Hello FreeSurfer Developers, I'm attempting to run recon-all after unpacking data. It is exiting with errors - mri_cc: no WM voxels found with norm > 40 -- check skull stripping I've attached the recon-all.log in case it's of any use.
1) FreeSurfer version: freesurfer-Linux-centos7_x86_64-stable-v6-20161229-80ac5eb 2) Platform: centos7_x86_64 3) uname -a: Linux lemmiwinks.nmr.mgh.harvard.edu 3.10.0-1062.4.3.el7.x86_64 #1 SMP Wed Nov 13 23:58:53 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached Thank you!
Mon Jan 13 10:46:26 EST 2020 /autofs/cluster/animal/scan_data/sleep_eeg/SLEEP_TTRA_M_89/recons/FS6 /usr/local/freesurfer/stable6/bin/recon-all -s FS6 -i raw/MPRAGE/004/mprage.mgz -all subjid FS6 setenv SUBJECTS_DIR /autofs/cluster/animal/scan_data/sleep_eeg/SLEEP_TTRA_M_89/recons 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 lemmiwinks.nmr.mgh.harvard.edu 3.10.0-1062.4.3.el7.x86_64 #1 SMP Wed Nov 13 23:58:53 UTC 2019 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 240728 maxlocks unlimited maxsignal 240728 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 61668864 1925908 53876912 309808 5866044 58918992 Swap: 25165820 0 25165820 ######################################## 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: 2020/01/13-15:46:26-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: td744 Machine: lemmiwinks.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.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: 2020/01/13-15:46:26-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: td744 Machine: lemmiwinks.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.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: 2020/01/13-15:46:26-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: td744 Machine: lemmiwinks.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/01/13-15:46:26-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: td744 Machine: lemmiwinks.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/01/13-15:46:26-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: td744 Machine: lemmiwinks.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/01/13-15:46:26-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: td744 Machine: lemmiwinks.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/01/13-15:46:26-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: td744 Machine: lemmiwinks.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/01/13-15:46:26-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: td744 Machine: lemmiwinks.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/01/13-15:46:27-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: td744 Machine: lemmiwinks.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/01/13-15:46:27-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: td744 Machine: lemmiwinks.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/01/13-15:46:27-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: td744 Machine: lemmiwinks.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/01/13-15:46:27-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: td744 Machine: lemmiwinks.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/01/13-15:46:27-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: td744 Machine: lemmiwinks.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/01/13-15:46:27-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: td744 Machine: lemmiwinks.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/01/13-15:46:27-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: td744 Machine: lemmiwinks.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/01/13-15:46:27-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: td744 Machine: lemmiwinks.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/01/13-15:46:27-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: td744 Machine: lemmiwinks.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/01/13-15:46:27-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: td744 Machine: lemmiwinks.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/01/13-15:46:27-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: td744 Machine: lemmiwinks.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/01/13-15:46:27-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: td744 Machine: lemmiwinks.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/01/13-15:46:27-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: td744 Machine: lemmiwinks.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/01/13-15:46:27-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: td744 Machine: lemmiwinks.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/01/13-15:46:27-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: td744 Machine: lemmiwinks.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/01/13-15:46:27-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: td744 Machine: lemmiwinks.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/01/13-15:46:28-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: td744 Machine: lemmiwinks.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/01/13-15:46:28-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: td744 Machine: lemmiwinks.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/01/13-15:46:28-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: td744 Machine: lemmiwinks.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2020/01/13-15:46:28-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: td744 Machine: lemmiwinks.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/01/13-15:46:28-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: td744 Machine: lemmiwinks.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/01/13-15:46:28-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: td744 Machine: lemmiwinks.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/01/13-15:46:28-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: td744 Machine: lemmiwinks.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/01/13-15:46:28-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: td744 Machine: lemmiwinks.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.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: 2020/01/13-15:46:28-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: td744 Machine: lemmiwinks.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.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: 2020/01/13-15:46:28-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: td744 Machine: lemmiwinks.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/01/13-15:46:28-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: td744 Machine: lemmiwinks.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/01/13-15:46:28-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: td744 Machine: lemmiwinks.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/01/13-15:46:28-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: td744 Machine: lemmiwinks.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/01/13-15:46:28-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: td744 Machine: lemmiwinks.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/01/13-15:46:28-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: td744 Machine: lemmiwinks.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-1062.4.3.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/cluster/animal/scan_data/sleep_eeg/SLEEP_TTRA_M_89/recons/FS6 mri_convert /autofs/cluster/animal/scan_data/sleep_eeg/SLEEP_TTRA_M_89/raw/MPRAGE/004/mprage.mgz /autofs/cluster/animal/scan_data/sleep_eeg/SLEEP_TTRA_M_89/recons/FS6/mri/orig/001.mgz mri_convert.bin /autofs/cluster/animal/scan_data/sleep_eeg/SLEEP_TTRA_M_89/raw/MPRAGE/004/mprage.mgz /autofs/cluster/animal/scan_data/sleep_eeg/SLEEP_TTRA_M_89/recons/FS6/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/cluster/animal/scan_data/sleep_eeg/SLEEP_TTRA_M_89/raw/MPRAGE/004/mprage.mgz... TR=2300.00, TE=2.96, TI=900.00, flip angle=9.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (-1, -0, 0) writing to /autofs/cluster/animal/scan_data/sleep_eeg/SLEEP_TTRA_M_89/recons/FS6/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Mon Jan 13 10:46:32 EST 2020 Found 1 runs /autofs/cluster/animal/scan_data/sleep_eeg/SLEEP_TTRA_M_89/recons/FS6/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/cluster/animal/scan_data/sleep_eeg/SLEEP_TTRA_M_89/recons/FS6/mri/orig/001.mgz /autofs/cluster/animal/scan_data/sleep_eeg/SLEEP_TTRA_M_89/recons/FS6/mri/rawavg.mgz /autofs/cluster/animal/scan_data/sleep_eeg/SLEEP_TTRA_M_89/recons/FS6 mri_convert /autofs/cluster/animal/scan_data/sleep_eeg/SLEEP_TTRA_M_89/recons/FS6/mri/rawavg.mgz /autofs/cluster/animal/scan_data/sleep_eeg/SLEEP_TTRA_M_89/recons/FS6/mri/orig.mgz --conform mri_convert.bin /autofs/cluster/animal/scan_data/sleep_eeg/SLEEP_TTRA_M_89/recons/FS6/mri/rawavg.mgz /autofs/cluster/animal/scan_data/sleep_eeg/SLEEP_TTRA_M_89/recons/FS6/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/cluster/animal/scan_data/sleep_eeg/SLEEP_TTRA_M_89/recons/FS6/mri/rawavg.mgz... TR=2300.00, TE=2.96, TI=900.00, flip angle=9.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (-1, -0, 0) changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /autofs/cluster/animal/scan_data/sleep_eeg/SLEEP_TTRA_M_89/recons/FS6/mri/orig.mgz... mri_add_xform_to_header -c /autofs/cluster/animal/scan_data/sleep_eeg/SLEEP_TTRA_M_89/recons/FS6/mri/transforms/talairach.xfm /autofs/cluster/animal/scan_data/sleep_eeg/SLEEP_TTRA_M_89/recons/FS6/mri/orig.mgz /autofs/cluster/animal/scan_data/sleep_eeg/SLEEP_TTRA_M_89/recons/FS6/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Mon Jan 13 10:46:44 EST 2020 /autofs/cluster/animal/scan_data/sleep_eeg/SLEEP_TTRA_M_89/recons/FS6/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /autofs/cluster/animal/scan_data/sleep_eeg/SLEEP_TTRA_M_89/recons/FS6/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 lemmiwinks.nmr.mgh.harvard.edu 3.10.0-1062.4.3.el7.x86_64 #1 SMP Wed Nov 13 23:58:53 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux Mon Jan 13 10:46:44 EST 2020 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.18442 /autofs/cluster/animal/scan_data/sleep_eeg/SLEEP_TTRA_M_89/recons/FS6/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.18442/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.18442/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=2300.00, TE=2.96, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.18442/nu0.mnc... -------------------------------------------------------- Iteration 1 Mon Jan 13 10:46:47 EST 2020 nu_correct -clobber ./tmp.mri_nu_correct.mni.18442/nu0.mnc ./tmp.mri_nu_correct.mni.18442/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.18442/0/ -iterations 1000 -distance 50 [td...@lemmiwinks.nmr.mgh.harvard.edu:/autofs/cluster/animal/scan_data/sleep_eeg/SLEEP_TTRA_M_89/recons/FS6/mri/] [2020-01-13 10:46:47] 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.18442/0/ ./tmp.mri_nu_correct.mni.18442/nu0.mnc ./tmp.mri_nu_correct.mni.18442/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 44 CV of field change: 0.000992581 mri_convert ./tmp.mri_nu_correct.mni.18442/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.18442/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.18442/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz... Mon Jan 13 10:48:10 EST 2020 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at Mon Jan 13 10:48:10 EST 2020 Ended at Mon Jan 13 10:48:50 EST 2020 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Mon Jan 13 10:48:52 EST 2020 /autofs/cluster/animal/scan_data/sleep_eeg/SLEEP_TTRA_M_89/recons/FS6/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7698, pval=0.6675 >= threshold=0.0050) awk -f /usr/local/freesurfer/stable6/bin/extract_talairach_avi_QA.awk /autofs/cluster/animal/scan_data/sleep_eeg/SLEEP_TTRA_M_89/recons/FS6/mri/transforms/talairach_avi.log tal_QC_AZS /autofs/cluster/animal/scan_data/sleep_eeg/SLEEP_TTRA_M_89/recons/FS6/mri/transforms/talairach_avi.log TalAviQA: 0.97889 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Mon Jan 13 10:48:52 EST 2020 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /autofs/cluster/animal/scan_data/sleep_eeg/SLEEP_TTRA_M_89/recons/FS6/mri /usr/local/freesurfer/stable6/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux lemmiwinks.nmr.mgh.harvard.edu 3.10.0-1062.4.3.el7.x86_64 #1 SMP Wed Nov 13 23:58:53 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux Mon Jan 13 10:48:52 EST 2020 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.19352 /autofs/cluster/animal/scan_data/sleep_eeg/SLEEP_TTRA_M_89/recons/FS6/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.19352/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.19352/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=2300.00, TE=2.96, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.19352/nu0.mnc... -------------------------------------------------------- Iteration 1 Mon Jan 13 10:48:55 EST 2020 nu_correct -clobber ./tmp.mri_nu_correct.mni.19352/nu0.mnc ./tmp.mri_nu_correct.mni.19352/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.19352/0/ [td...@lemmiwinks.nmr.mgh.harvard.edu:/autofs/cluster/animal/scan_data/sleep_eeg/SLEEP_TTRA_M_89/recons/FS6/mri/] [2020-01-13 10:48:55] running: /usr/local/freesurfer/stable6/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.19352/0/ ./tmp.mri_nu_correct.mni.19352/nu0.mnc ./tmp.mri_nu_correct.mni.19352/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 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./tmp.mri_nu_correct.mni.19352/nu1.mnc ./tmp.mri_nu_correct.mni.19352/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.19352/1/ [td...@lemmiwinks.nmr.mgh.harvard.edu:/autofs/cluster/animal/scan_data/sleep_eeg/SLEEP_TTRA_M_89/recons/FS6/mri/] [2020-01-13 10:49:57] 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.19352/1/ ./tmp.mri_nu_correct.mni.19352/nu1.mnc ./tmp.mri_nu_correct.mni.19352/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 19 CV of field change: 0.000982866 mri_binarize --i ./tmp.mri_nu_correct.mni.19352/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.19352/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /autofs/cluster/animal/scan_data/sleep_eeg/SLEEP_TTRA_M_89/recons/FS6/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.19352/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.19352/ones.mgz sysname Linux hostname lemmiwinks.nmr.mgh.harvard.edu machine x86_64 user td744 input ./tmp.mri_nu_correct.mni.19352/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.19352/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 16777216 values in range Counting number of voxels in first frame Found 16777216 voxels in final mask Count: 16777216 16777216.000000 16777216 100.000000 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.19352/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.19352/sum.junk --avgwf ./tmp.mri_nu_correct.mni.19352/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.19352/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.19352/sum.junk --avgwf ./tmp.mri_nu_correct.mni.19352/input.mean.dat sysname Linux hostname lemmiwinks.nmr.mgh.harvard.edu machine x86_64 user td744 UseRobust 0 Loading ./tmp.mri_nu_correct.mni.19352/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.19352/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.19352/ones.mgz --i ./tmp.mri_nu_correct.mni.19352/nu2.mnc --sum ./tmp.mri_nu_correct.mni.19352/sum.junk --avgwf ./tmp.mri_nu_correct.mni.19352/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.19352/ones.mgz --i ./tmp.mri_nu_correct.mni.19352/nu2.mnc --sum ./tmp.mri_nu_correct.mni.19352/sum.junk --avgwf ./tmp.mri_nu_correct.mni.19352/output.mean.dat sysname Linux hostname lemmiwinks.nmr.mgh.harvard.edu machine x86_64 user td744 UseRobust 0 Loading ./tmp.mri_nu_correct.mni.19352/ones.mgz Loading ./tmp.mri_nu_correct.mni.19352/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.19352/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.19352/nu2.mnc ./tmp.mri_nu_correct.mni.19352/nu2.mnc mul 1.00611939938923528661 Saving result to './tmp.mri_nu_correct.mni.19352/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.19352/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.19352/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.19352/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 11 seconds. mapping ( 8, 142) to ( 3, 110) Mon Jan 13 10:51:25 EST 2020 mri_nu_correct.mni done mri_add_xform_to_header -c /autofs/cluster/animal/scan_data/sleep_eeg/SLEEP_TTRA_M_89/recons/FS6/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Mon Jan 13 10:51:26 EST 2020 /autofs/cluster/animal/scan_data/sleep_eeg/SLEEP_TTRA_M_89/recons/FS6/mri mri_normalize -g 1 -mprage nu.mgz T1.mgz using max gradient = 1.000 assuming input volume is MGH (Van der Kouwe) MP-RAGE reading from nu.mgz... normalizing image... talairach transform 1.02774 0.06281 0.02630 -1.89609; -0.04769 1.08921 0.11363 -39.57262; -0.04738 -0.07843 1.17599 -12.67232; 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 = 19 Starting OpenSpline(): npoints = 19 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 105 gm peak at 66 (66), valley at 32 (32) csf peak at 33, setting threshold to 55 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 64 (64), valley at 31 (31) csf peak at 32, setting threshold to 53 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 56 seconds. #-------------------------------------------- #@# Skull Stripping Mon Jan 13 10:54:23 EST 2020 /autofs/cluster/animal/scan_data/sleep_eeg/SLEEP_TTRA_M_89/recons/FS6/mri mri_em_register -rusage /autofs/cluster/animal/scan_data/sleep_eeg/SLEEP_TTRA_M_89/recons/FS6/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 = 1 == reading 1 input volumes... logging results to talairach_with_skull.log reading '/usr/local/freesurfer/stable6/average/RB_all_withskull_2016-05-10.vc700.gca'... average std = 22.9 using min determinant for regularization = 52.6 0 singular and 9002 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 8.7 or > 569.1 total sample mean = 77.6 (1399 zeros) ************************************************ spacing=8, using 3243 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3243, passno 0, spacing 8 resetting wm mean[0]: 100 --> 108 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=5.0 skull bounding box = (43, 101, 26) --> (211, 255, 220) using (99, 152, 123) as brain centroid... mean wm in atlas = 108, using box (78,133,99) --> (119, 170,146) to find MRI wm before smoothing, mri peak at 102 robust fit to distribution - 102 +- 7.3 after smoothing, mri peak at 102, scaling input intensities by 1.059 scaling channel 0 by 1.05882 initial log_p = -5.037 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.580850 @ (-9.091, -45.455, -9.091) max log p = -4.419268 @ (4.545, -4.545, -4.545) max log p = -4.362124 @ (2.273, -2.273, -2.273) max log p = -4.348638 @ (1.136, -1.136, 1.136) max log p = -4.313070 @ (-0.568, 0.568, -0.568) max log p = -4.313070 @ (0.000, 0.000, 0.000) Found translation: (-1.7, -52.8, -15.3): log p = -4.313 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.988, old_max_log_p =-4.313 (thresh=-4.3) 1.06375 0.00000 0.00000 -9.77401; 0.00000 1.22567 0.16136 -117.22506; 0.00000 -0.15011 1.14016 3.73448; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.939, old_max_log_p =-3.988 (thresh=-4.0) 1.05465 0.15998 0.02106 -42.48047; -0.14926 1.30633 0.17198 -115.40096; 0.00000 -0.13885 1.05465 11.77363; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.939, old_max_log_p =-3.939 (thresh=-3.9) 1.05465 0.15998 0.02106 -42.48047; -0.14926 1.30633 0.17198 -115.40096; 0.00000 -0.13885 1.05465 11.77363; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.839, old_max_log_p =-3.939 (thresh=-3.9) 1.02439 0.02700 -0.01488 -10.17288; -0.04058 1.27359 0.06423 -111.71187; 0.02002 0.00098 1.08592 -23.76962; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.828, old_max_log_p =-3.839 (thresh=-3.8) 1.02319 0.02696 -0.05040 -5.69355; -0.03982 1.24971 0.06303 -108.82650; 0.05353 0.00187 1.08485 -28.11615; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.828, old_max_log_p =-3.828 (thresh=-3.8) 1.02319 0.02696 -0.05040 -5.69355; -0.03982 1.24971 0.06303 -108.82650; 0.05353 0.00187 1.08485 -28.11615; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.809, old_max_log_p =-3.828 (thresh=-3.8) 1.02359 0.04746 -0.04942 -9.00207; -0.05636 1.24471 0.06362 -104.84605; 0.05353 0.00187 1.08485 -28.11615; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.795, old_max_log_p =-3.809 (thresh=-3.8) 1.02117 0.03688 -0.03223 -10.08512; -0.04716 1.24784 0.08129 -107.37074; 0.03769 -0.01927 1.08433 -21.37857; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 8 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.791, old_max_log_p =-3.795 (thresh=-3.8) 1.02117 0.03688 -0.03223 -10.08512; -0.04700 1.24345 0.08101 -106.49411; 0.03764 -0.01925 1.08306 -21.22353; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 9 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.788, old_max_log_p =-3.791 (thresh=-3.8) 1.02117 0.03688 -0.03223 -10.08512; -0.04694 1.24199 0.08091 -106.20201; 0.03777 -0.01932 1.08687 -21.68846; 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 1.02117 0.03688 -0.03223 -10.08512; -0.04694 1.24199 0.08091 -106.20201; 0.03777 -0.01932 1.08687 -21.68846; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 1.02117 0.03688 -0.03223 -10.08512; -0.04694 1.24199 0.08091 -106.20201; 0.03777 -0.01932 1.08687 -21.68846; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 012: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.02117 0.03688 -0.03223 -10.08512; -0.04694 1.24199 0.08091 -106.20201; 0.03777 -0.01932 1.08687 -21.68846; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.788 (old=-5.037) transform before final EM align: 1.02117 0.03688 -0.03223 -10.08512; -0.04694 1.24199 0.08091 -106.20201; 0.03777 -0.01932 1.08687 -21.68846; 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 1.02117 0.03688 -0.03223 -10.08512; -0.04694 1.24199 0.08091 -106.20201; 0.03777 -0.01932 1.08687 -21.68846; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 1.02117 0.03688 -0.03223 -10.08512; -0.04694 1.24199 0.08091 -106.20201; 0.03777 -0.01932 1.08687 -21.68846; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 014: -log(p) = 4.2 tol 0.000000 final transform: 1.02117 0.03688 -0.03223 -10.08512; -0.04694 1.24199 0.08091 -106.20201; 0.03777 -0.01932 1.08687 -21.68846; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 1591.459167 mri_em_register stimesec 3.195054 mri_em_register ru_maxrss 609860 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 157380 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 67 mri_em_register ru_nivcsw 5473 registration took 26 minutes and 35 seconds. mri_watershed -rusage /autofs/cluster/animal/scan_data/sleep_eeg/SLEEP_TTRA_M_89/recons/FS6/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 Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=127 y=170 z=120 r=71 first estimation of the main basin volume: 1544218 voxels Looking for seedpoints 2 found in the cerebellum 15 found in the rest of the brain global maximum in x=149, y=166, z=87, Imax=255 CSF=16, 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=9346969007 voxels, voxel volume =1.000 = 9346969007 mmm3 = 9346968.576 cm3 done. PostAnalyze...Basin Prior 102 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=128,y=178, z=115, r=9459 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=28 , nb = 45540 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=24 , nb = 3150 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=23 , nb = 2916 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=24 , nb = 19764 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=28 , nb = 18936 OTHER CSF_MIN=0, CSF_intensity=7, CSF_MAX=44 , nb = 774 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 28, 32, 37, 59 after analyzing : 28, 35, 37, 41 RIGHT_CER before analyzing : 24, 36, 47, 64 after analyzing : 24, 43, 47, 48 LEFT_CER before analyzing : 23, 29, 37, 59 after analyzing : 23, 34, 37, 40 RIGHT_BRAIN before analyzing : 24, 29, 36, 60 after analyzing : 24, 33, 36, 39 LEFT_BRAIN before analyzing : 28, 32, 37, 59 after analyzing : 28, 35, 37, 41 OTHER before analyzing : 44, 81, 88, 95 after analyzing : 44, 85, 88, 87 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...68 iterations *********************VALIDATION********************* curvature mean = -0.014, std = 0.012 curvature mean = 67.614, std = 7.710 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 5.17, sigma = 7.43 after rotation: sse = 5.17, sigma = 7.43 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 5.56, its var is 6.74 before Erosion-Dilatation 1.78% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...50 iterations mri_strip_skull: done peeling brain Brain Size = 1546548 voxels, voxel volume = 1.000 mm3 = 1546548 mmm3 = 1546.548 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 28.086126 mri_watershed stimesec 0.430078 mri_watershed ru_maxrss 825240 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 211668 mri_watershed ru_majflt 1 mri_watershed ru_nswap 0 mri_watershed ru_inblock 9224 mri_watershed ru_oublock 2664 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 140 mri_watershed ru_nivcsw 18 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Mon Jan 13 11:21:28 EST 2020 /autofs/cluster/animal/scan_data/sleep_eeg/SLEEP_TTRA_M_89/recons/FS6/mri mri_em_register -rusage /autofs/cluster/animal/scan_data/sleep_eeg/SLEEP_TTRA_M_89/recons/FS6/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 = 1 == reading 1 input volumes... logging results to talairach.log reading '/usr/local/freesurfer/stable6/average/RB_all_2016-05-10.vc700.gca'... average std = 7.3 using min determinant for regularization = 5.3 0 singular and 841 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 6.3 or > 503.7 total sample mean = 78.8 (1011 zeros) ************************************************ spacing=8, using 2830 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2830, passno 0, spacing 8 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=20.9 skull bounding box = (57, 125, 42) --> (200, 235, 199) using (105, 162, 121) as brain centroid... mean wm in atlas = 107, using box (87,149,102) --> (122, 175,140) to find MRI wm before smoothing, mri peak at 104 robust fit to distribution - 103 +- 6.3 after smoothing, mri peak at 103, scaling input intensities by 1.039 scaling channel 0 by 1.03883 initial log_p = -4.726 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.242296 @ (-9.091, -45.455, -9.091) max log p = -4.053308 @ (4.545, -4.545, -4.545) max log p = -4.001093 @ (2.273, 2.273, 2.273) max log p = -3.931850 @ (1.136, -3.409, -1.136) max log p = -3.915412 @ (-0.568, 0.568, 0.568) max log p = -3.915412 @ (0.000, 0.000, 0.000) Found translation: (-1.7, -50.6, -11.9): log p = -3.915 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.744, old_max_log_p =-3.915 (thresh=-3.9) 0.99144 0.13053 0.00000 -22.77666; -0.14032 1.06580 0.00000 -51.22304; 0.00000 0.00000 1.06375 -19.41455; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.636, old_max_log_p =-3.744 (thresh=-3.7) 0.99562 -0.03168 -0.13766 21.52342; -0.02930 1.13967 -0.01676 -76.47118; 0.12941 0.01704 1.05465 -37.86182; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.636, old_max_log_p =-3.636 (thresh=-3.6) 0.99562 -0.03168 -0.13766 21.52342; -0.02930 1.13967 -0.01676 -76.47118; 0.12941 0.01704 1.05465 -37.86182; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.473, old_max_log_p =-3.636 (thresh=-3.6) 0.99869 0.03899 -0.06263 -2.28073; -0.08569 1.15711 0.09291 -88.92015; 0.06754 -0.09429 1.07780 -9.06441; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.473, old_max_log_p =-3.473 (thresh=-3.5) 0.99869 0.03899 -0.06263 -2.28073; -0.08569 1.15711 0.09291 -88.92015; 0.06754 -0.09429 1.07780 -9.06441; 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=-3.450, old_max_log_p =-3.473 (thresh=-3.5) 1.00125 0.03632 -0.03624 -4.20740; -0.08530 1.16037 0.10208 -90.59559; 0.04386 -0.10505 1.08201 -5.48932; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.450, old_max_log_p =-3.450 (thresh=-3.4) 1.00125 0.03632 -0.03624 -4.20740; -0.08530 1.16037 0.10208 -90.59559; 0.04386 -0.10505 1.08201 -5.48932; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2830 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.00125 0.03632 -0.03624 -4.20740; -0.08530 1.16037 0.10208 -90.59559; 0.04386 -0.10505 1.08201 -5.48932; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.00125 0.03632 -0.03624 -4.20740; -0.08530 1.16037 0.10208 -90.59559; 0.04386 -0.10505 1.08201 -5.48932; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.00125 0.03632 -0.03624 -4.20740; -0.08530 1.16037 0.10208 -90.59559; 0.04386 -0.10505 1.08201 -5.48932; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.450 (old=-4.726) transform before final EM align: 1.00125 0.03632 -0.03624 -4.20740; -0.08530 1.16037 0.10208 -90.59559; 0.04386 -0.10505 1.08201 -5.48932; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 315557 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.00125 0.03632 -0.03624 -4.20740; -0.08530 1.16037 0.10208 -90.59559; 0.04386 -0.10505 1.08201 -5.48932; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 1.00125 0.03632 -0.03624 -4.20740; -0.08530 1.16037 0.10208 -90.59559; 0.04386 -0.10505 1.08201 -5.48932; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 010: -log(p) = 8.1 after pass:transform: ( 0.99, 0.04, -0.12, -4.21) ( 0.46, 1.84, 0.54, -90.60) ( 0.09, 0.04, 1.18, -5.49) THE SEARCH DIRECTION IS NOT A DESCENT DIRECTION pass 2 through quasi-newton minimization... THE SEARCH DIRECTION IS NOT A DESCENT DIRECTION outof QuasiNewtonEMA: 012: -log(p) = 8.1 tol 0.000000 final transform: 0.98781 0.03541 -0.12316 -4.20740; 0.46473 1.84231 0.53944 -90.59559; 0.09368 0.04027 1.18099 -5.48932; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 962.264122 mri_em_register stimesec 2.355953 mri_em_register ru_maxrss 598988 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 159147 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 72 mri_em_register ru_nivcsw 1317 registration took 16 minutes and 5 seconds. #-------------------------------------- #@# CA Normalize Mon Jan 13 11:37:33 EST 2020 /autofs/cluster/animal/scan_data/sleep_eeg/SLEEP_TTRA_M_89/recons/FS6/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/stable6/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/usr/local/freesurfer/stable6/average/RB_all_2016-05-10.vc700.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=20.9 skull bounding box = (57, 125, 42) --> (200, 235, 199) using (105, 162, 121) as brain centroid... mean wm in atlas = 107, using box (87,149,102) --> (122, 175,140) to find MRI wm before smoothing, mri peak at 104 robust fit to distribution - 103 +- 6.3 after smoothing, mri peak at 103, scaling input intensities by 1.039 scaling channel 0 by 1.03883 using 246344 sample points... INFO: compute sample coordinates transform 0.98781 0.03541 -0.12316 -4.20740; 0.46473 1.84231 0.53944 -90.59559; 0.09368 0.04027 1.18099 -5.48932; 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 (131, 9, 12) --> (207, 91, 155) finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (73, 15, 15) --> (146, 94, 157) finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (136, 71, 30) --> (186, 96, 76) finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (90, 74, 30) --> (137, 106, 80) finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (123, 60, 59) --> (157, 104, 88) skipping region 1 with no control points detected finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (131, 9, 12) --> (207, 91, 155) finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (73, 15, 15) --> (146, 94, 157) finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (136, 71, 30) --> (186, 96, 76) finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (90, 74, 30) --> (137, 106, 80) finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (123, 60, 59) --> (157, 104, 88) skipping region 2 with no control points detected finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (131, 9, 12) --> (207, 91, 155) finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (73, 15, 15) --> (146, 94, 157) finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (136, 71, 30) --> (186, 96, 76) finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (90, 74, 30) --> (137, 106, 80) finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (123, 60, 59) --> (157, 104, 88) skipping region 3 with no control points detected writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 0 minutes and 30 seconds. #-------------------------------------- #@# CA Reg Mon Jan 13 11:38:03 EST 2020 /autofs/cluster/animal/scan_data/sleep_eeg/SLEEP_TTRA_M_89/recons/FS6/mri mri_ca_register -rusage /autofs/cluster/animal/scan_data/sleep_eeg/SLEEP_TTRA_M_89/recons/FS6/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 = 1 == 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) = 2.13 (predicted orig area = 3.8) 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=2.181, neg=0, invalid=762 0001: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0002: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0003: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0004: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0005: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0006: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0007: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0008: dt=0.000000, rms=2.177 (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=2.181, neg=0, invalid=762 0009: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0010: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0011: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0012: dt=0.000000, rms=2.177 (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=2.181, neg=0, invalid=762 0013: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0014: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0015: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0016: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0017: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0018: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0019: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0020: dt=0.000000, rms=2.177 (0.000%), 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=2.181, neg=0, invalid=762 0021: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0022: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0023: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0024: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.15565 (16) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.26829 (96) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.20183 (93) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.21683 (55) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.30730 (58) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.11430 (101) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.12076 (102) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.14995 (59) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.15082 (58) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.14161 (67) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.15243 (71) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13336 (57) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13252 (56) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.18181 (84) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.20573 (83) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.21969 (57) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.39313 (56) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.14181 (85) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.11978 (83) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13399 (79) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.14159 (79) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.10025 (80) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13281 (86) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.12801 (89) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.20494 (23) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.15061 (21) uniform distribution in MR - rejecting arbitrary fit gca peak Unknown = 0.94835 ( 0) gca peak Left_Cerebral_White_Matter = 0.12076 (102) gca peak Left_Cerebral_Cortex = 0.14995 (59) gca peak Left_Lateral_Ventricle = 0.10027 (20) gca peak Left_Inf_Lat_Vent = 0.18056 (32) gca peak Left_Cerebellum_White_Matter = 0.18181 (84) gca peak Left_Cerebellum_Cortex = 0.13336 (57) gca peak Left_Thalamus = 0.64095 (94) gca peak Left_Thalamus_Proper = 0.14181 (85) gca peak Left_Caudate = 0.15243 (71) gca peak Left_Putamen = 0.13399 (79) gca peak Left_Pallidum = 0.20183 (93) gca peak Third_Ventricle = 0.20494 (23) gca peak Fourth_Ventricle = 0.15061 (21) gca peak Brain_Stem = 0.10025 (80) gca peak Left_Hippocampus = 0.30730 (58) gca peak Left_Amygdala = 0.21969 (57) gca peak CSF = 0.20999 (34) gca peak Left_Accumbens_area = 0.39030 (62) gca peak Left_VentralDC = 0.12801 (89) 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_Cerebral_White_Matter = 0.11430 (101) gca peak Right_Cerebral_Cortex = 0.15082 (58) gca peak Right_Lateral_Ventricle = 0.15565 (16) gca peak Right_Inf_Lat_Vent = 0.23544 (26) gca peak Right_Cerebellum_White_Matter = 0.20573 (83) gca peak Right_Cerebellum_Cortex = 0.13252 (56) gca peak Right_Thalamus_Proper = 0.11978 (83) gca peak Right_Caudate = 0.14161 (67) gca peak Right_Putamen = 0.14159 (79) gca peak Right_Pallidum = 0.26829 (96) gca peak Right_Hippocampus = 0.21683 (55) gca peak Right_Amygdala = 0.39313 (56) gca peak Right_Accumbens_area = 0.30312 (64) gca peak Right_VentralDC = 0.13281 (86) gca peak Right_vessel = 0.46315 (51) gca peak Right_choroid_plexus = 0.14086 (44) gca peak Fifth_Ventricle = 0.51669 (36) gca peak WM_hypointensities = 0.09722 (76) gca peak non_WM_hypointensities = 0.11899 (47) gca peak Optic_Chiasm = 0.39033 (72) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.00 x + 0.0 setting left cbm cortex = 1.00 x + 0.00 setting right cbm cortex = 1.00 x + 0.00 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=2.181, neg=0, invalid=762 0025: dt=0.005645, rms=2.177 (0.184%), neg=0, invalid=762 0026: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 0027: dt=0.850000, rms=2.177 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0028: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0029: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 0030: dt=0.850000, rms=2.177 (-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=2.181, neg=0, invalid=762 0031: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0032: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 0033: dt=0.450000, rms=2.177 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0034: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0035: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 0036: dt=0.450000, rms=2.177 (-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=2.181, neg=0, invalid=762 0037: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0038: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 0039: dt=0.250000, rms=2.177 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0040: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0041: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 0042: dt=0.250000, rms=2.177 (-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=2.181, neg=0, invalid=762 0043: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0044: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 0045: dt=0.150000, rms=2.177 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0046: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0047: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 0048: dt=0.150000, rms=2.177 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0049: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0050: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 0051: dt=0.100000, rms=2.177 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0052: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0053: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 0054: dt=0.100000, rms=2.177 (-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=2.181, neg=0, invalid=762 0055: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0056: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 0057: dt=0.050000, rms=2.177 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0058: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0059: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 0060: dt=0.050000, rms=2.177 (-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=2.181, neg=0, invalid=762 0061: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0062: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0063: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0064: dt=0.000000, rms=2.177 (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=2.181, neg=0, invalid=762 0065: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0066: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0067: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0068: dt=0.000000, rms=2.177 (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=2.181, neg=0, invalid=762 0069: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0070: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0071: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0072: dt=0.000000, rms=2.177 (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=2.181, neg=0, invalid=762 0073: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0074: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0075: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0076: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0077: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0078: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0079: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0080: dt=0.000000, rms=2.177 (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=2.181, neg=0, invalid=762 0081: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0082: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0083: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762 0084: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0085: dt=4734.976000, rms=2.181 (0.000%), neg=0, invalid=762 0086: dt=4734.976000, rms=2.181 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0087: dt=0.000000, rms=2.181 (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=2.181, neg=0, invalid=762 0088: dt=0.000000, rms=2.181 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0089: dt=0.000000, rms=2.181 (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=2.181, neg=0, invalid=762 0090: dt=716.800000, rms=2.181 (0.000%), neg=0, invalid=762 0091: dt=716.800000, rms=2.181 (0.000%), neg=0, invalid=762 0092: dt=716.800000, rms=2.181 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0093: dt=0.000000, rms=2.181 (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=2.181, neg=0, invalid=762 0094: dt=46.080000, rms=2.181 (0.000%), neg=0, invalid=762 0095: dt=46.080000, rms=2.181 (0.000%), neg=0, invalid=762 0096: dt=46.080000, rms=2.181 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0097: dt=46.080000, rms=2.181 (0.000%), neg=0, invalid=762 0098: dt=46.080000, rms=2.181 (0.000%), neg=0, invalid=762 0099: dt=46.080000, rms=2.181 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0100: dt=5.120000, rms=2.181 (0.000%), neg=0, invalid=762 0101: dt=5.120000, rms=2.181 (0.000%), neg=0, invalid=762 0102: dt=5.120000, rms=2.181 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0103: dt=16.384000, rms=2.181 (0.000%), neg=0, invalid=762 0104: dt=16.384000, rms=2.181 (-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=2.181, neg=0, invalid=762 0105: dt=0.000000, rms=2.181 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.181, neg=0, invalid=762 0106: dt=0.000000, rms=2.181 (0.000%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 1 hours, 4 minutes and 53 seconds. mri_ca_register utimesec 3889.775684 mri_ca_register stimesec 2.460031 mri_ca_register ru_maxrss 1311848 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 1006615 mri_ca_register ru_majflt 0 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 232 mri_ca_register ru_oublock 58688 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 285 mri_ca_register ru_nivcsw 7962 FSRUNTIME@ mri_ca_register 1.0813 hours 1 threads #-------------------------------------- #@# SubCort Seg Mon Jan 13 12:42:56 EST 2020 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 lemmiwinks.nmr.mgh.harvard.edu machine x86_64 setenv SUBJECTS_DIR /autofs/cluster/animal/scan_data/sleep_eeg/SLEEP_TTRA_M_89/recons cd /autofs/cluster/animal/scan_data/sleep_eeg/SLEEP_TTRA_M_89/recons/FS6/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 = 1 == relabeling unlikely voxels with window_size = 9 and prior threshold 0.30 using Gibbs prior factor = 0.500 renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes reading classifier array from /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 3.76 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) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.17677 (13) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.28129 (95) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.16930 (96) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.24553 (55) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.30264 (59) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.07580 (103) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.07714 (104) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.09712 (58) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.11620 (58) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.30970 (66) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.15280 (69) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13902 (56) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.14777 (55) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.16765 (84) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.18739 (84) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.29869 (57) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.33601 (57) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.11131 (90) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.11793 (83) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.08324 (81) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.10360 (77) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.08424 (78) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.12631 (89) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.14500 (87) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.14975 (24) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.19357 (14) uniform distribution in MR - rejecting arbitrary fit gca peak Unknown = 0.94835 ( 0) gca peak Left_Cerebral_White_Matter = 0.07714 (104) gca peak Left_Cerebral_Cortex = 0.09712 (58) gca peak Left_Lateral_Ventricle = 0.16259 (20) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Cerebellum_White_Matter = 0.16765 (84) gca peak Left_Cerebellum_Cortex = 0.13902 (56) gca peak Left_Thalamus = 1.00000 (94) gca peak Left_Thalamus_Proper = 0.11131 (90) gca peak Left_Caudate = 0.15280 (69) gca peak Left_Putamen = 0.08324 (81) gca peak Left_Pallidum = 0.16930 (96) gca peak Third_Ventricle = 0.14975 (24) gca peak Fourth_Ventricle = 0.19357 (14) gca peak Brain_Stem = 0.08424 (78) gca peak Left_Hippocampus = 0.30264 (59) gca peak Left_Amygdala = 0.29869 (57) gca peak CSF = 0.23379 (36) gca peak Left_Accumbens_area = 0.70037 (62) gca peak Left_VentralDC = 0.14500 (87) 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_Cerebral_White_Matter = 0.07580 (103) gca peak Right_Cerebral_Cortex = 0.11620 (58) gca peak Right_Lateral_Ventricle = 0.17677 (13) gca peak Right_Inf_Lat_Vent = 0.24655 (23) gca peak Right_Cerebellum_White_Matter = 0.18739 (84) gca peak Right_Cerebellum_Cortex = 0.14777 (55) gca peak Right_Thalamus_Proper = 0.11793 (83) gca peak Right_Caudate = 0.30970 (66) gca peak Right_Putamen = 0.10360 (77) gca peak Right_Pallidum = 0.28129 (95) gca peak Right_Hippocampus = 0.24553 (55) gca peak Right_Amygdala = 0.33601 (57) gca peak Right_Accumbens_area = 0.45042 (65) gca peak Right_VentralDC = 0.12631 (89) 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 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.00 x + 0.0 setting left cbm cortex = 1.00 x + 0.00 setting right cbm cortex = 1.00 x + 0.00 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.16259 (20) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.17677 (13) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.28129 (95) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.16930 (96) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.24553 (55) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.30264 (59) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.07580 (103) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.07714 (104) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.09712 (58) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.11620 (58) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.30970 (66) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.15280 (69) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13902 (56) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.14777 (55) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.16765 (84) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.18739 (84) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.29869 (57) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.33601 (57) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.11131 (90) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.11793 (83) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.08324 (81) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.10360 (77) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.08424 (78) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.12631 (89) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.14500 (87) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.14975 (24) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.19357 (14) uniform distribution in MR - rejecting arbitrary fit gca peak Unknown = 0.94835 ( 0) gca peak Left_Cerebral_White_Matter = 0.07714 (104) gca peak Left_Cerebral_Cortex = 0.09712 (58) gca peak Left_Lateral_Ventricle = 0.16259 (20) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Cerebellum_White_Matter = 0.16765 (84) gca peak Left_Cerebellum_Cortex = 0.13902 (56) gca peak Left_Thalamus = 1.00000 (94) gca peak Left_Thalamus_Proper = 0.11131 (90) gca peak Left_Caudate = 0.15280 (69) gca peak Left_Putamen = 0.08324 (81) gca peak Left_Pallidum = 0.16930 (96) gca peak Third_Ventricle = 0.14975 (24) gca peak Fourth_Ventricle = 0.19357 (14) gca peak Brain_Stem = 0.08424 (78) gca peak Left_Hippocampus = 0.30264 (59) gca peak Left_Amygdala = 0.29869 (57) gca peak CSF = 0.23379 (36) gca peak Left_Accumbens_area = 0.70037 (62) gca peak Left_VentralDC = 0.14500 (87) 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_Cerebral_White_Matter = 0.07580 (103) gca peak Right_Cerebral_Cortex = 0.11620 (58) gca peak Right_Lateral_Ventricle = 0.17677 (13) gca peak Right_Inf_Lat_Vent = 0.24655 (23) gca peak Right_Cerebellum_White_Matter = 0.18739 (84) gca peak Right_Cerebellum_Cortex = 0.14777 (55) gca peak Right_Thalamus_Proper = 0.11793 (83) gca peak Right_Caudate = 0.30970 (66) gca peak Right_Putamen = 0.10360 (77) gca peak Right_Pallidum = 0.28129 (95) gca peak Right_Hippocampus = 0.24553 (55) gca peak Right_Amygdala = 0.33601 (57) gca peak Right_Accumbens_area = 0.45042 (65) gca peak Right_VentralDC = 0.12631 (89) 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 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.00 x + 0.0 setting left cbm cortex = 1.00 x + 0.00 setting right cbm cortex = 1.00 x + 0.00 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 9061 voxels changed in iteration 0 of unlikely voxel relabeling 0 voxels changed in iteration 1 of unlikely voxel relabeling 144 gm and wm labels changed (%100 to gray, % 0 to white out of all changed labels) 231 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 15130 changed. image ll: -9.672, PF=0.500 pass 2: 2561 changed. 6212 voxels changed in iteration 0 of unlikely voxel relabeling 7 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 3965 voxels changed in iteration 0 of unlikely voxel relabeling 42 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 2608 voxels changed in iteration 0 of unlikely voxel relabeling 12 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 5185 voxels changed in iteration 0 of unlikely voxel relabeling 13 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling MRItoUCHAR: min=0, max=80 MRItoUCHAR: converting to UCHAR writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 4079.121263 mri_ca_label stimesec 1.373296 mri_ca_label ru_maxrss 2097272 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 535303 mri_ca_label ru_majflt 1 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 1208 mri_ca_label ru_oublock 264 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 228 mri_ca_label ru_nivcsw 8517 auto-labeling took 68 minutes and 1 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /autofs/cluster/animal/scan_data/sleep_eeg/SLEEP_TTRA_M_89/recons/FS6/mri/transforms/cc_up.lta FS6 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /autofs/cluster/animal/scan_data/sleep_eeg/SLEEP_TTRA_M_89/recons/FS6/mri/transforms/cc_up.lta reading aseg from /autofs/cluster/animal/scan_data/sleep_eeg/SLEEP_TTRA_M_89/recons/FS6/mri/aseg.auto_noCCseg.mgz reading norm from /autofs/cluster/animal/scan_data/sleep_eeg/SLEEP_TTRA_M_89/recons/FS6/mri/norm.mgz 3392 voxels in left wm, 15737 in right wm, xrange [132, 149] searching rotation angles z=[-10 4], y=[-13 1] searching scale 1 Z rot -10.3 searching scale 1 Z rot -10.1 searching scale 1 Z rot -9.8 searching scale 1 Z rot -9.6 searching scale 1 Z rot -9.3 searching scale 1 Z rot -9.1 searching scale 1 Z rot -8.8 searching scale 1 Z rot -8.6 searching scale 1 Z rot -8.3 searching scale 1 Z rot -8.1 searching scale 1 Z rot -7.8 searching scale 1 Z rot -7.6 searching scale 1 Z rot -7.3 searching scale 1 Z rot -7.1 searching scale 1 Z rot -6.8 searching scale 1 Z rot -6.6 searching scale 1 Z rot -6.3 searching scale 1 Z rot -6.1 searching scale 1 Z rot -5.8 searching scale 1 Z rot -5.6 searching scale 1 Z rot -5.3 searching scale 1 Z rot -5.1 searching scale 1 Z rot -4.8 searching scale 1 Z rot -4.6 searching scale 1 Z rot -4.3 searching scale 1 Z rot -4.1 searching scale 1 Z rot -3.8 searching scale 1 Z rot -3.6 searching scale 1 Z rot -3.3 searching scale 1 Z rot -3.1 searching scale 1 Z rot -2.8 searching scale 1 Z rot -2.6 searching scale 1 Z rot -2.3 searching scale 1 Z rot -2.1 global minimum found at slice 141.0, rotations (-7.05, -8.83) final transformation (x=141.0, yr=-7.050, zr=-8.832): 0.98067 0.15354 -0.12129 -8.55582; -0.15238 0.98814 0.01885 96.59499; 0.12274 0.00000 0.99244 31.29823; 0.00000 0.00000 0.00000 1.00000; mri_cc: no WM voxels found with norm > 40 -- check skull stripping Linux lemmiwinks.nmr.mgh.harvard.edu 3.10.0-1062.4.3.el7.x86_64 #1 SMP Wed Nov 13 23:58:53 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s FS6 exited with ERRORS at Mon Jan 13 13:51:23 EST 2020 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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