, invalid=762 0063: dt=36.288000, rms=0.792 (0.090%), neg=0, invalid=762 0064: dt=36.288000, rms=0.791 (0.042%), neg=0, invalid=762 0065: dt=36.288000, rms=0.791 (0.048%), neg=0, invalid=762 0066: dt=36.288000, rms=0.791 (0.041%), neg=0, invalid=762 0067: dt=36.288000, rms=0.790 (0.065%), neg=0, invalid=762 0068: dt=36.288000, rms=0.790 (0.066%), neg=0, invalid=762 0069: dt=36.288000, rms=0.789 (0.068%), neg=0, invalid=762 0070: dt=36.288000, rms=0.788 (0.067%), neg=0, invalid=762 0071: dt=145.152000, rms=0.788 (0.053%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.789, neg=0, invalid=762 0072: dt=25.920000, rms=0.788 (0.147%), neg=0, invalid=762 0073: dt=0.000000, rms=0.788 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.840, neg=0, invalid=762 0074: dt=23.448276, rms=0.837 (0.376%), neg=0, invalid=762 0075: dt=60.540541, rms=0.832 (0.646%), neg=0, invalid=762 0076: dt=44.800000, rms=0.828 (0.428%), neg=0, invalid=762 0077: dt=32.000000, rms=0.825 (0.367%), neg=0, invalid=762 0078: dt=25.600000, rms=0.824 (0.112%), neg=0, invalid=762 0079: dt=25.600000, rms=0.823 (0.180%), neg=0, invalid=762 0080: dt=25.600000, rms=0.821 (0.239%), neg=0, invalid=762 0081: dt=25.600000, rms=0.818 (0.304%), neg=0, invalid=762 0082: dt=25.600000, rms=0.816 (0.254%), neg=0, invalid=762 0083: dt=25.600000, rms=0.814 (0.261%), neg=0, invalid=762 0084: dt=25.600000, rms=0.812 (0.215%), neg=0, invalid=762 0085: dt=25.600000, rms=0.811 (0.127%), neg=0, invalid=762 0086: dt=25.600000, rms=0.811 (0.089%), neg=0, invalid=762 0087: dt=25.600000, rms=0.810 (0.087%), neg=0, invalid=762 0088: dt=44.800000, rms=0.809 (0.085%), neg=0, invalid=762 0089: dt=44.800000, rms=0.809 (-0.093%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.810, neg=0, invalid=762 0090: dt=0.000000, rms=0.809 (0.063%), neg=0, invalid=762 0091: dt=0.000000, rms=0.809 (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=0.873, neg=0, invalid=762 0092: dt=1.230769, rms=0.872 (0.117%), neg=0, invalid=762 0093: dt=0.036000, rms=0.872 (0.006%), neg=0, invalid=762 0094: dt=0.036000, rms=0.872 (0.001%), neg=0, invalid=762 0095: dt=0.036000, rms=0.872 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.873, neg=0, invalid=762 0096: dt=0.108000, rms=0.872 (0.061%), neg=0, invalid=762 0097: dt=0.013500, rms=0.872 (0.000%), neg=0, invalid=762 0098: dt=0.013500, rms=0.872 (-0.001%), neg=0, invalid=762 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.980, neg=0, invalid=762 0099: dt=1.629050, rms=0.961 (1.980%), neg=0, invalid=762 0100: dt=1.536000, rms=0.952 (0.896%), neg=0, invalid=762 0101: dt=1.280000, rms=0.948 (0.432%), neg=0, invalid=762 0102: dt=1.280000, rms=0.945 (0.283%), neg=0, invalid=762 0103: dt=1.536000, rms=0.943 (0.263%), neg=0, invalid=762 0104: dt=1.024000, rms=0.941 (0.138%), neg=0, invalid=762 0105: dt=1.024000, rms=0.940 (0.155%), neg=0, invalid=762 0106: dt=1.024000, rms=0.938 (0.150%), neg=0, invalid=762 0107: dt=1.024000, rms=0.937 (0.107%), neg=0, invalid=762 0108: dt=1.024000, rms=0.937 (-0.001%), neg=0, invalid=762 0109: dt=4.096000, rms=0.936 (0.141%), neg=0, invalid=762 0110: dt=1.280000, rms=0.935 (0.085%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.936, neg=0, invalid=762 0111: dt=0.448000, rms=0.935 (0.098%), neg=0, invalid=762 0112: dt=1.280000, rms=0.935 (0.029%), neg=0, invalid=762 0113: dt=1.280000, rms=0.934 (0.057%), neg=0, invalid=762 0114: dt=1.280000, rms=0.934 (0.039%), neg=0, invalid=762 0115: dt=1.280000, rms=0.934 (0.007%), 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=0.893, neg=0, invalid=762 0116: dt=0.692140, rms=0.877 (1.764%), neg=0, invalid=762 0117: dt=0.064000, rms=0.876 (0.039%), neg=0, invalid=762 0118: dt=0.064000, rms=0.876 (-0.043%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.877, neg=0, invalid=762 0119: dt=0.028000, rms=0.876 (0.094%), neg=0, invalid=762 0120: dt=0.020000, rms=0.876 (0.001%), neg=0, invalid=762 0121: dt=0.020000, rms=0.876 (-0.005%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.07447 (44) Left_Lateral_Ventricle (4): linear fit = 2.17 x + 0.0 (5389 voxels, overlap=0.046) Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (5389 voxels, peak = 44), gca=30.0 gca peak = 0.15565 (16) mri peak = 0.08298 (44) Right_Lateral_Ventricle (43): linear fit = 2.86 x + 0.0 (4377 voxels, overlap=0.004) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (4377 voxels, peak = 46), gca=24.0 gca peak = 0.26829 (96) mri peak = 0.07411 (103) Right_Pallidum (52): linear fit = 1.07 x + 0.0 (3191 voxels, overlap=0.993) Right_Pallidum (52): linear fit = 1.07 x + 0.0 (3191 voxels, peak = 102), gca=102.2 gca peak = 0.20183 (93) mri peak = 0.05495 (93) Left_Pallidum (13): linear fit = 0.96 x + 0.0 (2917 voxels, overlap=1.011) Left_Pallidum (13): linear fit = 0.96 x + 0.0 (2917 voxels, peak = 90), gca=89.7 gca peak = 0.21683 (55) mri peak = 0.06512 (68) Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (2977 voxels, overlap=0.022) Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (2977 voxels, peak = 67), gca=67.4 gca peak = 0.30730 (58) mri peak = 0.05957 (66) Left_Hippocampus (17): linear fit = 1.16 x + 0.0 (2170 voxels, overlap=0.104) Left_Hippocampus (17): linear fit = 1.16 x + 0.0 (2170 voxels, peak = 68), gca=67.6 gca peak = 0.11430 (101) mri peak = 0.09756 (105) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (260441 voxels, overlap=0.687) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (260441 voxels, peak = 105), gca=104.5 gca peak = 0.12076 (102) mri peak = 0.09424 (105) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (263697 voxels, overlap=0.656) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (263697 voxels, peak = 107), gca=106.6 gca peak = 0.14995 (59) mri peak = 0.04337 (88) Left_Cerebral_Cortex (3): linear fit = 1.49 x + 0.0 (133192 voxels, overlap=0.000) Left_Cerebral_Cortex (3): linear fit = 1.49 x + 0.0 (133192 voxels, peak = 88), gca=87.6 gca peak = 0.15082 (58) mri peak = 0.03805 (88) Right_Cerebral_Cortex (42): linear fit = 1.48 x + 0.0 (134491 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.48 x + 0.0 (134491 voxels, peak = 86), gca=85.6 gca peak = 0.14161 (67) mri peak = 0.06668 (89) Right_Caudate (50): linear fit = 1.30 x + 0.0 (2910 voxels, overlap=0.026) Right_Caudate (50): linear fit = 1.30 x + 0.0 (2910 voxels, peak = 87), gca=87.4 gca peak = 0.15243 (71) mri peak = 0.09407 (93) Left_Caudate (11): linear fit = 1.25 x + 0.0 (4377 voxels, overlap=0.019) Left_Caudate (11): linear fit = 1.25 x + 0.0 (4377 voxels, peak = 89), gca=89.1 gca peak = 0.13336 (57) mri peak = 0.01777 (90) Left_Cerebellum_Cortex (8): linear fit = 1.58 x + 0.0 (36346 voxels, overlap=0.000) Left_Cerebellum_Cortex (8): linear fit = 1.58 x + 0.0 (36346 voxels, peak = 90), gca=89.8 gca peak = 0.13252 (56) mri peak = 0.02676 (70) Right_Cerebellum_Cortex (47): linear fit = 1.30 x + 0.0 (41104 voxels, overlap=0.000) Right_Cerebellum_Cortex (47): linear fit = 1.30 x + 0.0 (41104 voxels, peak = 73), gca=73.1 gca peak = 0.18181 (84) mri peak = 0.03366 (77) Left_Cerebellum_White_Matter (7): linear fit = 0.98 x + 0.0 (15826 voxels, overlap=0.716) Left_Cerebellum_White_Matter (7): linear fit = 0.98 x + 0.0 (15826 voxels, peak = 82), gca=81.9 gca peak = 0.20573 (83) mri peak = 0.04004 (85) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (17148 voxels, overlap=0.979) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (17148 voxels, peak = 86), gca=85.9 gca peak = 0.21969 (57) mri peak = 0.05689 (86) Left_Amygdala (18): linear fit = 1.40 x + 0.0 (1129 voxels, overlap=0.081) Left_Amygdala (18): linear fit = 1.40 x + 0.0 (1129 voxels, peak = 80), gca=80.1 gca peak = 0.39313 (56) mri peak = 0.06176 (88) Right_Amygdala (54): linear fit = 1.50 x + 0.0 (1478 voxels, overlap=0.064) Right_Amygdala (54): linear fit = 1.50 x + 0.0 (1478 voxels, peak = 84), gca=83.7 gca peak = 0.14181 (85) mri peak = 0.09787 (101) Left_Thalamus_Proper (10): linear fit = 1.16 x + 0.0 (17365 voxels, overlap=0.030) Left_Thalamus_Proper (10): linear fit = 1.16 x + 0.0 (17365 voxels, peak = 99), gca=99.0 gca peak = 0.11978 (83) mri peak = 0.11462 (101) Right_Thalamus_Proper (49): linear fit = 1.18 x + 0.0 (14546 voxels, overlap=0.006) Right_Thalamus_Proper (49): linear fit = 1.18 x + 0.0 (14546 voxels, peak = 98), gca=98.4 gca peak = 0.13399 (79) mri peak = 0.05109 (98) Left_Putamen (12): linear fit = 1.22 x + 0.0 (8150 voxels, overlap=0.157) Left_Putamen (12): linear fit = 1.22 x + 0.0 (8150 voxels, peak = 96), gca=96.0 gca peak = 0.14159 (79) mri peak = 0.05488 (97) Right_Putamen (51): linear fit = 1.22 x + 0.0 (8534 voxels, overlap=0.015) Right_Putamen (51): linear fit = 1.22 x + 0.0 (8534 voxels, peak = 96), gca=96.0 gca peak = 0.10025 (80) mri peak = 0.07777 (90) Brain_Stem (16): linear fit = 1.15 x + 0.0 (24171 voxels, overlap=0.204) Brain_Stem (16): linear fit = 1.15 x + 0.0 (24171 voxels, peak = 92), gca=92.4 gca peak = 0.13281 (86) mri peak = 0.07531 (97) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (3621 voxels, overlap=0.462) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (3621 voxels, peak = 93), gca=93.3 gca peak = 0.12801 (89) mri peak = 0.07037 (93) Left_VentralDC (28): linear fit = 1.07 x + 0.0 (3689 voxels, overlap=0.706) Left_VentralDC (28): linear fit = 1.07 x + 0.0 (3689 voxels, peak = 95), gca=94.8 gca peak = 0.20494 (23) mri peak = 0.09951 (44) Third_Ventricle (14): linear fit = 1.79 x + 0.0 (322 voxels, overlap=0.030) Third_Ventricle (14): linear fit = 1.79 x + 0.0 (322 voxels, peak = 41), gca=41.3 gca peak = 0.15061 (21) mri peak = 0.05508 (26) Fourth_Ventricle (15): linear fit = 1.53 x + 0.0 (1578 voxels, overlap=0.503) Fourth_Ventricle (15): linear fit = 1.53 x + 0.0 (1578 voxels, peak = 32), gca=32.2 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18056 (32) gca peak Left_Cerebellum_Cortex = 0.13336 (57) gca peak Left_Thalamus = 0.64095 (94) gca peak Third_Ventricle = 0.20494 (23) gca peak Fourth_Ventricle = 0.15061 (21) gca peak CSF = 0.20999 (34) gca peak Left_Accumbens_area = 0.39030 (62) gca peak Left_undetermined = 0.95280 (25) gca peak Left_vessel = 0.67734 (53) gca peak Left_choroid_plexus = 0.09433 (44) gca peak Right_Inf_Lat_Vent = 0.23544 (26) gca peak Right_Accumbens_area = 0.30312 (64) gca peak Right_vessel = 0.46315 (51) gca peak Right_choroid_plexus = 0.14086 (44) gca peak Fifth_Ventricle = 0.51669 (36) gca peak WM_hypointensities = 0.09722 (76) gca peak non_WM_hypointensities = 0.11899 (47) gca peak Optic_Chiasm = 0.39033 (72) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means setting label Left_Cerebellum_Cortex based on Right_Cerebellum_Cortex = 1.30 x + 0: 73 estimating mean gm scale to be 1.38 x + 0.0 estimating mean wm scale to be 1.04 x + 0.0 estimating mean csf scale to be 1.50 x + 0.0 Left_Putamen too bright - rescaling by 0.990 (from 1.215) to 95.0 (was 96.0) Right_Putamen too bright - rescaling by 0.990 (from 1.215) to 95.0 (was 96.0) Right_Pallidum too bright - rescaling by 1.002 (from 1.065) to 102.4 (was 102.2) 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=0.851, neg=0, invalid=762 0122: dt=236.482774, rms=0.805 (5.454%), neg=0, invalid=762 0123: dt=517.888000, rms=0.784 (2.583%), neg=0, invalid=762 0124: dt=221.952000, rms=0.780 (0.517%), neg=0, invalid=762 0125: dt=1183.744000, rms=0.772 (1.044%), neg=0, invalid=762 0126: dt=141.803922, rms=0.767 (0.570%), neg=0, invalid=762 0127: dt=517.888000, rms=0.765 (0.259%), neg=0, invalid=762 0128: dt=369.920000, rms=0.763 (0.282%), neg=0, invalid=762 0129: dt=129.472000, rms=0.762 (0.119%), neg=0, invalid=762 0130: dt=1775.616000, rms=0.759 (0.429%), neg=0, invalid=762 0131: dt=140.985507, rms=0.756 (0.405%), neg=0, invalid=762 0132: dt=1183.744000, rms=0.753 (0.338%), neg=0, invalid=762 0133: dt=129.472000, rms=0.753 (0.116%), neg=0, invalid=762 0134: dt=129.472000, rms=0.752 (0.011%), neg=0, invalid=762 0135: dt=129.472000, rms=0.752 (0.019%), neg=0, invalid=762 0136: dt=129.472000, rms=0.752 (0.039%), neg=0, invalid=762 0137: dt=129.472000, rms=0.752 (0.063%), neg=0, invalid=762 0138: dt=129.472000, rms=0.751 (0.093%), neg=0, invalid=762 0139: dt=129.472000, rms=0.750 (0.117%), neg=0, invalid=762 0140: dt=129.472000, rms=0.749 (0.129%), neg=0, invalid=762 0141: dt=129.472000, rms=0.748 (0.117%), neg=0, invalid=762 0142: dt=129.472000, rms=0.747 (0.108%), neg=0, invalid=762 0143: dt=129.472000, rms=0.747 (0.113%), neg=0, invalid=762 0144: dt=129.472000, rms=0.746 (0.111%), neg=0, invalid=762 0145: dt=129.472000, rms=0.745 (0.112%), neg=0, invalid=762 0146: dt=129.472000, rms=0.744 (0.119%), neg=0, invalid=762 0147: dt=129.472000, rms=0.743 (0.103%), neg=0, invalid=762 0148: dt=129.472000, rms=0.743 (0.088%), neg=0, invalid=762 0149: dt=129.472000, rms=0.742 (0.076%), neg=0, invalid=762 0150: dt=129.472000, rms=0.742 (0.053%), neg=0, invalid=762 0151: dt=129.472000, rms=0.741 (0.056%), neg=0, invalid=762 0152: dt=129.472000, rms=0.741 (0.060%), neg=0, invalid=762 0153: dt=129.472000, rms=0.740 (0.068%), neg=0, invalid=762 0154: dt=129.472000, rms=0.740 (0.078%), neg=0, invalid=762 0155: dt=129.472000, rms=0.739 (0.077%), neg=0, invalid=762 0156: dt=129.472000, rms=0.739 (0.076%), neg=0, invalid=762 0157: dt=129.472000, rms=0.738 (0.067%), neg=0, invalid=762 0158: dt=129.472000, rms=0.738 (0.064%), neg=0, invalid=762 0159: dt=129.472000, rms=0.737 (0.060%), neg=0, invalid=762 0160: dt=129.472000, rms=0.737 (0.061%), neg=0, invalid=762 0161: dt=129.472000, rms=0.736 (0.066%), neg=0, invalid=762 0162: dt=129.472000, rms=0.736 (0.069%), neg=0, invalid=762 0163: dt=129.472000, rms=0.735 (0.058%), neg=0, invalid=762 0164: dt=129.472000, rms=0.735 (0.052%), neg=0, invalid=762 0165: dt=129.472000, rms=0.735 (0.044%), neg=0, invalid=762 0166: dt=129.472000, rms=0.734 (0.040%), neg=0, invalid=762 0167: dt=129.472000, rms=0.734 (0.046%), neg=0, invalid=762 0168: dt=129.472000, rms=0.734 (0.047%), neg=0, invalid=762 0169: dt=129.472000, rms=0.733 (0.045%), neg=0, invalid=762 0170: dt=129.472000, rms=0.733 (0.042%), neg=0, invalid=762 0171: dt=129.472000, rms=0.733 (0.045%), neg=0, invalid=762 0172: dt=129.472000, rms=0.732 (0.039%), neg=0, invalid=762 0173: dt=129.472000, rms=0.732 (0.038%), neg=0, invalid=762 0174: dt=129.472000, rms=0.732 (0.044%), neg=0, invalid=762 0175: dt=129.472000, rms=0.731 (0.043%), neg=0, invalid=762 0176: dt=129.472000, rms=0.731 (0.038%), neg=0, invalid=762 0177: dt=129.472000, rms=0.731 (0.039%), neg=0, invalid=762 0178: dt=129.472000, rms=0.731 (0.032%), neg=0, invalid=762 0179: dt=129.472000, rms=0.730 (0.031%), neg=0, invalid=762 0180: dt=129.472000, rms=0.730 (0.028%), neg=0, invalid=762 0181: dt=129.472000, rms=0.730 (0.032%), neg=0, invalid=762 0182: dt=129.472000, rms=0.730 (0.031%), neg=0, invalid=762 0183: dt=129.472000, rms=0.730 (0.029%), neg=0, invalid=762 0184: dt=129.472000, rms=0.729 (0.029%), neg=0, invalid=762 0185: dt=129.472000, rms=0.729 (0.023%), neg=0, invalid=762 0186: dt=129.472000, rms=0.729 (0.020%), neg=0, invalid=762 0187: dt=1775.616000, rms=0.729 (0.017%), neg=0, invalid=762 0188: dt=1775.616000, rms=0.729 (-0.267%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.729, neg=0, invalid=762 0189: dt=129.472000, rms=0.729 (0.081%), neg=0, invalid=762 0190: dt=221.952000, rms=0.729 (0.017%), neg=0, invalid=762 0191: dt=221.952000, rms=0.728 (0.019%), neg=0, invalid=762 0192: dt=221.952000, rms=0.728 (0.032%), neg=0, invalid=762 0193: dt=221.952000, rms=0.728 (0.030%), neg=0, invalid=762 0194: dt=221.952000, rms=0.728 (0.027%), neg=0, invalid=762 0195: dt=221.952000, rms=0.727 (0.036%), neg=0, invalid=762 0196: dt=221.952000, rms=0.727 (0.060%), neg=0, invalid=762 0197: dt=221.952000, rms=0.727 (0.069%), neg=0, invalid=762 0198: dt=221.952000, rms=0.726 (0.063%), neg=0, invalid=762 0199: dt=221.952000, rms=0.726 (0.057%), neg=0, invalid=762 0200: dt=221.952000, rms=0.725 (0.036%), neg=0, invalid=762 0201: dt=221.952000, rms=0.725 (0.012%), neg=0, invalid=762 0202: dt=221.952000, rms=0.725 (0.011%), neg=0, invalid=762 0203: dt=517.888000, rms=0.725 (0.017%), neg=0, invalid=762 0204: dt=0.000000, rms=0.725 (0.001%), neg=0, invalid=762 0205: dt=0.850000, rms=0.725 (-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=0.728, neg=0, invalid=762 0206: dt=145.152000, rms=0.723 (0.610%), neg=0, invalid=762 0207: dt=145.152000, rms=0.721 (0.383%), neg=0, invalid=762 0208: dt=103.680000, rms=0.719 (0.260%), neg=0, invalid=762 0209: dt=2.268000, rms=0.719 (0.005%), neg=0, invalid=762 0210: dt=0.567000, rms=0.719 (0.001%), neg=0, invalid=762 0211: dt=0.283500, rms=0.719 (0.001%), neg=0, invalid=762 0212: dt=0.141750, rms=0.719 (0.000%), neg=0, invalid=762 0213: dt=0.000000, rms=0.719 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.719, neg=0, invalid=762 0214: dt=145.152000, rms=0.716 (0.412%), neg=0, invalid=762 0215: dt=414.720000, rms=0.712 (0.559%), neg=0, invalid=762 0216: dt=88.859504, rms=0.710 (0.289%), neg=0, invalid=762 0217: dt=580.608000, rms=0.705 (0.659%), neg=0, invalid=762 0218: dt=82.944000, rms=0.704 (0.186%), neg=0, invalid=762 0219: dt=580.608000, rms=0.701 (0.401%), neg=0, invalid=762 0220: dt=82.944000, rms=0.700 (0.149%), neg=0, invalid=762 0221: dt=414.720000, rms=0.698 (0.301%), neg=0, invalid=762 0222: dt=103.680000, rms=0.697 (0.118%), neg=0, invalid=762 0223: dt=414.720000, rms=0.696 (0.207%), neg=0, invalid=762 0224: dt=65.465649, rms=0.695 (0.106%), neg=0, invalid=762 0225: dt=414.720000, rms=0.694 (0.138%), neg=0, invalid=762 0226: dt=145.152000, rms=0.693 (0.216%), neg=0, invalid=762 0227: dt=62.208000, rms=0.692 (0.047%), neg=0, invalid=762 0228: dt=62.208000, rms=0.692 (0.033%), neg=0, invalid=762 0229: dt=62.208000, rms=0.692 (0.061%), neg=0, invalid=762 0230: dt=62.208000, rms=0.691 (0.100%), neg=0, invalid=762 0231: dt=62.208000, rms=0.690 (0.128%), neg=0, invalid=762 0232: dt=62.208000, rms=0.689 (0.145%), neg=0, invalid=762 0233: dt=7.776000, rms=0.689 (0.006%), neg=0, invalid=762 0234: dt=0.972000, rms=0.689 (0.001%), neg=0, invalid=762 0235: dt=0.121500, rms=0.689 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.697, neg=0, invalid=762 0236: dt=0.001953, rms=0.697 (0.063%), neg=0, invalid=762 0237: dt=0.000000, rms=0.697 (0.000%), neg=0, invalid=762 0238: dt=0.000122, rms=0.697 (0.000%), neg=0, invalid=762 0239: dt=0.000061, rms=0.697 (0.000%), neg=0, invalid=762 0240: dt=0.000031, rms=0.697 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.697, neg=0, invalid=762 0241: dt=186.874142, rms=0.683 (2.117%), neg=0, invalid=762 0242: dt=11.200000, rms=0.680 (0.396%), neg=0, invalid=762 0243: dt=11.200000, rms=0.678 (0.306%), neg=0, invalid=762 0244: dt=11.200000, rms=0.676 (0.243%), neg=0, invalid=762 0245: dt=2.800000, rms=0.676 (0.053%), neg=0, invalid=762 0246: dt=2.800000, rms=0.676 (0.048%), neg=0, invalid=762 0247: dt=1.400000, rms=0.675 (0.024%), neg=0, invalid=762 0248: dt=0.700000, rms=0.675 (0.011%), neg=0, invalid=762 0249: dt=0.001367, rms=0.675 (0.000%), neg=0, invalid=762 0250: dt=0.000000, rms=0.675 (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=0.697, neg=0, invalid=762 0251: dt=16.128000, rms=0.683 (1.970%), neg=0, invalid=762 0252: dt=11.520000, rms=0.678 (0.856%), neg=0, invalid=762 0253: dt=16.128000, rms=0.673 (0.750%), neg=0, invalid=762 0254: dt=16.128000, rms=0.670 (0.448%), neg=0, invalid=762 0255: dt=16.128000, rms=0.668 (0.299%), neg=0, invalid=762 0256: dt=11.520000, rms=0.666 (0.179%), neg=0, invalid=762 0257: dt=55.296000, rms=0.662 (0.616%), neg=0, invalid=762 0258: dt=4.032000, rms=0.662 (0.038%), neg=0, invalid=762 0259: dt=4.032000, rms=0.662 (0.044%), neg=0, invalid=762 0260: dt=4.032000, rms=0.662 (0.030%), neg=0, invalid=762 0261: dt=4.032000, rms=0.661 (0.030%), neg=0, invalid=762 0262: dt=4.032000, rms=0.661 (0.024%), neg=0, invalid=762 0263: dt=2.016000, rms=0.661 (0.009%), neg=0, invalid=762 0264: dt=1.008000, rms=0.661 (0.005%), neg=0, invalid=762 0265: dt=1.008000, rms=0.661 (0.003%), neg=0, invalid=762 0266: dt=0.063000, rms=0.661 (0.003%), neg=0, invalid=762 0267: dt=0.031500, rms=0.661 (0.001%), neg=0, invalid=762 0268: dt=0.007875, rms=0.661 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.661, neg=0, invalid=762 0269: dt=0.000000, rms=0.661 (0.053%), neg=0, invalid=762 0270: dt=0.000000, rms=0.661 (0.000%), neg=0, invalid=762 0271: dt=0.150000, rms=0.661 (-0.002%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.694, neg=0, invalid=762 0272: dt=0.000000, rms=0.693 (0.049%), neg=0, invalid=762 0273: dt=0.000000, rms=0.693 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.694, neg=0, invalid=762 0274: dt=0.000000, rms=0.693 (0.049%), neg=0, invalid=762 0275: dt=0.000000, rms=0.693 (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=0.639, neg=0, invalid=762 0276: dt=0.320000, rms=0.627 (1.823%), neg=0, invalid=762 0277: dt=0.320000, rms=0.621 (0.944%), neg=0, invalid=762 0278: dt=0.320000, rms=0.618 (0.516%), neg=0, invalid=762 0279: dt=0.320000, rms=0.616 (0.303%), neg=0, invalid=762 0280: dt=0.320000, rms=0.615 (0.193%), neg=0, invalid=762 0281: dt=0.320000, rms=0.614 (0.139%), neg=0, invalid=762 0282: dt=0.320000, rms=0.613 (0.104%), neg=0, invalid=762 0283: dt=0.320000, rms=0.613 (0.089%), neg=0, invalid=762 0284: dt=0.320000, rms=0.613 (0.069%), neg=0, invalid=762 0285: dt=0.320000, rms=0.612 (0.064%), neg=0, invalid=762 0286: dt=0.320000, rms=0.612 (0.048%), neg=0, invalid=762 0287: dt=0.320000, rms=0.612 (0.049%), neg=0, invalid=762 0288: dt=0.320000, rms=0.611 (0.080%), neg=0, invalid=762 0289: dt=0.160000, rms=0.611 (0.016%), neg=0, invalid=762 0290: dt=0.160000, rms=0.611 (0.034%), neg=0, invalid=762 0291: dt=0.160000, rms=0.610 (0.045%), neg=0, invalid=762 0292: dt=0.160000, rms=0.610 (0.052%), neg=0, invalid=762 0293: dt=0.160000, rms=0.610 (0.057%), neg=0, invalid=762 0294: dt=0.160000, rms=0.609 (0.056%), neg=0, invalid=762 0295: dt=0.160000, rms=0.609 (0.055%), neg=0, invalid=762 0296: dt=0.160000, rms=0.609 (0.005%), neg=0, invalid=762 0297: dt=0.160000, rms=0.609 (0.008%), neg=0, invalid=762 0298: dt=0.160000, rms=0.609 (0.008%), neg=0, invalid=762 0299: dt=0.112000, rms=0.609 (0.004%), neg=0, invalid=762 0300: dt=0.112000, rms=0.609 (0.004%), neg=0, invalid=762 0301: dt=0.112000, rms=0.609 (0.004%), neg=0, invalid=762 0302: dt=0.112000, rms=0.609 (0.010%), neg=0, invalid=762 0303: dt=0.112000, rms=0.609 (0.008%), neg=0, invalid=762 0304: dt=0.112000, rms=0.609 (0.010%), neg=0, invalid=762 0305: dt=0.112000, rms=0.609 (0.012%), neg=0, invalid=762 0306: dt=0.112000, rms=0.609 (0.015%), neg=0, invalid=762 0307: dt=0.112000, rms=0.609 (0.012%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.609, neg=0, invalid=762 0308: dt=0.112000, rms=0.607 (0.341%), neg=0, invalid=762 0309: dt=0.234375, rms=0.604 (0.459%), neg=0, invalid=762 0310: dt=0.112000, rms=0.603 (0.130%), neg=0, invalid=762 0311: dt=0.112000, rms=0.603 (0.109%), neg=0, invalid=762 0312: dt=0.112000, rms=0.602 (0.086%), neg=0, invalid=762 0313: dt=0.112000, rms=0.602 (0.072%), neg=0, invalid=762 0314: dt=0.112000, rms=0.601 (0.057%), neg=0, invalid=762 0315: dt=0.112000, rms=0.601 (0.048%), neg=0, invalid=762 0316: dt=0.112000, rms=0.601 (0.036%), neg=0, invalid=762 0317: dt=0.112000, rms=0.600 (0.068%), neg=0, invalid=762 0318: dt=0.112000, rms=0.600 (0.077%), neg=0, invalid=762 0319: dt=0.112000, rms=0.600 (0.068%), neg=0, invalid=762 0320: dt=0.112000, rms=0.599 (0.048%), neg=0, invalid=762 0321: dt=0.112000, rms=0.599 (0.018%), neg=0, invalid=762 0322: dt=0.112000, rms=0.599 (-0.014%), neg=0, invalid=762 0323: dt=0.000000, rms=0.599 (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=0.597, neg=0, invalid=762 0324: dt=73.984000, rms=0.596 (0.090%), neg=0, invalid=762 0325: dt=73.984000, rms=0.596 (0.010%), neg=0, invalid=762 0326: dt=73.984000, rms=0.596 (0.006%), neg=0, invalid=762 0327: dt=73.984000, rms=0.596 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.596, neg=0, invalid=762 0328: dt=110.976000, rms=0.596 (0.136%), neg=0, invalid=762 0329: dt=295.936000, rms=0.595 (0.073%), neg=0, invalid=762 0330: dt=295.936000, rms=0.595 (-0.233%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.596, neg=0, invalid=762 0331: dt=36.288000, rms=0.594 (0.205%), neg=0, invalid=762 0332: dt=62.208000, rms=0.594 (0.076%), neg=0, invalid=762 0333: dt=62.208000, rms=0.594 (0.060%), neg=0, invalid=762 0334: dt=62.208000, rms=0.593 (0.026%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 3 iterations, nbhd size=0, neg = 0 0335: dt=62.208000, rms=0.594 (-0.058%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.594, neg=0, invalid=762 0336: dt=87.225806, rms=0.592 (0.376%), neg=0, invalid=762 0337: dt=124.416000, rms=0.591 (0.175%), neg=0, invalid=762 0338: dt=124.416000, rms=0.591 (-0.116%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.591, neg=0, invalid=762 iter 0, gcam->neg = 14 after 4 iterations, nbhd size=0, neg = 0 0339: dt=52.612613, rms=0.587 (0.784%), neg=0, invalid=762 0340: dt=62.500000, rms=0.583 (0.557%), neg=0, invalid=762 iter 0, gcam->neg = 9 after 3 iterations, nbhd size=0, neg = 0 0341: dt=38.400000, rms=0.582 (0.333%), neg=0, invalid=762 0342: dt=44.800000, rms=0.580 (0.271%), neg=0, invalid=762 0343: dt=38.400000, rms=0.579 (0.161%), neg=0, invalid=762 0344: dt=38.400000, rms=0.579 (0.077%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 2 iterations, nbhd size=0, neg = 0 0345: dt=38.400000, rms=0.577 (0.224%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 4 iterations, nbhd size=0, neg = 0 0346: dt=38.400000, rms=0.576 (0.300%), neg=0, invalid=762 iter 0, gcam->neg = 9 after 9 iterations, nbhd size=1, neg = 0 0347: dt=38.400000, rms=0.574 (0.213%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 9 iterations, nbhd size=1, neg = 0 0348: dt=38.400000, rms=0.573 (0.220%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 9 iterations, nbhd size=1, neg = 0 0349: dt=38.400000, rms=0.572 (0.224%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 9 iterations, nbhd size=1, neg = 0 0350: dt=38.400000, rms=0.571 (0.214%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0351: dt=38.400000, rms=0.570 (0.134%), neg=0, invalid=762 iter 0, gcam->neg = 9 after 9 iterations, nbhd size=0, neg = 0 0352: dt=38.400000, rms=0.569 (0.071%), neg=0, invalid=762 iter 0, gcam->neg = 11 after 21 iterations, nbhd size=1, neg = 0 0353: dt=38.400000, rms=0.569 (0.078%), neg=0, invalid=762 iter 0, gcam->neg = 24 after 8 iterations, nbhd size=0, neg = 0 0354: dt=38.400000, rms=0.568 (0.175%), neg=0, invalid=762 iter 0, gcam->neg = 47 after 7 iterations, nbhd size=0, neg = 0 0355: dt=38.400000, rms=0.568 (0.044%), neg=0, invalid=762 iter 0, gcam->neg = 47 after 31 iterations, nbhd size=2, neg = 0 0356: dt=38.400000, rms=0.568 (-0.035%), neg=0, invalid=762 0357: dt=11.200000, rms=0.568 (0.025%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 10 iterations, nbhd size=1, neg = 0 0358: dt=11.200000, rms=0.568 (0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.568, neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0359: dt=58.181818, rms=0.564 (0.652%), neg=0, invalid=762 0360: dt=44.800000, rms=0.562 (0.306%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0361: dt=32.000000, rms=0.562 (0.107%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0362: dt=32.000000, rms=0.561 (0.096%), neg=0, invalid=762 0363: dt=32.000000, rms=0.561 (0.103%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=0, neg = 0 0364: dt=32.000000, rms=0.560 (0.069%), neg=0, invalid=762 0365: dt=32.000000, rms=0.560 (0.013%), neg=0, invalid=762 0366: dt=44.800000, rms=0.560 (0.091%), neg=0, invalid=762 0367: dt=25.600000, rms=0.560 (0.029%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.569, neg=0, invalid=762 0368: dt=2.750000, rms=0.568 (0.101%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0369: dt=0.576000, rms=0.568 (0.001%), neg=0, invalid=762 0370: dt=0.576000, rms=0.568 (0.000%), neg=0, invalid=762 0371: dt=0.576000, rms=0.568 (-0.007%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.569, neg=0, invalid=762 0372: dt=4.032000, rms=0.568 (0.118%), neg=0, invalid=762 0373: dt=3.456000, rms=0.568 (0.020%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0374: dt=3.456000, rms=0.568 (0.009%), neg=0, invalid=762 0375: dt=3.456000, rms=0.568 (-0.012%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.580, neg=0, invalid=762 0376: dt=0.448000, rms=0.579 (0.104%), neg=0, invalid=762 0377: dt=0.448000, rms=0.579 (0.013%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 3 iterations, nbhd size=0, neg = 0 0378: dt=0.448000, rms=0.579 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.579, neg=0, invalid=762 iter 0, gcam->neg = 2 after 4 iterations, nbhd size=0, neg = 0 0379: dt=1.792000, rms=0.577 (0.360%), neg=0, invalid=762 0380: dt=1.792000, rms=0.577 (0.135%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0381: dt=1.792000, rms=0.576 (0.080%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0382: dt=1.792000, rms=0.576 (0.013%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0383: dt=1.792000, rms=0.576 (-0.148%), 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=0.570, neg=0, invalid=762 iter 0, gcam->neg = 423 after 13 iterations, nbhd size=1, neg = 0 0384: dt=2.164716, rms=0.532 (6.570%), neg=0, invalid=762 0385: dt=0.112000, rms=0.532 (0.104%), neg=0, invalid=762 0386: dt=0.112000, rms=0.532 (-0.049%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.532, neg=0, invalid=762 0387: dt=0.112000, rms=0.531 (0.168%), neg=0, invalid=762 0388: dt=0.020000, rms=0.531 (-0.001%), 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=0.514, neg=0, invalid=762 0389: dt=0.003387, rms=0.514 (0.000%), neg=0, invalid=762 0390: dt=0.000000, rms=0.514 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.514, neg=0, invalid=762 0391: dt=13.872000, rms=0.514 (0.001%), neg=0, invalid=762 0392: dt=4.624000, rms=0.514 (0.000%), neg=0, invalid=762 0393: dt=4.624000, rms=0.514 (-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=0.514, neg=0, invalid=762 0394: dt=9.072000, rms=0.514 (0.007%), neg=0, invalid=762 0395: dt=3.888000, rms=0.514 (0.001%), neg=0, invalid=762 0396: dt=3.888000, rms=0.514 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.514, neg=0, invalid=762 0397: dt=36.288000, rms=0.514 (0.057%), neg=0, invalid=762 0398: dt=103.680000, rms=0.514 (0.051%), neg=0, invalid=762 0399: dt=103.680000, rms=0.513 (0.074%), neg=0, invalid=762 0400: dt=103.680000, rms=0.513 (0.040%), neg=0, invalid=762 0401: dt=103.680000, rms=0.513 (-0.002%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.514, neg=0, invalid=762 0402: dt=11.200000, rms=0.513 (0.157%), neg=0, invalid=762 0403: dt=11.200000, rms=0.513 (0.065%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0404: dt=11.200000, rms=0.513 (0.032%), neg=0, invalid=762 0405: dt=11.200000, rms=0.513 (-0.013%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.513, neg=0, invalid=762 0406: dt=38.400000, rms=0.510 (0.512%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0407: dt=77.473684, rms=0.508 (0.376%), neg=0, invalid=762 0408: dt=23.172414, rms=0.507 (0.252%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 8 iterations, nbhd size=1, neg = 0 0409: dt=153.600000, rms=0.505 (0.285%), neg=0, invalid=762 0410: dt=24.228571, rms=0.504 (0.172%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0411: dt=24.228571, rms=0.504 (0.073%), neg=0, invalid=762 0412: dt=24.228571, rms=0.504 (0.084%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0413: dt=24.228571, rms=0.503 (0.095%), neg=0, invalid=762 0414: dt=24.228571, rms=0.503 (0.098%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0415: dt=24.228571, rms=0.502 (0.109%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0416: dt=24.228571, rms=0.502 (0.110%), neg=0, invalid=762 0417: dt=24.228571, rms=0.501 (0.097%), neg=0, invalid=762 0418: dt=24.228571, rms=0.501 (0.099%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 3 iterations, nbhd size=0, neg = 0 0419: dt=24.228571, rms=0.500 (0.092%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0420: dt=76.800000, rms=0.500 (0.058%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.505, neg=0, invalid=762 0421: dt=1.008000, rms=0.505 (0.007%), neg=0, invalid=762 0422: dt=0.252000, rms=0.505 (0.000%), neg=0, invalid=762 0423: dt=0.252000, rms=0.505 (0.000%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0424: dt=0.252000, rms=0.505 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.505, neg=0, invalid=762 0425: dt=4.032000, rms=0.505 (0.039%), neg=0, invalid=762 0426: dt=3.456000, rms=0.505 (0.013%), neg=0, invalid=762 0427: dt=3.456000, rms=0.505 (0.004%), neg=0, invalid=762 0428: dt=3.456000, rms=0.505 (-0.019%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.514, neg=0, invalid=762 0429: dt=0.000000, rms=0.514 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.514, neg=0, invalid=762 0430: dt=0.000000, rms=0.514 (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=0.499, neg=0, invalid=762 iter 0, gcam->neg = 381 after 18 iterations, nbhd size=1, neg = 0 0431: dt=1.536000, rms=0.485 (2.745%), neg=0, invalid=762 0432: dt=0.007000, rms=0.485 (0.001%), neg=0, invalid=762 0433: dt=0.007000, rms=0.485 (0.000%), neg=0, invalid=762 0434: dt=0.007000, rms=0.485 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.485, neg=0, invalid=762 0435: dt=0.112000, rms=0.484 (0.104%), neg=0, invalid=762 0436: dt=0.080000, rms=0.484 (0.024%), neg=0, invalid=762 0437: dt=0.080000, rms=0.484 (-0.001%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 1 hours, 38 minutes and 43 seconds. mri_ca_register utimesec 7398.002575 mri_ca_register stimesec 65.787555 mri_ca_register ru_maxrss 1661332 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 80895275 mri_ca_register ru_majflt 0 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 232 mri_ca_register ru_oublock 63656 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 48108 mri_ca_register ru_nivcsw 4968 FSRUNTIME@ mri_ca_register 1.6453 hours 4 threads #-------------------------------------- #@# SubCort Seg Wed Feb 20 17:12:00 EST 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/SUBJECTS_DIR cd /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/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 18.65 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 = 0.07612 (41) Left_Lateral_Ventricle (4): linear fit = 2.16 x + 0.0 (4615 voxels, overlap=0.020) Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (4615 voxels, peak = 43), gca=30.0 gca peak = 0.17677 (13) mri peak = 0.07848 (44) Right_Lateral_Ventricle (43): linear fit = 3.28 x + 0.0 (2986 voxels, overlap=0.012) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (2986 voxels, peak = 43), gca=19.5 gca peak = 0.28129 (95) mri peak = 0.13204 (102) Right_Pallidum (52): linear fit = 1.07 x + 0.0 (2887 voxels, overlap=0.279) Right_Pallidum (52): linear fit = 1.07 x + 0.0 (2887 voxels, peak = 101), gca=101.2 gca peak = 0.16930 (96) mri peak = 0.11411 (102) Left_Pallidum (13): linear fit = 1.08 x + 0.0 (2752 voxels, overlap=0.504) Left_Pallidum (13): linear fit = 1.08 x + 0.0 (2752 voxels, peak = 103), gca=103.2 gca peak = 0.24553 (55) mri peak = 0.06236 (74) Right_Hippocampus (53): linear fit = 1.26 x + 0.0 (2806 voxels, overlap=0.029) Right_Hippocampus (53): linear fit = 1.26 x + 0.0 (2806 voxels, peak = 70), gca=69.6 gca peak = 0.30264 (59) mri peak = 0.05650 (71) Left_Hippocampus (17): linear fit = 1.29 x + 0.0 (2168 voxels, overlap=0.027) Left_Hippocampus (17): linear fit = 1.29 x + 0.0 (2168 voxels, peak = 76), gca=76.4 gca peak = 0.07580 (103) mri peak = 0.10767 (104) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (195876 voxels, overlap=0.641) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (195876 voxels, peak = 104), gca=103.5 gca peak = 0.07714 (104) mri peak = 0.10476 (105) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (186869 voxels, overlap=0.612) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (186869 voxels, peak = 106), gca=105.6 gca peak = 0.09712 (58) mri peak = 0.04644 (88) Left_Cerebral_Cortex (3): linear fit = 1.47 x + 0.0 (156465 voxels, overlap=0.000) Left_Cerebral_Cortex (3): linear fit = 1.47 x + 0.0 (156465 voxels, peak = 85), gca=85.0 gca peak = 0.11620 (58) mri peak = 0.04009 (87) Right_Cerebral_Cortex (42): linear fit = 1.47 x + 0.0 (150750 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.47 x + 0.0 (150750 voxels, peak = 85), gca=85.0 gca peak = 0.30970 (66) mri peak = 0.10233 (92) Right_Caudate (50): linear fit = 1.36 x + 0.0 (3380 voxels, overlap=0.023) Right_Caudate (50): linear fit = 1.36 x + 0.0 (3380 voxels, peak = 89), gca=89.4 gca peak = 0.15280 (69) mri peak = 0.09452 (95) Left_Caudate (11): linear fit = 1.25 x + 0.0 (3653 voxels, overlap=0.022) Left_Caudate (11): linear fit = 1.25 x + 0.0 (3653 voxels, peak = 87), gca=86.6 gca peak = 0.13902 (56) mri peak = 0.03064 (83) Left_Cerebellum_Cortex (8): linear fit = 1.46 x + 0.0 (27795 voxels, overlap=0.001) Left_Cerebellum_Cortex (8): linear fit = 1.46 x + 0.0 (27795 voxels, peak = 81), gca=81.5 gca peak = 0.14777 (55) mri peak = 0.03818 (70) Right_Cerebellum_Cortex (47): linear fit = 1.26 x + 0.0 (43737 voxels, overlap=0.040) Right_Cerebellum_Cortex (47): linear fit = 1.26 x + 0.0 (43737 voxels, peak = 70), gca=69.6 gca peak = 0.16765 (84) mri peak = 0.05992 (90) Left_Cerebellum_White_Matter (7): linear fit = 1.12 x + 0.0 (15689 voxels, overlap=0.638) Left_Cerebellum_White_Matter (7): linear fit = 1.12 x + 0.0 (15689 voxels, peak = 94), gca=93.7 gca peak = 0.18739 (84) mri peak = 0.08135 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (11444 voxels, overlap=0.862) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (11444 voxels, peak = 89), gca=89.5 gca peak = 0.29869 (57) mri peak = 0.09202 (77) Left_Amygdala (18): linear fit = 1.38 x + 0.0 (702 voxels, overlap=0.065) Left_Amygdala (18): linear fit = 1.38 x + 0.0 (702 voxels, peak = 79), gca=78.9 gca peak = 0.33601 (57) mri peak = 0.07528 (78) Right_Amygdala (54): linear fit = 1.46 x + 0.0 (1279 voxels, overlap=0.060) Right_Amygdala (54): linear fit = 1.46 x + 0.0 (1279 voxels, peak = 83), gca=82.9 gca peak = 0.11131 (90) mri peak = 0.09714 (101) Left_Thalamus_Proper (10): linear fit = 1.13 x + 0.0 (13178 voxels, overlap=0.092) Left_Thalamus_Proper (10): linear fit = 1.13 x + 0.0 (13178 voxels, peak = 102), gca=102.2 gca peak = 0.11793 (83) mri peak = 0.10544 (101) Right_Thalamus_Proper (49): linear fit = 1.21 x + 0.0 (12514 voxels, overlap=0.008) Right_Thalamus_Proper (49): linear fit = 1.21 x + 0.0 (12514 voxels, peak = 100), gca=100.0 gca peak = 0.08324 (81) mri peak = 0.08454 (101) Left_Putamen (12): linear fit = 1.24 x + 0.0 (6409 voxels, overlap=0.014) Left_Putamen (12): linear fit = 1.24 x + 0.0 (6409 voxels, peak = 100), gca=100.0 gca peak = 0.10360 (77) mri peak = 0.06307 (97) Right_Putamen (51): linear fit = 1.21 x + 0.0 (7513 voxels, overlap=0.049) Right_Putamen (51): linear fit = 1.21 x + 0.0 (7513 voxels, peak = 93), gca=92.8 gca peak = 0.08424 (78) mri peak = 0.07345 (90) Brain_Stem (16): linear fit = 1.13 x + 0.0 (27221 voxels, overlap=0.415) Brain_Stem (16): linear fit = 1.13 x + 0.0 (27221 voxels, peak = 89), gca=88.5 gca peak = 0.12631 (89) mri peak = 0.07880 (97) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (4747 voxels, overlap=0.393) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (4747 voxels, peak = 97), gca=97.5 gca peak = 0.14500 (87) mri peak = 0.09089 (97) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (4700 voxels, overlap=0.474) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (4700 voxels, peak = 96), gca=96.1 gca peak = 0.14975 (24) mri peak = 0.13987 (45) Third_Ventricle (14): linear fit = 1.73 x + 0.0 (151 voxels, overlap=0.057) Third_Ventricle (14): linear fit = 1.73 x + 0.0 (151 voxels, peak = 41), gca=41.4 gca peak = 0.19357 (14) mri peak = 0.07903 (23) Fourth_Ventricle (15): linear fit = 1.40 x + 0.0 (981 voxels, overlap=0.930) Fourth_Ventricle (15): linear fit = 1.40 x + 0.0 (981 voxels, peak = 20), gca=19.7 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 1.39 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 Left_Putamen too bright - rescaling by 0.941 (from 1.235) to 94.1 (was 100.0) Left_Pallidum too bright - rescaling by 0.983 (from 1.075) to 101.4 (was 103.2) Right_Pallidum too bright - rescaling by 1.002 (from 1.065) to 101.4 (was 101.2) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.12544 (31) mri peak = 0.07612 (41) Left_Lateral_Ventricle (4): linear fit = 1.38 x + 0.0 (4615 voxels, overlap=0.253) Left_Lateral_Ventricle (4): linear fit = 1.38 x + 0.0 (4615 voxels, peak = 43), gca=42.6 gca peak = 0.13981 (19) mri peak = 0.07848 (44) Right_Lateral_Ventricle (43): linear fit = 2.15 x + 0.0 (2986 voxels, overlap=0.123) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (2986 voxels, peak = 41), gca=28.5 gca peak = 0.26316 (102) mri peak = 0.13204 (102) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (2887 voxels, overlap=1.002) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (2887 voxels, peak = 103), gca=102.5 gca peak = 0.16987 (102) mri peak = 0.11411 (102) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (2752 voxels, overlap=0.999) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (2752 voxels, peak = 104), gca=103.5 gca peak = 0.20097 (70) mri peak = 0.06236 (74) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (2806 voxels, overlap=1.005) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (2806 voxels, peak = 70), gca=70.0 gca peak = 0.24998 (73) mri peak = 0.05650 (71) Left_Hippocampus (17): linear fit = 0.96 x + 0.0 (2168 voxels, overlap=1.004) Left_Hippocampus (17): linear fit = 0.96 x + 0.0 (2168 voxels, peak = 70), gca=70.4 gca peak = 0.07859 (103) mri peak = 0.10767 (104) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (195876 voxels, overlap=0.665) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (195876 voxels, peak = 103), gca=103.0 gca peak = 0.07821 (106) mri peak = 0.10476 (105) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (186869 voxels, overlap=0.679) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (186869 voxels, peak = 105), gca=105.5 gca peak = 0.06701 (85) mri peak = 0.04644 (88) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (156465 voxels, overlap=0.925) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (156465 voxels, peak = 85), gca=85.4 gca peak = 0.08269 (85) mri peak = 0.04009 (87) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (150750 voxels, overlap=0.955) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (150750 voxels, peak = 85), gca=85.0 gca peak = 0.21176 (89) mri peak = 0.10233 (92) Right_Caudate (50): linear fit = 1.00 x + 0.0 (3380 voxels, overlap=1.001) Right_Caudate (50): linear fit = 1.00 x + 0.0 (3380 voxels, peak = 89), gca=89.0 gca peak = 0.14849 (97) mri peak = 0.09452 (95) Left_Caudate (11): linear fit = 1.00 x + 0.0 (3653 voxels, overlap=0.996) Left_Caudate (11): linear fit = 1.00 x + 0.0 (3653 voxels, peak = 97), gca=97.0 gca peak = 0.09779 (80) mri peak = 0.03064 (83) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (27795 voxels, overlap=0.891) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (27795 voxels, peak = 80), gca=79.6 gca peak = 0.12189 (69) mri peak = 0.03818 (70) Right_Cerebellum_Cortex (47): linear fit = 1.03 x + 0.0 (43737 voxels, overlap=0.991) Right_Cerebellum_Cortex (47): linear fit = 1.03 x + 0.0 (43737 voxels, peak = 71), gca=71.4 gca peak = 0.15147 (94) mri peak = 0.05992 (90) Left_Cerebellum_White_Matter (7): linear fit = 0.98 x + 0.0 (15689 voxels, overlap=0.988) Left_Cerebellum_White_Matter (7): linear fit = 0.98 x + 0.0 (15689 voxels, peak = 92), gca=91.7 gca peak = 0.15165 (90) mri peak = 0.08135 (88) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (11444 voxels, overlap=0.989) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (11444 voxels, peak = 89), gca=88.7 gca peak = 0.29298 (79) mri peak = 0.09202 (77) Left_Amygdala (18): linear fit = 0.99 x + 0.0 (702 voxels, overlap=1.004) Left_Amygdala (18): linear fit = 0.99 x + 0.0 (702 voxels, peak = 78), gca=77.8 gca peak = 0.29171 (83) mri peak = 0.07528 (78) Right_Amygdala (54): linear fit = 0.99 x + 0.0 (1279 voxels, overlap=1.004) Right_Amygdala (54): linear fit = 0.99 x + 0.0 (1279 voxels, peak = 82), gca=81.8 gca peak = 0.10617 (100) mri peak = 0.09714 (101) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (13178 voxels, overlap=0.855) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (13178 voxels, peak = 100), gca=100.5 gca peak = 0.08433 (97) mri peak = 0.10544 (101) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (12514 voxels, overlap=0.876) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (12514 voxels, peak = 97), gca=96.5 gca peak = 0.07535 (94) mri peak = 0.08454 (101) Left_Putamen (12): linear fit = 1.07 x + 0.0 (6409 voxels, overlap=0.690) Left_Putamen (12): linear fit = 1.07 x + 0.0 (6409 voxels, peak = 100), gca=100.1 gca peak = 0.08541 (91) mri peak = 0.06307 (97) Right_Putamen (51): linear fit = 1.00 x + 0.0 (7513 voxels, overlap=0.944) Right_Putamen (51): linear fit = 1.00 x + 0.0 (7513 voxels, peak = 91), gca=91.5 gca peak = 0.07622 (89) mri peak = 0.07345 (90) Brain_Stem (16): linear fit = 0.99 x + 0.0 (27221 voxels, overlap=0.867) Brain_Stem (16): linear fit = 0.99 x + 0.0 (27221 voxels, peak = 88), gca=87.7 gca peak = 0.12070 (97) mri peak = 0.07880 (97) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (4747 voxels, overlap=0.809) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (4747 voxels, peak = 98), gca=98.5 gca peak = 0.15002 (96) mri peak = 0.09089 (97) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (4700 voxels, overlap=0.865) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (4700 voxels, peak = 96), gca=95.5 gca peak = 0.12452 (38) mri peak = 0.13987 (45) Third_Ventricle (14): linear fit = 1.18 x + 0.0 (151 voxels, overlap=0.443) Third_Ventricle (14): linear fit = 1.18 x + 0.0 (151 voxels, peak = 45), gca=45.0 gca peak = 0.14887 (21) mri peak = 0.07903 (23) Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (981 voxels, overlap=0.828) Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (981 voxels, peak = 22), gca=21.5 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.17746 (35) gca peak Left_Thalamus = 0.72551 (105) gca peak CSF = 0.15453 (54) gca peak Left_Accumbens_area = 0.57643 (78) 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 = 0.19572 (29) gca peak Right_Accumbens_area = 0.29664 (87) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14504 (37) gca peak Fifth_Ventricle = 0.51780 (45) gca peak WM_hypointensities = 0.07850 (77) gca peak non_WM_hypointensities = 0.12165 (55) gca peak Optic_Chiasm = 0.57465 (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 1.27 x + 0.0 Left_Putamen too bright - rescaling by 0.937 (from 1.065) to 93.8 (was 100.1) Left_Pallidum too bright - rescaling by 0.977 (from 1.015) to 101.1 (was 103.5) Right_Pallidum too bright - rescaling by 0.986 (from 1.005) to 101.1 (was 102.5) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 308920 voxels changed in iteration 0 of unlikely voxel relabeling 1553 voxels changed in iteration 1 of unlikely voxel relabeling 47 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 457131 gm and wm labels changed (%29 to gray, %71 to white out of all changed labels) 1204 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 259481 changed. image ll: -2.289, PF=0.500 pass 2: 70393 changed. image ll: -2.285, PF=0.500 pass 3: 26997 changed. pass 4: 12337 changed. pass 5: 6307 changed. pass 6: 3552 changed. 391859 voxels changed in iteration 0 of unlikely voxel relabeling 2520 voxels changed in iteration 1 of unlikely voxel relabeling 578 voxels changed in iteration 2 of unlikely voxel relabeling 427 voxels changed in iteration 3 of unlikely voxel relabeling 137 voxels changed in iteration 4 of unlikely voxel relabeling 21850 voxels changed in iteration 0 of unlikely voxel relabeling 524 voxels changed in iteration 1 of unlikely voxel relabeling 27 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 18477 voxels changed in iteration 0 of unlikely voxel relabeling 444 voxels changed in iteration 1 of unlikely voxel relabeling 104 voxels changed in iteration 2 of unlikely voxel relabeling 29 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 16911 voxels changed in iteration 0 of unlikely voxel relabeling 97 voxels changed in iteration 1 of unlikely voxel relabeling 1 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling MRItoUCHAR: min=0, max=85 MRItoUCHAR: converting to UCHAR writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 8235.304800 mri_ca_label stimesec 22.004629 mri_ca_label ru_maxrss 3229624 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 28757555 mri_ca_label ru_majflt 1 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 1208 mri_ca_label ru_oublock 984 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 925 mri_ca_label ru_nivcsw 2586 auto-labeling took 136 minutes and 6 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/mri/transforms/cc_up.lta inul_loom2_7T 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/SUBJECTS_DIR/inul_loom2_7T/mri/transforms/cc_up.lta reading aseg from /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/mri/aseg.auto_noCCseg.mgz reading norm from /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/mri/norm.mgz 136740 voxels in left wm, 148391 in right wm, xrange [146, 159] searching rotation angles z=[-4 10], y=[-8 6] searching scale 1 Z rot -4.4 searching scale 1 Z rot -4.2 searching scale 1 Z rot -3.9 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.4 searching scale 1 Z rot -3.2 searching scale 1 Z rot -2.9 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.4 searching scale 1 Z rot -2.2 searching scale 1 Z rot -1.9 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.4 searching scale 1 Z rot -1.2 searching scale 1 Z rot -0.9 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.4 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.1 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.6 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.1 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.6 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.1 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.6 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.1 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.6 searching scale 1 Z rot 3.8 searching scale 1 Z rot 4.1 searching scale 1 Z rot 4.3 searching scale 1 Z rot 4.6 searching scale 1 Z rot 4.8 searching scale 1 Z rot 5.1 searching scale 1 Z rot 5.3 searching scale 1 Z rot 5.6 searching scale 1 Z rot 5.8 searching scale 1 Z rot 6.1 searching scale 1 Z rot 6.3 searching scale 1 Z rot 6.6 searching scale 1 Z rot 6.8 searching scale 1 Z rot 7.1 searching scale 1 Z rot 7.3 searching scale 1 Z rot 7.6 searching scale 1 Z rot 7.8 searching scale 1 Z rot 8.1 searching scale 1 Z rot 8.3 searching scale 1 Z rot 8.6 searching scale 1 Z rot 8.8 searching scale 1 Z rot 9.1 searching scale 1 Z rot 9.3 global minimum found at slice 152.2, rotations (-0.84, 2.55) final transformation (x=152.2, yr=-0.842, zr=2.551): 0.99890 -0.04451 -0.01467 -17.50867; 0.04451 0.99901 -0.00065 18.41436; 0.01469 -0.00000 0.99989 -5.22135; 0.00000 0.00000 0.00000 1.00000; updating x range to be [126, 132] in xformed coordinates best xformed slice 129 cc center is found at 129 103 131 eigenvectors: -0.00146 0.00598 0.99998; -0.17047 -0.98535 0.00565; 0.98536 -0.17046 0.00246; writing aseg with callosum to /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/mri/aseg.auto.mgz... corpus callosum segmentation took 1.7 minutes #-------------------------------------- #@# Merge ASeg Wed Feb 20 19:29:51 EST 2019 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Wed Feb 20 19:29:51 EST 2019 /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/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... 3652 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 109 gm peak at 87 (87), valley at 31 (31) csf peak at 11, setting threshold to 61 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 86 (86), valley at 30 (30) csf peak at 10, setting threshold to 60 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 5 minutes and 31 seconds. #-------------------------------------------- #@# Mask BFS Wed Feb 20 19:35:23 EST 2019 /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 4206914 voxels in mask (pct= 12.84) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Wed Feb 20 19:35:26 EST 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): 104.4 +- 7.2 [79.0 --> 125.0] GM (72.0) : 70.5 +- 11.7 [30.0 --> 95.0] setting bottom of white matter range to 82.3 setting top of gray matter range to 94.0 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, 6932 filled 19974 bright non-wm voxels segmented. 19563 diagonally connected voxels added... white matter segmentation took 3.5 minutes writing output to wm.seg.mgz... assuming input volume is MGH (Van der Kouwe) MP-RAGE mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.91 minutes reading wm segmentation from wm.seg.mgz... 718 voxels added to wm to prevent paths from MTL structures to cortex 7600 additional wm voxels added 0 additional wm voxels added SEG EDIT: 77718 voxels turned on, 73891 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 0 new 0 115,126,128 old 0 new 0 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 102 found - 102 modified | TOTAL: 102 pass 2 (xy+): 0 found - 102 modified | TOTAL: 102 pass 1 (xy-): 89 found - 89 modified | TOTAL: 191 pass 2 (xy-): 0 found - 89 modified | TOTAL: 191 pass 1 (yz+): 108 found - 108 modified | TOTAL: 299 pass 2 (yz+): 0 found - 108 modified | TOTAL: 299 pass 1 (yz-): 99 found - 99 modified | TOTAL: 398 pass 2 (yz-): 0 found - 99 modified | TOTAL: 398 pass 1 (xz+): 89 found - 89 modified | TOTAL: 487 pass 2 (xz+): 0 found - 89 modified | TOTAL: 487 pass 1 (xz-): 108 found - 108 modified | TOTAL: 595 pass 2 (xz-): 0 found - 108 modified | TOTAL: 595 Iteration Number : 1 pass 1 (+++): 357 found - 357 modified | TOTAL: 357 pass 2 (+++): 0 found - 357 modified | TOTAL: 357 pass 1 (+++): 274 found - 274 modified | TOTAL: 631 pass 2 (+++): 0 found - 274 modified | TOTAL: 631 pass 1 (+++): 292 found - 292 modified | TOTAL: 923 pass 2 (+++): 0 found - 292 modified | TOTAL: 923 pass 1 (+++): 297 found - 297 modified | TOTAL: 1220 pass 2 (+++): 0 found - 297 modified | TOTAL: 1220 Iteration Number : 1 pass 1 (++): 515 found - 515 modified | TOTAL: 515 pass 2 (++): 0 found - 515 modified | TOTAL: 515 pass 1 (+-): 400 found - 400 modified | TOTAL: 915 pass 2 (+-): 1 found - 401 modified | TOTAL: 916 pass 3 (+-): 0 found - 401 modified | TOTAL: 916 pass 1 (--): 424 found - 424 modified | TOTAL: 1340 pass 2 (--): 2 found - 426 modified | TOTAL: 1342 pass 3 (--): 0 found - 426 modified | TOTAL: 1342 pass 1 (-+): 369 found - 369 modified | TOTAL: 1711 pass 2 (-+): 0 found - 369 modified | TOTAL: 1711 Iteration Number : 2 pass 1 (xy+): 89 found - 89 modified | TOTAL: 89 pass 2 (xy+): 0 found - 89 modified | TOTAL: 89 pass 1 (xy-): 83 found - 83 modified | TOTAL: 172 pass 2 (xy-): 0 found - 83 modified | TOTAL: 172 pass 1 (yz+): 88 found - 88 modified | TOTAL: 260 pass 2 (yz+): 0 found - 88 modified | TOTAL: 260 pass 1 (yz-): 63 found - 63 modified | TOTAL: 323 pass 2 (yz-): 0 found - 63 modified | TOTAL: 323 pass 1 (xz+): 97 found - 97 modified | TOTAL: 420 pass 2 (xz+): 0 found - 97 modified | TOTAL: 420 pass 1 (xz-): 81 found - 81 modified | TOTAL: 501 pass 2 (xz-): 0 found - 81 modified | TOTAL: 501 Iteration Number : 2 pass 1 (+++): 21 found - 21 modified | TOTAL: 21 pass 2 (+++): 0 found - 21 modified | TOTAL: 21 pass 1 (+++): 30 found - 30 modified | TOTAL: 51 pass 2 (+++): 0 found - 30 modified | TOTAL: 51 pass 1 (+++): 23 found - 23 modified | TOTAL: 74 pass 2 (+++): 0 found - 23 modified | TOTAL: 74 pass 1 (+++): 20 found - 20 modified | TOTAL: 94 pass 2 (+++): 0 found - 20 modified | TOTAL: 94 Iteration Number : 2 pass 1 (++): 48 found - 48 modified | TOTAL: 48 pass 2 (++): 0 found - 48 modified | TOTAL: 48 pass 1 (+-): 39 found - 39 modified | TOTAL: 87 pass 2 (+-): 0 found - 39 modified | TOTAL: 87 pass 1 (--): 38 found - 38 modified | TOTAL: 125 pass 2 (--): 0 found - 38 modified | TOTAL: 125 pass 1 (-+): 42 found - 42 modified | TOTAL: 167 pass 2 (-+): 0 found - 42 modified | TOTAL: 167 Iteration Number : 3 pass 1 (xy+): 11 found - 11 modified | TOTAL: 11 pass 2 (xy+): 0 found - 11 modified | TOTAL: 11 pass 1 (xy-): 7 found - 7 modified | TOTAL: 18 pass 2 (xy-): 0 found - 7 modified | TOTAL: 18 pass 1 (yz+): 8 found - 8 modified | TOTAL: 26 pass 2 (yz+): 0 found - 8 modified | TOTAL: 26 pass 1 (yz-): 9 found - 9 modified | TOTAL: 35 pass 2 (yz-): 0 found - 9 modified | TOTAL: 35 pass 1 (xz+): 7 found - 7 modified | TOTAL: 42 pass 2 (xz+): 0 found - 7 modified | TOTAL: 42 pass 1 (xz-): 8 found - 8 modified | TOTAL: 50 pass 2 (xz-): 0 found - 8 modified | TOTAL: 50 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 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 : 3 pass 1 (++): 4 found - 4 modified | TOTAL: 4 pass 2 (++): 0 found - 4 modified | TOTAL: 4 pass 1 (+-): 3 found - 3 modified | TOTAL: 7 pass 2 (+-): 0 found - 3 modified | TOTAL: 7 pass 1 (--): 6 found - 6 modified | TOTAL: 13 pass 2 (--): 0 found - 6 modified | TOTAL: 13 pass 1 (-+): 5 found - 5 modified | TOTAL: 18 pass 2 (-+): 0 found - 5 modified | TOTAL: 18 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 1 found - 1 modified | TOTAL: 2 pass 2 (xz+): 0 found - 1 modified | TOTAL: 2 pass 1 (xz-): 2 found - 2 modified | TOTAL: 4 pass 2 (xz-): 0 found - 2 modified | TOTAL: 4 Iteration Number : 4 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 : 4 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 1 found - 1 modified | TOTAL: 2 pass 2 (--): 0 found - 1 modified | TOTAL: 2 pass 1 (-+): 0 found - 0 modified | TOTAL: 2 Iteration Number : 5 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 5 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 5 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 6 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 6 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 6 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 4371 (out of 1777466: 0.245912) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Wed Feb 20 19:39:57 EST 2019 /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/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 1.04285 -0.00402 -0.03539 1.85782; 0.01855 0.94717 0.38433 -28.67044; 0.03596 -0.35799 0.88293 54.36340; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.04285 -0.00402 -0.03539 1.85782; 0.01855 0.94717 0.38433 -28.67044; 0.03596 -0.35799 0.88293 54.36340; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (622, 2489) area[0] = 1620 (min = 622, max = 2489), aspect = 0.54 (min = 0.10, max = 0.75) no need to search using seed (158, 138, 110), TAL = (1.5, -37.5, 16.5) talairach voxel to voxel transform 0.95754 0.01594 0.03144 -3.03102; -0.00252 0.90658 -0.39472 47.45517; -0.04002 0.36693 0.97127 -42.20714; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (158, 138, 110) --> (1.5, -37.5, 16.5) done. writing output to filled.mgz... filling took 1.0 minutes badRH = 511/856195, badLH=15114/883702 Please check filled volume. Cerebellum may be included. talairach cc position changed to (1.50, -37.50, 16.50) Erasing brainstem...done. seed_search_size = 12, min_neighbors = 5 search rh wm seed point around talairach space:(19.50, -37.50, 16.50) SRC: (130.94, 128.81, 109.91) search lh wm seed point around talairach space (-16.50, -37.50, 16.50), SRC: (176.90, 128.69, 107.99) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Wed Feb 20 19:40:59 EST 2019 /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.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-): 6 found - 6 modified | TOTAL: 14 pass 2 (xy-): 0 found - 6 modified | TOTAL: 14 pass 1 (yz+): 3 found - 3 modified | TOTAL: 17 pass 2 (yz+): 0 found - 3 modified | TOTAL: 17 pass 1 (yz-): 8 found - 8 modified | TOTAL: 25 pass 2 (yz-): 0 found - 8 modified | TOTAL: 25 pass 1 (xz+): 10 found - 10 modified | TOTAL: 35 pass 2 (xz+): 0 found - 10 modified | TOTAL: 35 pass 1 (xz-): 2 found - 2 modified | TOTAL: 37 pass 2 (xz-): 0 found - 2 modified | TOTAL: 37 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 4 Iteration Number : 1 pass 1 (++): 4 found - 4 modified | TOTAL: 4 pass 2 (++): 0 found - 4 modified | TOTAL: 4 pass 1 (+-): 3 found - 3 modified | TOTAL: 7 pass 2 (+-): 0 found - 3 modified | TOTAL: 7 pass 1 (--): 6 found - 6 modified | TOTAL: 13 pass 2 (--): 0 found - 6 modified | TOTAL: 13 pass 1 (-+): 1 found - 1 modified | TOTAL: 14 pass 2 (-+): 0 found - 1 modified | TOTAL: 14 Iteration Number : 2 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 1 found - 1 modified | TOTAL: 2 pass 2 (xy-): 0 found - 1 modified | TOTAL: 2 pass 1 (yz+): 2 found - 2 modified | TOTAL: 4 pass 2 (yz+): 0 found - 2 modified | TOTAL: 4 pass 1 (yz-): 1 found - 1 modified | TOTAL: 5 pass 2 (yz-): 0 found - 1 modified | TOTAL: 5 pass 1 (xz+): 0 found - 0 modified | TOTAL: 5 pass 1 (xz-): 0 found - 0 modified | TOTAL: 5 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 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 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 = 61 (out of 883763: 0.006902) 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: 1512 vertices, 1734 faces slice 40: 14490 vertices, 15143 faces slice 50: 34021 vertices, 34896 faces slice 60: 57595 vertices, 58584 faces slice 70: 83521 vertices, 84645 faces slice 80: 109454 vertices, 110535 faces slice 90: 131736 vertices, 132748 faces slice 100: 152755 vertices, 153835 faces slice 110: 172003 vertices, 173129 faces slice 120: 192898 vertices, 194005 faces slice 130: 212396 vertices, 213640 faces slice 140: 231927 vertices, 233193 faces slice 150: 251785 vertices, 253210 faces slice 160: 273575 vertices, 275175 faces slice 170: 296525 vertices, 298240 faces slice 180: 316008 vertices, 317815 faces slice 190: 333925 vertices, 335762 faces slice 200: 350335 vertices, 352154 faces slice 210: 366232 vertices, 368111 faces slice 220: 380493 vertices, 382418 faces slice 230: 394862 vertices, 396855 faces slice 240: 406831 vertices, 408751 faces slice 250: 414540 vertices, 416363 faces slice 260: 416810 vertices, 418428 faces slice 270: 416810 vertices, 418428 faces slice 280: 416810 vertices, 418428 faces slice 290: 416810 vertices, 418428 faces slice 300: 416810 vertices, 418428 faces slice 310: 416810 vertices, 418428 faces slice 320: 416810 vertices, 418428 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -0.75000 0.00000 0.00000 120.00000; 0.00000 0.00000 0.75000 -120.00000; 0.00000 -0.75000 0.00000 120.00000; 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... 416810 voxel in cpt #1: X=-1618 [v=416810,e=1255284,f=836856] located at (-20.381742, -22.694338, 34.826656) For the whole surface: X=-1618 [v=416810,e=1255284,f=836856] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Wed Feb 20 19:41:14 EST 2019 /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 12 found - 12 modified | TOTAL: 12 pass 2 (xy+): 0 found - 12 modified | TOTAL: 12 pass 1 (xy-): 7 found - 7 modified | TOTAL: 19 pass 2 (xy-): 0 found - 7 modified | TOTAL: 19 pass 1 (yz+): 4 found - 4 modified | TOTAL: 23 pass 2 (yz+): 0 found - 4 modified | TOTAL: 23 pass 1 (yz-): 7 found - 7 modified | TOTAL: 30 pass 2 (yz-): 0 found - 7 modified | TOTAL: 30 pass 1 (xz+): 7 found - 7 modified | TOTAL: 37 pass 2 (xz+): 0 found - 7 modified | TOTAL: 37 pass 1 (xz-): 6 found - 6 modified | TOTAL: 43 pass 2 (xz-): 0 found - 6 modified | TOTAL: 43 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 1 pass 1 (++): 5 found - 5 modified | TOTAL: 5 pass 2 (++): 0 found - 5 modified | TOTAL: 5 pass 1 (+-): 2 found - 2 modified | TOTAL: 7 pass 2 (+-): 0 found - 2 modified | TOTAL: 7 pass 1 (--): 6 found - 6 modified | TOTAL: 13 pass 2 (--): 0 found - 6 modified | TOTAL: 13 pass 1 (-+): 4 found - 4 modified | TOTAL: 17 pass 2 (-+): 0 found - 4 modified | TOTAL: 17 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 1 found - 1 modified | TOTAL: 1 pass 2 (yz-): 0 found - 1 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 1 found - 1 modified | TOTAL: 2 pass 2 (xz-): 0 found - 1 modified | TOTAL: 2 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 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 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 = 65 (out of 856260: 0.007591) 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: 874 vertices, 1021 faces slice 40: 10012 vertices, 10515 faces slice 50: 25513 vertices, 26211 faces slice 60: 45163 vertices, 45917 faces slice 70: 67410 vertices, 68383 faces slice 80: 89233 vertices, 90228 faces slice 90: 112092 vertices, 113146 faces slice 100: 132828 vertices, 133833 faces slice 110: 150872 vertices, 151847 faces slice 120: 171034 vertices, 172120 faces slice 130: 190091 vertices, 191266 faces slice 140: 209598 vertices, 210850 faces slice 150: 228492 vertices, 229805 faces slice 160: 250439 vertices, 251918 faces slice 170: 272624 vertices, 274329 faces slice 180: 294662 vertices, 296370 faces slice 190: 315957 vertices, 317768 faces slice 200: 338056 vertices, 339911 faces slice 210: 356398 vertices, 358188 faces slice 220: 371843 vertices, 373702 faces slice 230: 388738 vertices, 390768 faces slice 240: 402862 vertices, 404871 faces slice 250: 412413 vertices, 414314 faces slice 260: 416931 vertices, 418594 faces slice 270: 416946 vertices, 418602 faces slice 280: 416946 vertices, 418602 faces slice 290: 416946 vertices, 418602 faces slice 300: 416946 vertices, 418602 faces slice 310: 416946 vertices, 418602 faces slice 320: 416946 vertices, 418602 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -0.75000 0.00000 0.00000 120.00000; 0.00000 0.00000 0.75000 -120.00000; 0.00000 -0.75000 0.00000 120.00000; 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... 416946 voxel in cpt #1: X=-1656 [v=416946,e=1255806,f=837204] located at (30.686216, -16.530703, 31.164127) For the whole surface: X=-1656 [v=416946,e=1255806,f=837204] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Wed Feb 20 19:41:29 EST 2019 /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix #-------------------------------------------- #@# Smooth1 rh Wed Feb 20 19:41:29 EST 2019 /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix Waiting for PID 8186 of (8186 8189) to complete... Waiting for PID 8189 of (8186 8189) 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 (8186 8189) completed and logs appended. #-------------------------------------------- #@# Inflation1 lh Wed Feb 20 19:41:47 EST 2019 /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/scripts mris_inflate -no-save-sulc -n 15 -w 10 ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix #-------------------------------------------- #@# Inflation1 rh Wed Feb 20 19:41:47 EST 2019 /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/scripts mris_inflate -no-save-sulc -n 15 -w 10 ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Waiting for PID 8264 of (8264 8267) to complete... Waiting for PID 8267 of (8264 8267) 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 = 53.2 mm, total surface area = 121980 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 1.7 minutes step 000: RMS=0.186 (target=0.015) step 005: RMS=0.151 (target=0.015) step 010: RMS=0.131 (target=0.015) step 015: RMS=0.121 (target=0.015) step 020: RMS=0.114 (target=0.015) step 025: RMS=0.109 (target=0.015) step 030: RMS=0.104 (target=0.015) step 035: RMS=0.100 (target=0.015) step 040: RMS=0.097 (target=0.015) step 045: RMS=0.094 (target=0.015) step 050: RMS=0.092 (target=0.015) step 055: RMS=0.090 (target=0.015) step 060: RMS=0.089 (target=0.015) step 065: RMS=0.088 (target=0.015) step 070: RMS=0.087 (target=0.015) step 075: RMS=0.086 (target=0.015) step 080: RMS=0.086 (target=0.015) step 085: RMS=0.086 (target=0.015) step 090: RMS=0.086 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 218.542244 mris_inflate stimesec 4.258732 mris_inflate ru_maxrss 644968 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 2901697 mris_inflate ru_majflt 1 mris_inflate ru_nswap 0 mris_inflate ru_inblock 648 mris_inflate ru_oublock 323344 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 171393 mris_inflate ru_nivcsw 145 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 = 52.5 mm, total surface area = 120962 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 1.9 minutes step 000: RMS=0.190 (target=0.015) step 005: RMS=0.154 (target=0.015) step 010: RMS=0.135 (target=0.015) step 015: RMS=0.126 (target=0.015) step 020: RMS=0.119 (target=0.015) step 025: RMS=0.114 (target=0.015) step 030: RMS=0.110 (target=0.015) step 035: RMS=0.106 (target=0.015) step 040: RMS=0.102 (target=0.015) step 045: RMS=0.100 (target=0.015) step 050: RMS=0.098 (target=0.015) step 055: RMS=0.096 (target=0.015) step 060: RMS=0.095 (target=0.015) step 065: RMS=0.094 (target=0.015) step 070: RMS=0.093 (target=0.015) step 075: RMS=0.093 (target=0.015) step 080: RMS=0.093 (target=0.015) step 085: RMS=0.093 (target=0.015) step 090: RMS=0.093 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 246.384845 mris_inflate stimesec 8.387705 mris_inflate ru_maxrss 645408 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 5790011 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 323456 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 178202 mris_inflate ru_nivcsw 347 PIDs (8264 8267) completed and logs appended. #-------------------------------------------- #@# QSphere lh Wed Feb 20 19:43:42 EST 2019 /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix #-------------------------------------------- #@# QSphere rh Wed Feb 20 19:43:42 EST 2019 /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix Waiting for PID 8445 of (8445 8448) to complete... Waiting for PID 8448 of (8445 8448) 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 0.59 +- 0.47 (0.00-->9.76) (max @ vno 247003 --> 248982) face area 0.01 +- 0.02 (-0.31-->0.41) == Number of threads available to mris_sphere for OpenMP = 4 == scaling brain by 0.260... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.499, avgs=0 005/300: dt: 0.9000, rms radial error=175.243, avgs=0 010/300: dt: 0.9000, rms radial error=174.692, avgs=0 015/300: dt: 0.9000, rms radial error=173.970, avgs=0 020/300: dt: 0.9000, rms radial error=173.146, avgs=0 025/300: dt: 0.9000, rms radial error=172.266, avgs=0 030/300: dt: 0.9000, rms radial error=171.353, avgs=0 035/300: dt: 0.9000, rms radial error=170.424, avgs=0 040/300: dt: 0.9000, rms radial error=169.486, avgs=0 045/300: dt: 0.9000, rms radial error=168.547, avgs=0 050/300: dt: 0.9000, rms radial error=167.607, avgs=0 055/300: dt: 0.9000, rms radial error=166.671, avgs=0 060/300: dt: 0.9000, rms radial error=165.738, avgs=0 065/300: dt: 0.9000, rms radial error=164.809, avgs=0 070/300: dt: 0.9000, rms radial error=163.884, avgs=0 075/300: dt: 0.9000, rms radial error=162.964, avgs=0 080/300: dt: 0.9000, rms radial error=162.049, avgs=0 085/300: dt: 0.9000, rms radial error=161.139, avgs=0 090/300: dt: 0.9000, rms radial error=160.234, avgs=0 095/300: dt: 0.9000, rms radial error=159.334, avgs=0 100/300: dt: 0.9000, rms radial error=158.438, avgs=0 105/300: dt: 0.9000, rms radial error=157.550, avgs=0 110/300: dt: 0.9000, rms radial error=156.667, avgs=0 115/300: dt: 0.9000, rms radial error=155.789, avgs=0 120/300: dt: 0.9000, rms radial error=154.915, avgs=0 125/300: dt: 0.9000, rms radial error=154.046, avgs=0 130/300: dt: 0.9000, rms radial error=153.181, avgs=0 135/300: dt: 0.9000, rms radial error=152.322, avgs=0 140/300: dt: 0.9000, rms radial error=151.470, avgs=0 145/300: dt: 0.9000, rms radial error=150.621, avgs=0 150/300: dt: 0.9000, rms radial error=149.778, avgs=0 155/300: dt: 0.9000, rms radial error=148.939, avgs=0 160/300: dt: 0.9000, rms radial error=148.103, avgs=0 165/300: dt: 0.9000, rms radial error=147.273, avgs=0 170/300: dt: 0.9000, rms radial error=146.446, avgs=0 175/300: dt: 0.9000, rms radial error=145.623, avgs=0 180/300: dt: 0.9000, rms radial error=144.803, avgs=0 185/300: dt: 0.9000, rms radial error=143.987, avgs=0 190/300: dt: 0.9000, rms radial error=143.175, avgs=0 195/300: dt: 0.9000, rms radial error=142.369, avgs=0 200/300: dt: 0.9000, rms radial error=141.567, avgs=0 205/300: dt: 0.9000, rms radial error=140.770, avgs=0 210/300: dt: 0.9000, rms radial error=139.977, avgs=0 215/300: dt: 0.9000, rms radial error=139.189, avgs=0 220/300: dt: 0.9000, rms radial error=138.405, avgs=0 225/300: dt: 0.9000, rms radial error=137.625, avgs=0 230/300: dt: 0.9000, rms radial error=136.850, avgs=0 235/300: dt: 0.9000, rms radial error=136.079, avgs=0 240/300: dt: 0.9000, rms radial error=135.312, avgs=0 245/300: dt: 0.9000, rms radial error=134.550, avgs=0 250/300: dt: 0.9000, rms radial error=133.792, avgs=0 255/300: dt: 0.9000, rms radial error=133.038, avgs=0 260/300: dt: 0.9000, rms radial error=132.289, avgs=0 265/300: dt: 0.9000, rms radial error=131.543, avgs=0 270/300: dt: 0.9000, rms radial error=130.802, avgs=0 275/300: dt: 0.9000, rms radial error=130.065, avgs=0 280/300: dt: 0.9000, rms radial error=129.332, avgs=0 285/300: dt: 0.9000, rms radial error=128.603, avgs=0 290/300: dt: 0.9000, rms radial error=127.878, avgs=0 295/300: dt: 0.9000, rms radial error=127.158, avgs=0 300/300: dt: 0.9000, rms radial error=126.441, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 54402.33 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00009 epoch 2 (K=40.0), pass 1, starting sse = 11730.80 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 = 2125.54 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/10 = 0.00122 epoch 4 (K=640.0), pass 1, starting sse = 371.99 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/10 = 0.00566 final distance error %35.83 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.09 hours mris_sphere utimesec 746.706086 mris_sphere stimesec 4.271504 mris_sphere ru_maxrss 645128 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 3613784 mris_sphere ru_majflt 1 mris_sphere ru_nswap 0 mris_sphere ru_inblock 896 mris_sphere ru_oublock 29432 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 159666 mris_sphere ru_nivcsw 331 FSRUNTIME@ mris_sphere 0.0891 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 0.58 +- 0.45 (0.00-->6.38) (max @ vno 247581 --> 249820) face area 0.01 +- 0.02 (-0.10-->0.55) == Number of threads available to mris_sphere for OpenMP = 4 == scaling brain by 0.258... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.957, avgs=0 005/300: dt: 0.9000, rms radial error=175.698, avgs=0 010/300: dt: 0.9000, rms radial error=175.141, avgs=0 015/300: dt: 0.9000, rms radial error=174.410, avgs=0 020/300: dt: 0.9000, rms radial error=173.578, avgs=0 025/300: dt: 0.9000, rms radial error=172.688, avgs=0 030/300: dt: 0.9000, rms radial error=171.765, avgs=0 035/300: dt: 0.9000, rms radial error=170.826, avgs=0 040/300: dt: 0.9000, rms radial error=169.879, avgs=0 045/300: dt: 0.9000, rms radial error=168.930, avgs=0 050/300: dt: 0.9000, rms radial error=167.984, avgs=0 055/300: dt: 0.9000, rms radial error=167.040, avgs=0 060/300: dt: 0.9000, rms radial error=166.099, avgs=0 065/300: dt: 0.9000, rms radial error=165.164, avgs=0 070/300: dt: 0.9000, rms radial error=164.234, avgs=0 075/300: dt: 0.9000, rms radial error=163.308, avgs=0 080/300: dt: 0.9000, rms radial error=162.387, avgs=0 085/300: dt: 0.9000, rms radial error=161.471, avgs=0 090/300: dt: 0.9000, rms radial error=160.560, avgs=0 095/300: dt: 0.9000, rms radial error=159.654, avgs=0 100/300: dt: 0.9000, rms radial error=158.753, avgs=0 105/300: dt: 0.9000, rms radial error=157.856, avgs=0 110/300: dt: 0.9000, rms radial error=156.965, avgs=0 115/300: dt: 0.9000, rms radial error=156.078, avgs=0 120/300: dt: 0.9000, rms radial error=155.196, avgs=0 125/300: dt: 0.9000, rms radial error=154.320, avgs=0 130/300: dt: 0.9000, rms radial error=153.452, avgs=0 135/300: dt: 0.9000, rms radial error=152.589, avgs=0 140/300: dt: 0.9000, rms radial error=151.730, avgs=0 145/300: dt: 0.9000, rms radial error=150.876, avgs=0 150/300: dt: 0.9000, rms radial error=150.026, avgs=0 155/300: dt: 0.9000, rms radial error=149.181, avgs=0 160/300: dt: 0.9000, rms radial error=148.340, avgs=0 165/300: dt: 0.9000, rms radial error=147.504, avgs=0 170/300: dt: 0.9000, rms radial error=146.673, avgs=0 175/300: dt: 0.9000, rms radial error=145.847, avgs=0 180/300: dt: 0.9000, rms radial error=145.025, avgs=0 185/300: dt: 0.9000, rms radial error=144.207, avgs=0 190/300: dt: 0.9000, rms radial error=143.394, avgs=0 195/300: dt: 0.9000, rms radial error=142.586, avgs=0 200/300: dt: 0.9000, rms radial error=141.782, avgs=0 205/300: dt: 0.9000, rms radial error=140.983, avgs=0 210/300: dt: 0.9000, rms radial error=140.188, avgs=0 215/300: dt: 0.9000, rms radial error=139.397, avgs=0 220/300: dt: 0.9000, rms radial error=138.611, avgs=0 225/300: dt: 0.9000, rms radial error=137.829, avgs=0 230/300: dt: 0.9000, rms radial error=137.051, avgs=0 235/300: dt: 0.9000, rms radial error=136.278, avgs=0 240/300: dt: 0.9000, rms radial error=135.509, avgs=0 245/300: dt: 0.9000, rms radial error=134.745, avgs=0 250/300: dt: 0.9000, rms radial error=133.984, avgs=0 255/300: dt: 0.9000, rms radial error=133.228, avgs=0 260/300: dt: 0.9000, rms radial error=132.476, avgs=0 265/300: dt: 0.9000, rms radial error=131.729, avgs=0 270/300: dt: 0.9000, rms radial error=130.985, avgs=0 275/300: dt: 0.9000, rms radial error=130.246, avgs=0 280/300: dt: 0.9000, rms radial error=129.511, avgs=0 285/300: dt: 0.9000, rms radial error=128.780, avgs=0 290/300: dt: 0.9000, rms radial error=128.053, avgs=0 295/300: dt: 0.9000, rms radial error=127.330, avgs=0 300/300: dt: 0.9000, rms radial error=126.611, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 54445.66 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 = 11707.75 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00002 epoch 3 (K=160.0), pass 1, starting sse = 2123.50 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/10 = 0.00121 epoch 4 (K=640.0), pass 1, starting sse = 393.52 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/10 = 0.00563 final distance error %33.90 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.10 hours mris_sphere utimesec 839.244793 mris_sphere stimesec 17.410281 mris_sphere ru_maxrss 645624 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 14579457 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 29440 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 253184 mris_sphere ru_nivcsw 969 FSRUNTIME@ mris_sphere 0.1041 hours 1 threads PIDs (8445 8448) completed and logs appended. #-------------------------------------------- #@# Fix Topology Copy lh Wed Feb 20 19:49:57 EST 2019 /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Wed Feb 20 19:50:00 EST 2019 /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Wed Feb 20 19:50:03 EST 2019 mris_fix_topology -rusage /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 inul_loom2_7T lh #@# Fix Topology rh Wed Feb 20 19:50:03 EST 2019 mris_fix_topology -rusage /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 inul_loom2_7T rh Waiting for PID 8994 of (8994 8997) to complete...