External Email - Use Caution
I am trying to debug why all of our T1's are failing Freesurfer recon-all. It seems that most of the files are being created but it isn't getting to the stats steps to output those files. In the recon-all log it does say "recon-all -s 13265 exited with ERRORS."
I looked in the recon-all.error file and the only thing in that is "CMD mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix." Would this be the step where the error is happening?
I have checked the T1 thoroughly and it is good quality. What is the best way to debug why this is happening with our scans?
Hi Courtney
Can you send us the recon-all.log file and the full screen output from one job that failed?
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Courtney Haswell Sent: Thursday, December 3, 2020 9:52 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] recon-all issues debugging
External Email - Use Caution I am trying to debug why all of our T1's are failing Freesurfer recon-all. It seems that most of the files are being created but it isn't getting to the stats steps to output those files. In the recon-all log it does say "recon-all -s 13265 exited with ERRORS."
I looked in the recon-all.error file and the only thing in that is "CMD mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix." Would this be the step where the error is happening?
I have checked the T1 thoroughly and it is good quality. What is the best way to debug why this is happening with our scans?
External Email - Use Caution
I attached the recon-all.log file. I'm not sure what you mean by the full screen output. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Fischl, Bruce BFISCHL@mgh.harvard.edu Sent: Thursday, December 3, 2020 11:56 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all issues debugging
Hi Courtney
Can you send us the recon-all.log file and the full screen output from one job that failed?
Cheers
Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Courtney Haswell Sent: Thursday, December 3, 2020 9:52 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] recon-all issues debugging
External Email - Use Caution
I am trying to debug why all of our T1's are failing Freesurfer recon-all. It seems that most of the files are being created but it isn't getting to the stats steps to output those files. In the recon-all log it does say "recon-all -s 13265 exited with ERRORS."
I looked in the recon-all.error file and the only thing in that is "CMD mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix." Would this be the step where the error is happening?
I have checked the T1 thoroughly and it is good quality. What is the best way to debug why this is happening with our scans?
External Email - Use Caution
I could not attach but this is the log for recon-all.
Fri Nov 13 13:23:03 EST 2020 /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265 /usr/local/packages/freesurfer_v6.0.0/bin/recon-all -subjid 13265 -i /mnt/munin/Morey/Lab/T1Duke/T1s/13265.nii.gz -all subjid 13265 setenv SUBJECTS_DIR /mnt/munin/Morey/Lab/T1Duke/Freesurfer FREESURFER_HOME /usr/local/packages/freesurfer_v6.0.0 Actual FREESURFER_HOME /usr/local/packages/freesurfer_v6.0.0 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-4cfbf2a #freesurfer-Linux-centos6_x86_64-stable-v6-beta-20161028-4cfbf2a Linux blade21.dhe.duke.edu 3.10.0-1160.2.2.el7.x86_64 #1 SMP Mon Oct 19 10:20:12 CDT 2020 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize unlimited memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 1024 maxlocks unlimited maxsignal 514553 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited
total used free shared buff/cache available Mem: 131771700 11355116 105128156 220060 15288428 119570388 Swap: 0 0 0
######################################## program versions used $Id: recon-all,v 1.580.2.13 2016/10/18 14:39:30 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: 2020/11/13-18:23:03-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:03-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:03-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/11/13-18:23:03-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mri_normalize.c,v 1.88.2.1 2016/07/29 22:20:35 zkaufman Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:03-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:03-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/11/13-18:23:04-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/11/13-18:23:04-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mri_label2label.c,v 1.48.2.1 2016/08/02 20:14:55 zkaufman Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/11/13-18:23:04-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/11/13-18:23:04-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/11/13-18:23:04-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/11/13-18:23:04-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:04-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:04-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/11/13-18:23:04-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:04-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:04-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:04-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:04-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:04-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:04-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/11/13-18:23:04-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:04-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:04-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:04-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:04-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mris_make_surfaces.c,v 1.164 2016/05/13 18:03:58 fischl Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:05-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:05-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mris_volmask.cpp,v 1.26 2014/11/06 03:40:22 nicks Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:05-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:05-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:05-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:05-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $
ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:05-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $
ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:05-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:05-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:05-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:05-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:05-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:05-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/packages/freesurfer_v6.0.0/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/packages/freesurfer_v6.0.0/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265
mri_convert /mnt/munin/Morey/Lab/T1Duke/T1s/13265.nii.gz /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri/orig/001.mgz
mri_convert.bin /mnt/munin/Morey/Lab/T1Duke/T1s/13265.nii.gz /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /mnt/munin/Morey/Lab/T1Duke/T1s/13265.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Fri Nov 13 13:23:08 EST 2020 Found 1 runs /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/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 /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri/orig/001.mgz /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri/rawavg.mgz
/mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265
mri_convert /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri/rawavg.mgz /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri/orig.mgz --conform
mri_convert.bin /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri/rawavg.mgz /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri/orig.mgz...
mri_add_xform_to_header -c /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri/transforms/talairach.xfm /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri/orig.mgz /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri/orig.mgz
INFO: extension is mgz #-------------------------------------------- #@# Talairach Fri Nov 13 13:23:18 EST 2020 /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri
mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
/mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri /usr/local/packages/freesurfer_v6.0.0/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 blade21.dhe.duke.edu 3.10.0-1160.2.2.el7.x86_64 #1 SMP Mon Oct 19 10:20:12 CDT 2020 x86_64 x86_64 x86_64 GNU/Linux Fri Nov 13 13:23:18 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 /bin/bc tmpdir is ./tmp.mri_nu_correct.mni.10582 /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.10582/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.10582/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.10582/nu0.mnc...
-------------------------------------------------------- Iteration 1 Fri Nov 13 13:23:21 EST 2020 nu_correct -clobber ./tmp.mri_nu_correct.mni.10582/nu0.mnc ./tmp.mri_nu_correct.mni.10582/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.10582/0/ -iterations 1000 -distance 50 [ch186@blade21.dhe.duke.edu:/mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri/] [2020-11-13 13:23:21] running: /usr/local/packages/freesurfer_v6.0.0/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.10582/0/ ./tmp.mri_nu_correct.mni.10582/nu0.mnc ./tmp.mri_nu_correct.mni.10582/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 Number of iterations: 35 CV of field change: 0.000973337
mri_convert ./tmp.mri_nu_correct.mni.10582/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.10582/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.10582/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...
Fri Nov 13 13:24:34 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 Fri Nov 13 13:24:35 EST 2020 Ended at Fri Nov 13 13:24:59 EST 2020 talairach_avi done
cp transforms/talairach.auto.xfm transforms/talairach.xfm
#-------------------------------------------- #@# Talairach Failure Detection Fri Nov 13 13:25:01 EST 2020 /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7962, pval=0.8469 >= threshold=0.0050)
awk -f /usr/local/packages/freesurfer_v6.0.0/bin/extract_talairach_avi_QA.awk /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri/transforms/talairach_avi.log
tal_QC_AZS /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri/transforms/talairach_avi.log
TalAviQA: 0.97951 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Fri Nov 13 13:25:01 EST 2020
mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2
/mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri /usr/local/packages/freesurfer_v6.0.0/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 blade21.dhe.duke.edu 3.10.0-1160.2.2.el7.x86_64 #1 SMP Mon Oct 19 10:20:12 CDT 2020 x86_64 x86_64 x86_64 GNU/Linux Fri Nov 13 13:25:01 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 /bin/bc tmpdir is ./tmp.mri_nu_correct.mni.11553 /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.11553/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.11553/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.11553/nu0.mnc...
-------------------------------------------------------- Iteration 1 Fri Nov 13 13:25:04 EST 2020 nu_correct -clobber ./tmp.mri_nu_correct.mni.11553/nu0.mnc ./tmp.mri_nu_correct.mni.11553/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.11553/0/ [ch186@blade21.dhe.duke.edu:/mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri/] [2020-11-13 13:25:05] running: /usr/local/packages/freesurfer_v6.0.0/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.11553/0/ ./tmp.mri_nu_correct.mni.11553/nu0.mnc ./tmp.mri_nu_correct.mni.11553/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 Number of iterations: 28 CV of field change: 0.000986668
-------------------------------------------------------- Iteration 2 Fri Nov 13 13:25:57 EST 2020 nu_correct -clobber ./tmp.mri_nu_correct.mni.11553/nu1.mnc ./tmp.mri_nu_correct.mni.11553/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.11553/1/ [ch186@blade21.dhe.duke.edu:/mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri/] [2020-11-13 13:25:57] running: /usr/local/packages/freesurfer_v6.0.0/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.11553/1/ ./tmp.mri_nu_correct.mni.11553/nu1.mnc ./tmp.mri_nu_correct.mni.11553/nu2.imp
Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 20 CV of field change: 0.000971098
mri_binarize --i ./tmp.mri_nu_correct.mni.11553/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.11553/ones.mgz
$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.11553/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.11553/ones.mgz sysname Linux hostname blade21.dhe.duke.edu machine x86_64 user ch186
input ./tmp.mri_nu_correct.mni.11553/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.11553/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.11553/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.11553/sum.junk --avgwf ./tmp.mri_nu_correct.mni.11553/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.11553/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.11553/sum.junk --avgwf ./tmp.mri_nu_correct.mni.11553/input.mean.dat sysname Linux hostname blade21.dhe.duke.edu machine x86_64 user ch186 UseRobust 0 Loading ./tmp.mri_nu_correct.mni.11553/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.11553/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.11553/ones.mgz --i ./tmp.mri_nu_correct.mni.11553/nu2.mnc --sum ./tmp.mri_nu_correct.mni.11553/sum.junk --avgwf ./tmp.mri_nu_correct.mni.11553/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.11553/ones.mgz --i ./tmp.mri_nu_correct.mni.11553/nu2.mnc --sum ./tmp.mri_nu_correct.mni.11553/sum.junk --avgwf ./tmp.mri_nu_correct.mni.11553/output.mean.dat sysname Linux hostname blade21.dhe.duke.edu machine x86_64 user ch186 UseRobust 0 Loading ./tmp.mri_nu_correct.mni.11553/ones.mgz Loading ./tmp.mri_nu_correct.mni.11553/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.11553/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.11553/nu2.mnc ./tmp.mri_nu_correct.mni.11553/nu2.mnc mul 1.03361326205155151317 Saving result to './tmp.mri_nu_correct.mni.11553/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.11553/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.11553/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.11553/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 6 seconds. mapping (15, 94) to ( 3, 110)
Fri Nov 13 13:27:15 EST 2020 mri_nu_correct.mni done
mri_add_xform_to_header -c /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri/transforms/talairach.xfm nu.mgz nu.mgz
INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Fri Nov 13 13:27:16 EST 2020 /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/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 1.04893 0.01526 -0.00374 1.45294; -0.04316 1.00886 0.18821 -51.03661; -0.01136 -0.16057 1.13393 -0.98010; 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 109 gm peak at 66 (66), valley at 34 (34) 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 67 (67), valley at 32 (32) csf peak at 34, setting threshold to 56 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 30 seconds. #-------------------------------------------- #@# Skull Stripping Fri Nov 13 13:28:46 EST 2020 /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri
mri_em_register -rusage /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /usr/local/packages/freesurfer_v6.0.0/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/packages/freesurfer_v6.0.0/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=14.0 skull bounding box = (43, 52, 20) --> (215, 205, 233) using (100, 103, 127) as brain centroid... mean wm in atlas = 108, using box (79,84,101) --> (121, 121,153) to find MRI wm before smoothing, mri peak at 99 robust fit to distribution - 99 +- 7.9 after smoothing, mri peak at 99, scaling input intensities by 1.091 scaling channel 0 by 1.09091 initial log_p = -4.587 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.579605 @ (-9.091, -9.091, -9.091) max log p = -4.428650 @ (4.545, -4.545, -4.545) max log p = -4.397101 @ (2.273, 2.273, 2.273) max log p = -4.382682 @ (-1.136, 1.136, -1.136) max log p = -4.363797 @ (0.568, 0.568, -1.705) max log p = -4.363797 @ (0.000, 0.000, 0.000) Found translation: (-2.8, -9.7, -14.2): log p = -4.364 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.216, old_max_log_p =-4.364 (thresh=-4.4) 1.00000 0.00000 0.00000 -2.84091; 0.00000 1.15000 0.00000 -32.43408; 0.00000 0.00000 1.00000 -14.20455; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.216, old_max_log_p =-4.216 (thresh=-4.2) 1.00000 0.00000 0.00000 -2.84091; 0.00000 1.15000 0.00000 -32.43408; 0.00000 0.00000 1.00000 -14.20455; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.129, old_max_log_p =-4.216 (thresh=-4.2) 1.03686 0.00528 -0.03487 -3.98750; 0.00000 1.20510 0.13796 -54.24200; 0.03149 -0.15004 0.99099 5.68060; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.129, old_max_log_p =-4.129 (thresh=-4.1) 1.03686 0.00528 -0.03487 -3.98750; 0.00000 1.20510 0.13796 -54.24200; 0.03149 -0.15004 0.99099 5.68060; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.108, old_max_log_p =-4.129 (thresh=-4.1) 1.03533 0.04326 -0.02167 -11.08516; -0.03334 1.20174 0.16292 -52.12689; 0.02321 -0.17869 0.98412 11.38717; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.103, old_max_log_p =-4.108 (thresh=-4.1) 1.03533 0.04326 -0.02167 -11.08516; -0.03353 1.20315 0.15489 -50.83923; 0.02286 -0.16824 0.98196 10.15241; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.103, old_max_log_p =-4.103 (thresh=-4.1) 1.03533 0.04326 -0.02167 -11.08516; -0.03353 1.20315 0.15489 -50.83923; 0.02286 -0.16824 0.98196 10.15241; 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 1.03533 0.04326 -0.02167 -11.08516; -0.03353 1.20315 0.15489 -50.83923; 0.02286 -0.16824 0.98196 10.15241; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 1.03533 0.04326 -0.02167 -11.08516; -0.03353 1.20315 0.15489 -50.83923; 0.02286 -0.16824 0.98196 10.15241; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.03533 0.04326 -0.02167 -11.08516; -0.03353 1.20315 0.15489 -50.83923; 0.02286 -0.16824 0.98196 10.15241; 0.00000 0.00000 0.00000 1.00000;
pass 1, spacing 8: log(p) = -4.103 (old=-4.587) transform before final EM align: 1.03533 0.04326 -0.02167 -11.08516; -0.03353 1.20315 0.15489 -50.83923; 0.02286 -0.16824 0.98196 10.15241; 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 1.03533 0.04326 -0.02167 -11.08516; -0.03353 1.20315 0.15489 -50.83923; 0.02286 -0.16824 0.98196 10.15241; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 1.03533 0.04326 -0.02167 -11.08516; -0.03353 1.20315 0.15489 -50.83923; 0.02286 -0.16824 0.98196 10.15241; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = 4.5 tol 0.000000 final transform: 1.03533 0.04326 -0.02167 -11.08516; -0.03353 1.20315 0.15489 -50.83923; 0.02286 -0.16824 0.98196 10.15241; 0.00000 0.00000 0.00000 1.00000;
writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 846.321024 mri_em_register stimesec 2.335252 mri_em_register ru_maxrss 609856 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 820113 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 148912 mri_em_register ru_oublock 40 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 484 mri_em_register ru_nivcsw 85111 registration took 14 minutes and 9 seconds.
mri_watershed -rusage /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/touch/rusage.mri_watershed.dat -T1 -brain_atlas /usr/local/packages/freesurfer_v6.0.0/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=129 y=125 z=123 r=75 first estimation of the main basin volume: 1796098 voxels Looking for seedpoints 2 found in the cerebellum 18 found in the rest of the brain global maximum in x=150, y=115, z=87, Imax=255 CSF=21, 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=502583624 voxels, voxel volume =1.000 = 502583624 mmm3 = 502583.616 cm3 done. PostAnalyze...Basin Prior 77 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=132, z=119, r=9657 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^
GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 45457 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1035962766 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1103986758 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1077462120 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1077264638 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=23 , nb = 1070358796 Problem with the least square interpolation in GM_MIN calculation.
CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 4, 6, 38, 63 after analyzing : 4, 27, 38, 36 RIGHT_CER before analyzing : 4, 6, 41, 74 after analyzing : 4, 29, 41, 40 LEFT_CER before analyzing : 4, 5, 32, 70 after analyzing : 4, 23, 32, 34 RIGHT_BRAIN before analyzing : 4, 6, 37, 62 after analyzing : 4, 26, 37, 35 LEFT_BRAIN before analyzing : 4, 6, 38, 63 after analyzing : 4, 27, 38, 36 OTHER before analyzing : 23, 30, 45, 87 after analyzing : 23, 40, 45, 51 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...65 iterations
*********************VALIDATION********************* curvature mean = -0.013, std = 0.010 curvature mean = 71.464, std = 8.269
No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 1.98, sigma = 3.16 after rotation: sse = 1.98, sigma = 3.16 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 1.99, its var is 2.50 before Erosion-Dilatation 0.09% 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...36 iterations
mri_strip_skull: done peeling brain
Brain Size = 1628717 voxels, voxel volume = 1.000 mm3 = 1628717 mmm3 = 1628.717 cm3
****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 14.860329 mri_watershed stimesec 0.584423 mri_watershed ru_maxrss 824448 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 369932 mri_watershed ru_majflt 0 mri_watershed ru_nswap 0 mri_watershed ru_inblock 7960 mri_watershed ru_oublock 2608 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 930 mri_watershed ru_nivcsw 1562 mri_watershed done
cp brainmask.auto.mgz brainmask.mgz
#------------------------------------- #@# EM Registration Fri Nov 13 13:43:12 EST 2020 /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri
mri_em_register -rusage /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /usr/local/packages/freesurfer_v6.0.0/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/packages/freesurfer_v6.0.0/average/RB_all_2016-05-10.vc700.gca'... average std = 7.3 using min determinant for regularization = 5.3 0 singular and 841 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 6.3 or > 503.7 total sample mean = 78.8 (1011 zeros) ************************************************ spacing=8, using 2830 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2830, passno 0, spacing 8 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=23.1 skull bounding box = (62, 70, 41) --> (194, 193, 210) using (106, 111, 126) as brain centroid... mean wm in atlas = 107, using box (90,96,105) --> (122, 126,146) to find MRI wm before smoothing, mri peak at 100 robust fit to distribution - 100 +- 6.5 after smoothing, mri peak at 100, scaling input intensities by 1.070 scaling channel 0 by 1.07 initial log_p = -4.315 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.066327 @ (-9.091, -9.091, -9.091) max log p = -3.894957 @ (4.545, -4.545, -4.545) max log p = -3.818117 @ (2.273, 2.273, -2.273) max log p = -3.815683 @ (1.136, -1.136, 1.136) max log p = -3.770580 @ (0.568, 0.568, -0.568) max log p = -3.770580 @ (0.000, 0.000, 0.000) Found translation: (-0.6, -11.9, -15.3): log p = -3.771 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.692, old_max_log_p =-3.771 (thresh=-3.8) 1.00000 0.00000 0.00000 -0.56818; 0.00000 1.14016 0.13053 -46.08973; 0.00000 -0.15011 0.99144 5.38950; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.692, old_max_log_p =-3.692 (thresh=-3.7) 1.00000 0.00000 0.00000 -0.56818; 0.00000 1.14016 0.13053 -46.08973; 0.00000 -0.15011 0.99144 5.38950; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.601, old_max_log_p =-3.692 (thresh=-3.7) 1.03718 0.00318 -0.00461 -6.79167; -0.00210 1.16572 0.10116 -43.88010; -0.00502 -0.10923 0.97631 4.42902; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.576, old_max_log_p =-3.601 (thresh=-3.6) 1.01711 0.04041 -0.00025 -9.55984; -0.03687 1.18256 0.13563 -47.55101; -0.00504 -0.15008 0.99071 8.02897; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.576, old_max_log_p =-3.576 (thresh=-3.6) 1.01711 0.04041 -0.00025 -9.55984; -0.03687 1.18256 0.13563 -47.55101; -0.00504 -0.15008 0.99071 8.02897; 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=-3.569, old_max_log_p =-3.576 (thresh=-3.6) 1.01897 0.00293 -0.01249 -3.88443; -0.00353 1.18189 0.13522 -51.24036; 0.00304 -0.14943 0.98717 6.85401; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.568, old_max_log_p =-3.569 (thresh=-3.6) 1.01897 0.00293 -0.01249 -3.88443; -0.00353 1.18189 0.13522 -51.24036; 0.00303 -0.14908 0.98486 7.08509; 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 1.01897 0.00293 -0.01249 -3.88443; -0.00353 1.18189 0.13522 -51.24036; 0.00303 -0.14908 0.98486 7.08509; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.01897 0.00293 -0.01249 -3.88443; -0.00353 1.18189 0.13522 -51.24036; 0.00303 -0.14908 0.98486 7.08509; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.01897 0.00293 -0.01249 -3.88443; -0.00353 1.18189 0.13522 -51.24036; 0.00303 -0.14908 0.98486 7.08509; 0.00000 0.00000 0.00000 1.00000;
pass 1, spacing 8: log(p) = -3.568 (old=-4.315) transform before final EM align: 1.01897 0.00293 -0.01249 -3.88443; -0.00353 1.18189 0.13522 -51.24036; 0.00303 -0.14908 0.98486 7.08509; 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 1.01897 0.00293 -0.01249 -3.88443; -0.00353 1.18189 0.13522 -51.24036; 0.00303 -0.14908 0.98486 7.08509; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 1.01897 0.00293 -0.01249 -3.88443; -0.00353 1.18189 0.13522 -51.24036; 0.00303 -0.14908 0.98486 7.08509; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = 4.0 tol 0.000000 final transform: 1.01897 0.00293 -0.01249 -3.88443; -0.00353 1.18189 0.13522 -51.24036; 0.00303 -0.14908 0.98486 7.08509; 0.00000 0.00000 0.00000 1.00000;
writing output transformation to transforms/talairach.lta... mri_em_register utimesec 716.320693 mri_em_register stimesec 2.339274 mri_em_register ru_maxrss 599164 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 799686 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 140152 mri_em_register ru_oublock 40 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 655 mri_em_register ru_nivcsw 72101 registration took 11 minutes and 59 seconds. #-------------------------------------- #@# CA Normalize Fri Nov 13 13:55:11 EST 2020 /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri
mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/packages/freesurfer_v6.0.0/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/packages/freesurfer_v6.0.0/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=22.1 skull bounding box = (62, 69, 41) --> (194, 194, 210) using (106, 111, 126) as brain centroid... mean wm in atlas = 107, using box (90,96,105) --> (122, 126,146) to find MRI wm before smoothing, mri peak at 100 robust fit to distribution - 100 +- 6.5 after smoothing, mri peak at 100, scaling input intensities by 1.070 scaling channel 0 by 1.07 using 246344 sample points... INFO: compute sample coordinates transform 1.01897 0.00293 -0.01249 -3.88443; -0.00353 1.18189 0.13522 -51.24036; 0.00303 -0.14908 0.98486 7.08509; 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 (128, 74, 41) --> (193, 173, 209) Left_Cerebral_White_Matter: limiting intensities to 101.0 --> 132.0 1 of 169 (0.6%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (66, 76, 40) --> (131, 173, 209) Right_Cerebral_White_Matter: limiting intensities to 104.0 --> 132.0 1 of 124 (0.8%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (130, 150, 67) --> (177, 186, 122) Left_Cerebellum_White_Matter: limiting intensities to 121.0 --> 132.0 13 of 14 (92.9%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (85, 150, 65) --> (128, 185, 123) Right_Cerebellum_White_Matter: limiting intensities to 108.0 --> 132.0 0 of 17 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (113, 140, 104) --> (146, 200, 133) Brain_Stem: limiting intensities to 100.0 --> 132.0 1 of 19 (5.3%) samples deleted using 343 total control points for intensity normalization... bias field = 0.872 +- 0.082 0 of 327 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (128, 74, 41) --> (193, 173, 209) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 363 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (66, 76, 40) --> (131, 173, 209) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 301 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (130, 150, 67) --> (177, 186, 122) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 48 of 70 (68.6%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (85, 150, 65) --> (128, 185, 123) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 20 of 79 (25.3%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (113, 140, 104) --> (146, 200, 133) Brain_Stem: limiting intensities to 88.0 --> 132.0 72 of 117 (61.5%) samples deleted using 930 total control points for intensity normalization... bias field = 1.021 +- 0.063 0 of 785 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (128, 74, 41) --> (193, 173, 209) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 442 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (66, 76, 40) --> (131, 173, 209) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 418 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (130, 150, 67) --> (177, 186, 122) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 82 of 113 (72.6%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (85, 150, 65) --> (128, 185, 123) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 52 of 111 (46.8%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (113, 140, 104) --> (146, 200, 133) Brain_Stem: limiting intensities to 88.0 --> 132.0 164 of 225 (72.9%) samples deleted using 1309 total control points for intensity normalization... bias field = 1.008 +- 0.054 1 of 986 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 10 seconds. #-------------------------------------- #@# CA Reg Fri Nov 13 13:56:21 EST 2020 /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri
mri_ca_register -rusage /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /usr/local/packages/freesurfer_v6.0.0/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/packages/freesurfer_v6.0.0/average/RB_all_2016-05-10.vc700.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.21 (predicted orig area = 6.6) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.802, neg=0, invalid=4512 0001: dt=188.688327, rms=0.750 (6.513%), neg=0, invalid=4512 0002: dt=147.728155, rms=0.733 (2.209%), neg=0, invalid=4512 0003: dt=221.952000, rms=0.724 (1.206%), neg=0, invalid=4512 0004: dt=135.384615, rms=0.719 (0.662%), neg=0, invalid=4512 0005: dt=517.888000, rms=0.712 (1.016%), neg=0, invalid=4512 0006: dt=110.976000, rms=0.706 (0.787%), neg=0, invalid=4512 0007: dt=517.888000, rms=0.701 (0.820%), neg=0, invalid=4512 0008: dt=110.976000, rms=0.698 (0.328%), neg=0, invalid=4512 0009: dt=517.888000, rms=0.695 (0.455%), neg=0, invalid=4512 0010: dt=110.976000, rms=0.694 (0.120%), neg=0, invalid=4512 0011: dt=110.976000, rms=0.694 (0.071%), neg=0, invalid=4512 0012: dt=110.976000, rms=0.693 (0.114%), neg=0, invalid=4512 0013: dt=110.976000, rms=0.692 (0.136%), neg=0, invalid=4512 0014: dt=110.976000, rms=0.691 (0.155%), neg=0, invalid=4512 0015: dt=110.976000, rms=0.690 (0.164%), neg=0, invalid=4512 0016: dt=110.976000, rms=0.689 (0.165%), neg=0, invalid=4512 0017: dt=110.976000, rms=0.688 (0.154%), neg=0, invalid=4512 0018: dt=110.976000, rms=0.687 (0.143%), neg=0, invalid=4512 0019: dt=110.976000, rms=0.686 (0.131%), neg=0, invalid=4512 0020: dt=110.976000, rms=0.685 (0.137%), neg=0, invalid=4512 0021: dt=110.976000, rms=0.684 (0.134%), neg=0, invalid=4512 0022: dt=110.976000, rms=0.683 (0.121%), neg=0, invalid=4512 0023: dt=110.976000, rms=0.682 (0.106%), neg=0, invalid=4512 0024: dt=517.888000, rms=0.682 (0.062%), neg=0, invalid=4512 0025: dt=517.888000, rms=0.682 (-0.256%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.682, neg=0, invalid=4512 0026: dt=129.472000, rms=0.681 (0.175%), neg=0, invalid=4512 0027: dt=517.888000, rms=0.680 (0.213%), neg=0, invalid=4512 0028: dt=110.976000, rms=0.680 (0.015%), neg=0, invalid=4512 0029: dt=110.976000, rms=0.679 (0.028%), neg=0, invalid=4512 0030: dt=110.976000, rms=0.679 (0.038%), neg=0, invalid=4512 0031: dt=110.976000, rms=0.679 (0.051%), neg=0, invalid=4512 0032: dt=110.976000, rms=0.678 (0.065%), neg=0, invalid=4512 0033: dt=110.976000, rms=0.678 (0.082%), neg=0, invalid=4512 0034: dt=110.976000, rms=0.677 (0.090%), neg=0, invalid=4512 0035: dt=110.976000, rms=0.677 (0.088%), neg=0, invalid=4512 0036: dt=110.976000, rms=0.676 (0.086%), neg=0, invalid=4512 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.679, neg=0, invalid=4512 0037: dt=202.524444, rms=0.670 (1.334%), neg=0, invalid=4512 0038: dt=133.719149, rms=0.662 (1.223%), neg=0, invalid=4512 0039: dt=63.780571, rms=0.658 (0.613%), neg=0, invalid=4512 0040: dt=145.152000, rms=0.655 (0.444%), neg=0, invalid=4512 0041: dt=73.612648, rms=0.652 (0.448%), neg=0, invalid=4512 0042: dt=79.078534, rms=0.651 (0.241%), neg=0, invalid=4512 0043: dt=79.078534, rms=0.648 (0.321%), neg=0, invalid=4512 0044: dt=79.078534, rms=0.646 (0.451%), neg=0, invalid=4512 0045: dt=79.078534, rms=0.642 (0.548%), neg=0, invalid=4512 0046: dt=79.078534, rms=0.638 (0.651%), neg=0, invalid=4512 0047: dt=79.078534, rms=0.633 (0.716%), neg=0, invalid=4512 0048: dt=79.078534, rms=0.629 (0.632%), neg=0, invalid=4512 0049: dt=79.078534, rms=0.626 (0.571%), neg=0, invalid=4512 0050: dt=79.078534, rms=0.622 (0.531%), neg=0, invalid=4512 0051: dt=79.078534, rms=0.619 (0.467%), neg=0, invalid=4512 0052: dt=79.078534, rms=0.617 (0.343%), neg=0, invalid=4512 0053: dt=79.078534, rms=0.616 (0.271%), neg=0, invalid=4512 0054: dt=79.078534, rms=0.614 (0.281%), neg=0, invalid=4512 0055: dt=79.078534, rms=0.613 (0.216%), neg=0, invalid=4512 0056: dt=79.078534, rms=0.612 (0.164%), neg=0, invalid=4512 0057: dt=79.078534, rms=0.611 (0.124%), neg=0, invalid=4512 0058: dt=79.078534, rms=0.610 (0.183%), neg=0, invalid=4512 0059: dt=79.078534, rms=0.609 (0.131%), neg=0, invalid=4512 0060: dt=79.078534, rms=0.608 (0.107%), neg=0, invalid=4512 0061: dt=79.078534, rms=0.608 (0.068%), neg=0, invalid=4512 0062: dt=62.208000, rms=0.607 (0.069%), neg=0, invalid=4512 0063: dt=31.104000, rms=0.607 (0.004%), neg=0, invalid=4512 0064: dt=31.104000, rms=0.607 (0.008%), neg=0, invalid=4512 0065: dt=31.104000, rms=0.607 (0.013%), neg=0, invalid=4512 0066: dt=31.104000, rms=0.607 (0.019%), neg=0, invalid=4512 0067: dt=31.104000, rms=0.607 (0.020%), neg=0, invalid=4512 0068: dt=31.104000, rms=0.607 (0.021%), neg=0, invalid=4512 0069: dt=31.104000, rms=0.607 (0.019%), neg=0, invalid=4512 0070: dt=31.104000, rms=0.607 (0.013%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.607, neg=0, invalid=4512 0071: dt=145.152000, rms=0.605 (0.332%), neg=0, invalid=4512 0072: dt=103.680000, rms=0.605 (0.069%), neg=0, invalid=4512 0073: dt=103.680000, rms=0.605 (0.013%), neg=0, invalid=4512 0074: dt=103.680000, rms=0.605 (0.036%), neg=0, invalid=4512 0075: dt=103.680000, rms=0.604 (0.026%), neg=0, invalid=4512 0076: dt=103.680000, rms=0.604 (-0.001%), neg=0, invalid=4512 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.624, neg=0, invalid=4512 0077: dt=0.000000, rms=0.623 (0.090%), neg=0, invalid=4512 0078: dt=0.000000, rms=0.623 (0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.624, neg=0, invalid=4512 0079: dt=0.000000, rms=0.623 (0.090%), neg=0, invalid=4512 0080: dt=0.000000, rms=0.623 (0.000%), neg=0, invalid=4512 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.681, neg=0, invalid=4512 0081: dt=4.878049, rms=0.663 (2.572%), neg=0, invalid=4512 0082: dt=1.728000, rms=0.663 (0.064%), neg=0, invalid=4512 0083: dt=1.728000, rms=0.663 (-0.024%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.663, neg=0, invalid=4512 0084: dt=0.000000, rms=0.663 (0.061%), neg=0, invalid=4512 0085: dt=0.000000, rms=0.663 (0.000%), neg=0, invalid=4512 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.719, neg=0, invalid=4512 0086: dt=1.317507, rms=0.714 (0.755%), neg=0, invalid=4512 0087: dt=1.792000, rms=0.710 (0.565%), neg=0, invalid=4512 0088: dt=0.448000, rms=0.709 (0.029%), neg=0, invalid=4512 0089: dt=0.448000, rms=0.709 (0.026%), neg=0, invalid=4512 0090: dt=0.448000, rms=0.709 (0.011%), neg=0, invalid=4512 0091: dt=0.448000, rms=0.709 (-0.051%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.709, neg=0, invalid=4512 0092: dt=1.536000, rms=0.708 (0.220%), neg=0, invalid=4512 0093: dt=0.000000, rms=0.708 (-0.000%), neg=0, invalid=4512 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.670, neg=0, invalid=4512 0094: dt=0.916276, rms=0.649 (3.188%), neg=0, invalid=4512 0095: dt=0.080000, rms=0.648 (0.163%), neg=0, invalid=4512 0096: dt=0.080000, rms=0.648 (-0.083%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.648, neg=0, invalid=4512 0097: dt=0.028000, rms=0.648 (0.081%), neg=0, invalid=4512 0098: dt=0.007000, rms=0.648 (0.000%), neg=0, invalid=4512 0099: dt=0.007000, rms=0.648 (-0.000%), neg=0, invalid=4512 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.12287 (11) Left_Lateral_Ventricle (4): linear fit = 0.47 x + 0.0 (1254 voxels, overlap=0.360) Left_Lateral_Ventricle (4): linear fit = 0.47 x + 0.0 (1254 voxels, peak = 10), gca=9.5 gca peak = 0.15565 (16) mri peak = 0.08848 (10) Right_Lateral_Ventricle (43): linear fit = 0.51 x + 0.0 (503 voxels, overlap=0.224) Right_Lateral_Ventricle (43): linear fit = 0.51 x + 0.0 (503 voxels, peak = 8), gca=8.2 gca peak = 0.26829 (96) mri peak = 0.07737 (95) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (773 voxels, overlap=1.005) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (773 voxels, peak = 96), gca=96.5 gca peak = 0.20183 (93) mri peak = 0.05740 (87) Left_Pallidum (13): linear fit = 0.89 x + 0.0 (712 voxels, overlap=1.021) Left_Pallidum (13): linear fit = 0.89 x + 0.0 (712 voxels, peak = 83), gca=83.2 gca peak = 0.21683 (55) mri peak = 0.08078 (67) Right_Hippocampus (53): linear fit = 1.21 x + 0.0 (969 voxels, overlap=0.334) Right_Hippocampus (53): linear fit = 1.21 x + 0.0 (969 voxels, peak = 66), gca=66.3 gca peak = 0.30730 (58) mri peak = 0.08482 (69) Left_Hippocampus (17): linear fit = 1.16 x + 0.0 (696 voxels, overlap=0.564) Left_Hippocampus (17): linear fit = 1.16 x + 0.0 (696 voxels, peak = 68), gca=67.6 gca peak = 0.11430 (101) mri peak = 0.08210 (105) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (64908 voxels, overlap=0.687) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (64908 voxels, peak = 107), gca=106.6 gca peak = 0.12076 (102) mri peak = 0.08181 (106) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (61293 voxels, overlap=0.719) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (61293 voxels, peak = 108), gca=107.6 gca peak = 0.14995 (59) mri peak = 0.03500 (56) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (18356 voxels, overlap=0.973) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (18356 voxels, peak = 60), gca=60.5 gca peak = 0.15082 (58) mri peak = 0.03869 (56) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (20996 voxels, overlap=0.978) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (20996 voxels, peak = 59), gca=59.4 gca peak = 0.14161 (67) mri peak = 0.11457 (67) Right_Caudate (50): linear fit = 0.98 x + 0.0 (623 voxels, overlap=0.987) Right_Caudate (50): linear fit = 0.98 x + 0.0 (623 voxels, peak = 65), gca=65.3 gca peak = 0.15243 (71) mri peak = 0.08065 (73) Left_Caudate (11): linear fit = 1.00 x + 0.0 (944 voxels, overlap=0.987) Left_Caudate (11): linear fit = 1.00 x + 0.0 (944 voxels, peak = 71), gca=71.0 gca peak = 0.13336 (57) mri peak = 0.05185 (56) Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (19168 voxels, overlap=0.903) Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (19168 voxels, peak = 60), gca=59.6 gca peak = 0.13252 (56) mri peak = 0.05346 (63) Right_Cerebellum_Cortex (47): linear fit = 1.12 x + 0.0 (22877 voxels, overlap=0.758) Right_Cerebellum_Cortex (47): linear fit = 1.12 x + 0.0 (22877 voxels, peak = 62), gca=62.4 gca peak = 0.18181 (84) mri peak = 0.07035 (85) Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (8728 voxels, overlap=0.784) Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (8728 voxels, peak = 87), gca=86.9 gca peak = 0.20573 (83) mri peak = 0.07458 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (8456 voxels, overlap=0.749) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (8456 voxels, peak = 88), gca=87.6 gca peak = 0.21969 (57) mri peak = 0.09707 (66) Left_Amygdala (18): linear fit = 1.18 x + 0.0 (490 voxels, overlap=0.183) Left_Amygdala (18): linear fit = 1.18 x + 0.0 (490 voxels, peak = 68), gca=67.5 gca peak = 0.39313 (56) mri peak = 0.11141 (65) Right_Amygdala (54): linear fit = 1.13 x + 0.0 (551 voxels, overlap=0.300) Right_Amygdala (54): linear fit = 1.13 x + 0.0 (551 voxels, peak = 64), gca=63.6 gca peak = 0.14181 (85) mri peak = 0.04962 (99) Left_Thalamus_Proper (10): linear fit = 1.09 x + 0.0 (5514 voxels, overlap=0.764) Left_Thalamus_Proper (10): linear fit = 1.09 x + 0.0 (5514 voxels, peak = 92), gca=92.2 gca peak = 0.11978 (83) mri peak = 0.05466 (89) Right_Thalamus_Proper (49): linear fit = 1.07 x + 0.0 (4601 voxels, overlap=0.885) Right_Thalamus_Proper (49): linear fit = 1.07 x + 0.0 (4601 voxels, peak = 88), gca=88.4 gca peak = 0.13399 (79) mri peak = 0.06231 (84) Left_Putamen (12): linear fit = 1.04 x + 0.0 (1923 voxels, overlap=0.986) Left_Putamen (12): linear fit = 1.04 x + 0.0 (1923 voxels, peak = 83), gca=82.6 gca peak = 0.14159 (79) mri peak = 0.07409 (79) Right_Putamen (51): linear fit = 1.04 x + 0.0 (2385 voxels, overlap=0.998) Right_Putamen (51): linear fit = 1.04 x + 0.0 (2385 voxels, peak = 83), gca=82.6 gca peak = 0.10025 (80) mri peak = 0.08538 (82) Brain_Stem (16): linear fit = 1.10 x + 0.0 (13178 voxels, overlap=0.402) Brain_Stem (16): linear fit = 1.10 x + 0.0 (13178 voxels, peak = 88), gca=87.6 gca peak = 0.13281 (86) mri peak = 0.07803 (94) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1335 voxels, overlap=0.391) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1335 voxels, peak = 93), gca=93.3 gca peak = 0.12801 (89) mri peak = 0.09039 (95) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1400 voxels, overlap=0.291) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1400 voxels, peak = 97), gca=97.5 gca peak = 0.20494 (23) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.15061 (21) mri peak = 0.09801 (16) Fourth_Ventricle (15): linear fit = 0.88 x + 0.0 (252 voxels, overlap=0.533) Fourth_Ventricle (15): linear fit = 0.88 x + 0.0 (252 voxels, peak = 18), gca=18.4 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18056 (32) gca peak Left_Thalamus = 0.64095 (94) gca peak Third_Ventricle = 0.20494 (23) gca peak CSF = 0.20999 (34) gca peak Left_Accumbens_area = 0.39030 (62) gca peak Left_undetermined = 0.95280 (25) gca peak Left_vessel = 0.67734 (53) gca peak Left_choroid_plexus = 0.09433 (44) gca peak Right_Inf_Lat_Vent = 0.23544 (26) gca peak Right_Accumbens_area = 0.30312 (64) gca peak Right_vessel = 0.46315 (51) gca peak Right_choroid_plexus = 0.14086 (44) gca peak Fifth_Ventricle = 0.51669 (36) gca peak WM_hypointensities = 0.09722 (76) gca peak non_WM_hypointensities = 0.11899 (47) gca peak Optic_Chiasm = 0.39033 (72) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 1.12 x + 0.0 estimating mean wm scale to be 1.05 x + 0.0 estimating mean csf scale to be 0.62 x + 0.0 saving intensity scales to talairach.label_intensities.txt **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.663, neg=0, invalid=4512 0100: dt=129.472000, rms=0.659 (0.684%), neg=0, invalid=4512 0101: dt=369.920000, rms=0.655 (0.577%), neg=0, invalid=4512 0102: dt=92.480000, rms=0.654 (0.201%), neg=0, invalid=4512 0103: dt=295.936000, rms=0.653 (0.181%), neg=0, invalid=4512 0104: dt=110.976000, rms=0.652 (0.154%), neg=0, invalid=4512 0105: dt=129.472000, rms=0.651 (0.068%), neg=0, invalid=4512 0106: dt=129.472000, rms=0.651 (0.076%), neg=0, invalid=4512 0107: dt=129.472000, rms=0.650 (0.063%), neg=0, invalid=4512 0108: dt=129.472000, rms=0.650 (0.061%), neg=0, invalid=4512 0109: dt=221.952000, rms=0.649 (0.074%), neg=0, invalid=4512 0110: dt=92.480000, rms=0.649 (0.056%), neg=0, invalid=4512 0111: dt=369.920000, rms=0.648 (0.087%), neg=0, invalid=4512 0112: dt=73.984000, rms=0.648 (0.072%), neg=0, invalid=4512 0113: dt=1479.680000, rms=0.646 (0.247%), neg=0, invalid=4512 0114: dt=73.984000, rms=0.646 (0.109%), neg=0, invalid=4512 0115: dt=517.888000, rms=0.645 (0.060%), neg=0, invalid=4512 0116: dt=92.480000, rms=0.645 (0.029%), neg=0, invalid=4512 0117: dt=92.480000, rms=0.645 (0.017%), neg=0, invalid=4512 0118: dt=92.480000, rms=0.645 (0.029%), neg=0, invalid=4512 0119: dt=92.480000, rms=0.645 (0.038%), neg=0, invalid=4512 0120: dt=92.480000, rms=0.644 (0.041%), neg=0, invalid=4512 0121: dt=92.480000, rms=0.644 (0.042%), neg=0, invalid=4512 0122: dt=92.480000, rms=0.644 (0.047%), neg=0, invalid=4512 0123: dt=92.480000, rms=0.643 (0.047%), neg=0, invalid=4512 0124: dt=92.480000, rms=0.643 (0.049%), neg=0, invalid=4512 0125: dt=92.480000, rms=0.643 (0.053%), neg=0, invalid=4512 0126: dt=92.480000, rms=0.642 (0.056%), neg=0, invalid=4512 0127: dt=92.480000, rms=0.642 (0.059%), neg=0, invalid=4512 0128: dt=92.480000, rms=0.642 (0.056%), neg=0, invalid=4512 0129: dt=92.480000, rms=0.641 (0.051%), neg=0, invalid=4512 0130: dt=92.480000, rms=0.641 (0.047%), neg=0, invalid=4512 0131: dt=92.480000, rms=0.641 (0.046%), neg=0, invalid=4512 0132: dt=92.480000, rms=0.640 (0.048%), neg=0, invalid=4512 0133: dt=92.480000, rms=0.640 (0.044%), neg=0, invalid=4512 0134: dt=92.480000, rms=0.640 (0.041%), neg=0, invalid=4512 0135: dt=92.480000, rms=0.640 (0.043%), neg=0, invalid=4512 0136: dt=92.480000, rms=0.639 (0.042%), neg=0, invalid=4512 0137: dt=92.480000, rms=0.639 (0.043%), neg=0, invalid=4512 0138: dt=92.480000, rms=0.639 (0.043%), neg=0, invalid=4512 0139: dt=92.480000, rms=0.639 (0.040%), neg=0, invalid=4512 0140: dt=92.480000, rms=0.638 (0.041%), neg=0, invalid=4512 0141: dt=92.480000, rms=0.638 (0.040%), neg=0, invalid=4512 0142: dt=92.480000, rms=0.638 (0.038%), neg=0, invalid=4512 0143: dt=92.480000, rms=0.638 (0.037%), neg=0, invalid=4512 0144: dt=92.480000, rms=0.637 (0.037%), neg=0, invalid=4512 0145: dt=92.480000, rms=0.637 (0.036%), neg=0, invalid=4512 0146: dt=92.480000, rms=0.637 (0.035%), neg=0, invalid=4512 0147: dt=92.480000, rms=0.637 (0.032%), neg=0, invalid=4512 0148: dt=92.480000, rms=0.636 (0.030%), neg=0, invalid=4512 0149: dt=92.480000, rms=0.636 (0.030%), neg=0, invalid=4512 0150: dt=92.480000, rms=0.636 (0.029%), neg=0, invalid=4512 0151: dt=92.480000, rms=0.636 (0.030%), neg=0, invalid=4512 0152: dt=92.480000, rms=0.636 (0.028%), neg=0, invalid=4512 0153: dt=92.480000, rms=0.636 (0.028%), neg=0, invalid=4512 0154: dt=92.480000, rms=0.635 (0.028%), neg=0, invalid=4512 0155: dt=92.480000, rms=0.635 (0.028%), neg=0, invalid=4512 0156: dt=92.480000, rms=0.635 (0.026%), neg=0, invalid=4512 0157: dt=92.480000, rms=0.635 (0.022%), neg=0, invalid=4512 0158: dt=92.480000, rms=0.635 (0.023%), neg=0, invalid=4512 0159: dt=92.480000, rms=0.635 (0.023%), neg=0, invalid=4512 0160: dt=92.480000, rms=0.634 (0.022%), neg=0, invalid=4512 0161: dt=2071.552000, rms=0.634 (0.050%), neg=0, invalid=4512 0162: dt=32.368000, rms=0.634 (0.004%), neg=0, invalid=4512 0163: dt=32.368000, rms=0.634 (-0.001%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.634, neg=0, invalid=4512 0164: dt=221.952000, rms=0.633 (0.189%), neg=0, invalid=4512 0165: dt=129.472000, rms=0.633 (0.042%), neg=0, invalid=4512 0166: dt=129.472000, rms=0.633 (0.036%), neg=0, invalid=4512 0167: dt=129.472000, rms=0.633 (0.043%), neg=0, invalid=4512 0168: dt=129.472000, rms=0.632 (0.042%), neg=0, invalid=4512 0169: dt=129.472000, rms=0.632 (0.035%), neg=0, invalid=4512 0170: dt=129.472000, rms=0.632 (0.052%), neg=0, invalid=4512 0171: dt=129.472000, rms=0.631 (0.036%), neg=0, invalid=4512 0172: dt=129.472000, rms=0.631 (0.019%), neg=0, invalid=4512 0173: dt=129.472000, rms=0.631 (0.009%), neg=0, invalid=4512 0174: dt=129.472000, rms=0.631 (0.026%), neg=0, invalid=4512 0175: dt=0.000000, rms=0.631 (-0.000%), neg=0, invalid=4512 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.632, neg=0, invalid=4512 0176: dt=119.118367, rms=0.628 (0.593%), neg=0, invalid=4512 0177: dt=124.416000, rms=0.624 (0.653%), neg=0, invalid=4512 0178: dt=58.566038, rms=0.622 (0.384%), neg=0, invalid=4512 0179: dt=98.818653, rms=0.620 (0.335%), neg=0, invalid=4512 0180: dt=36.288000, rms=0.618 (0.247%), neg=0, invalid=4512 0181: dt=580.608000, rms=0.610 (1.291%), neg=0, invalid=4512 0182: dt=36.288000, rms=0.609 (0.231%), neg=0, invalid=4512 0183: dt=331.776000, rms=0.607 (0.390%), neg=0, invalid=4512 0184: dt=36.288000, rms=0.605 (0.265%), neg=0, invalid=4512 0185: dt=145.152000, rms=0.604 (0.167%), neg=0, invalid=4512 0186: dt=78.315789, rms=0.603 (0.162%), neg=0, invalid=4512 0187: dt=82.944000, rms=0.602 (0.078%), neg=0, invalid=4512 0188: dt=124.416000, rms=0.602 (0.153%), neg=0, invalid=4512 0189: dt=36.288000, rms=0.601 (0.085%), neg=0, invalid=4512 0190: dt=580.608000, rms=0.599 (0.317%), neg=0, invalid=4512 0191: dt=36.288000, rms=0.597 (0.328%), neg=0, invalid=4512 0192: dt=124.416000, rms=0.597 (0.102%), neg=0, invalid=4512 0193: dt=36.288000, rms=0.596 (0.067%), neg=0, invalid=4512 0194: dt=580.608000, rms=0.594 (0.283%), neg=0, invalid=4512 0195: dt=36.288000, rms=0.593 (0.191%), neg=0, invalid=4512 0196: dt=124.416000, rms=0.593 (0.074%), neg=0, invalid=4512 0197: dt=62.208000, rms=0.593 (0.059%), neg=0, invalid=4512 0198: dt=145.152000, rms=0.592 (0.085%), neg=0, invalid=4512 0199: dt=36.288000, rms=0.592 (0.038%), neg=0, invalid=4512 0200: dt=36.288000, rms=0.592 (0.022%), neg=0, invalid=4512 0201: dt=36.288000, rms=0.591 (0.043%), neg=0, invalid=4512 0202: dt=36.288000, rms=0.591 (0.060%), neg=0, invalid=4512 0203: dt=36.288000, rms=0.591 (0.076%), neg=0, invalid=4512 0204: dt=36.288000, rms=0.590 (0.085%), neg=0, invalid=4512 0205: dt=36.288000, rms=0.590 (0.093%), neg=0, invalid=4512 0206: dt=36.288000, rms=0.589 (0.098%), neg=0, invalid=4512 0207: dt=36.288000, rms=0.588 (0.105%), neg=0, invalid=4512 0208: dt=36.288000, rms=0.588 (0.111%), neg=0, invalid=4512 0209: dt=36.288000, rms=0.587 (0.110%), neg=0, invalid=4512 0210: dt=36.288000, rms=0.586 (0.108%), neg=0, invalid=4512 0211: dt=36.288000, rms=0.586 (0.107%), neg=0, invalid=4512 0212: dt=36.288000, rms=0.585 (0.103%), neg=0, invalid=4512 0213: dt=36.288000, rms=0.585 (0.103%), neg=0, invalid=4512 0214: dt=36.288000, rms=0.584 (0.100%), neg=0, invalid=4512 0215: dt=36.288000, rms=0.583 (0.096%), neg=0, invalid=4512 0216: dt=36.288000, rms=0.583 (0.094%), neg=0, invalid=4512 0217: dt=36.288000, rms=0.582 (0.092%), neg=0, invalid=4512 0218: dt=36.288000, rms=0.582 (0.090%), neg=0, invalid=4512 0219: dt=36.288000, rms=0.581 (0.087%), neg=0, invalid=4512 0220: dt=36.288000, rms=0.581 (0.082%), neg=0, invalid=4512 0221: dt=36.288000, rms=0.580 (0.080%), neg=0, invalid=4512 0222: dt=36.288000, rms=0.580 (0.082%), neg=0, invalid=4512 0223: dt=36.288000, rms=0.579 (0.080%), neg=0, invalid=4512 0224: dt=36.288000, rms=0.579 (0.077%), neg=0, invalid=4512 0225: dt=36.288000, rms=0.579 (0.074%), neg=0, invalid=4512 0226: dt=36.288000, rms=0.578 (0.071%), neg=0, invalid=4512 0227: dt=36.288000, rms=0.578 (0.070%), neg=0, invalid=4512 0228: dt=36.288000, rms=0.577 (0.069%), neg=0, invalid=4512 0229: dt=36.288000, rms=0.577 (0.065%), neg=0, invalid=4512 0230: dt=36.288000, rms=0.577 (0.063%), neg=0, invalid=4512 0231: dt=36.288000, rms=0.576 (0.060%), neg=0, invalid=4512 0232: dt=36.288000, rms=0.576 (0.057%), neg=0, invalid=4512 0233: dt=36.288000, rms=0.576 (0.055%), neg=0, invalid=4512 0234: dt=36.288000, rms=0.575 (0.052%), neg=0, invalid=4512 0235: dt=36.288000, rms=0.575 (0.049%), neg=0, invalid=4512 0236: dt=36.288000, rms=0.575 (0.049%), neg=0, invalid=4512 0237: dt=36.288000, rms=0.574 (0.047%), neg=0, invalid=4512 0238: dt=36.288000, rms=0.574 (0.047%), neg=0, invalid=4512 0239: dt=36.288000, rms=0.574 (0.045%), neg=0, invalid=4512 0240: dt=36.288000, rms=0.574 (0.045%), neg=0, invalid=4512 0241: dt=36.288000, rms=0.573 (0.044%), neg=0, invalid=4512 0242: dt=36.288000, rms=0.573 (0.043%), neg=0, invalid=4512 0243: dt=36.288000, rms=0.573 (0.042%), neg=0, invalid=4512 0244: dt=36.288000, rms=0.573 (0.039%), neg=0, invalid=4512 0245: dt=36.288000, rms=0.573 (0.040%), neg=0, invalid=4512 0246: dt=36.288000, rms=0.572 (0.036%), neg=0, invalid=4512 0247: dt=36.288000, rms=0.572 (0.034%), neg=0, invalid=4512 0248: dt=36.288000, rms=0.572 (0.035%), neg=0, invalid=4512 0249: dt=36.288000, rms=0.572 (0.036%), neg=0, invalid=4512 0250: dt=36.288000, rms=0.572 (0.034%), neg=0, invalid=4512 0251: dt=36.288000, rms=0.571 (0.034%), neg=0, invalid=4512 0252: dt=36.288000, rms=0.571 (0.031%), neg=0, invalid=4512 0253: dt=36.288000, rms=0.571 (0.031%), neg=0, invalid=4512 0254: dt=36.288000, rms=0.571 (0.032%), neg=0, invalid=4512 0255: dt=36.288000, rms=0.571 (0.033%), neg=0, invalid=4512 0256: dt=36.288000, rms=0.570 (0.034%), neg=0, invalid=4512 0257: dt=36.288000, rms=0.570 (0.031%), neg=0, invalid=4512 0258: dt=36.288000, rms=0.570 (0.029%), neg=0, invalid=4512 0259: dt=36.288000, rms=0.570 (0.027%), neg=0, invalid=4512 0260: dt=36.288000, rms=0.570 (0.025%), neg=0, invalid=4512 0261: dt=36.288000, rms=0.570 (0.027%), neg=0, invalid=4512 0262: dt=36.288000, rms=0.569 (0.027%), neg=0, invalid=4512 0263: dt=36.288000, rms=0.569 (0.028%), neg=0, invalid=4512 0264: dt=36.288000, rms=0.569 (0.003%), neg=0, invalid=4512 0265: dt=36.288000, rms=0.569 (0.003%), neg=0, invalid=4512 0266: dt=9.072000, rms=0.569 (0.001%), neg=0, invalid=4512 0267: dt=9.072000, rms=0.569 (0.001%), neg=0, invalid=4512 0268: dt=1.134000, rms=0.569 (0.000%), neg=0, invalid=4512 0269: dt=0.283500, rms=0.569 (-0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.570, neg=0, invalid=4512 0270: dt=145.152000, rms=0.567 (0.507%), neg=0, invalid=4512 0271: dt=62.208000, rms=0.566 (0.105%), neg=0, invalid=4512 0272: dt=145.152000, rms=0.566 (0.084%), neg=0, invalid=4512 0273: dt=36.288000, rms=0.566 (0.059%), neg=0, invalid=4512 0274: dt=497.664000, rms=0.565 (0.172%), neg=0, invalid=4512 0275: dt=36.288000, rms=0.564 (0.071%), neg=0, invalid=4512 0276: dt=124.416000, rms=0.564 (0.023%), neg=0, invalid=4512 0277: dt=124.416000, rms=0.564 (0.032%), neg=0, invalid=4512 0278: dt=124.416000, rms=0.564 (0.050%), neg=0, invalid=4512 0279: dt=124.416000, rms=0.563 (0.090%), neg=0, invalid=4512 0280: dt=124.416000, rms=0.563 (0.088%), neg=0, invalid=4512 0281: dt=124.416000, rms=0.562 (0.074%), neg=0, invalid=4512 0282: dt=124.416000, rms=0.561 (0.133%), neg=0, invalid=4512 0283: dt=124.416000, rms=0.561 (0.083%), neg=0, invalid=4512 0284: dt=124.416000, rms=0.561 (0.057%), neg=0, invalid=4512 0285: dt=124.416000, rms=0.560 (0.105%), neg=0, invalid=4512 0286: dt=124.416000, rms=0.560 (0.084%), neg=0, invalid=4512 0287: dt=124.416000, rms=0.559 (0.065%), neg=0, invalid=4512 0288: dt=124.416000, rms=0.559 (0.083%), neg=0, invalid=4512 0289: dt=124.416000, rms=0.558 (0.075%), neg=0, invalid=4512 0290: dt=124.416000, rms=0.558 (0.054%), neg=0, invalid=4512 0291: dt=124.416000, rms=0.558 (0.072%), neg=0, invalid=4512 0292: dt=124.416000, rms=0.557 (0.053%), neg=0, invalid=4512 0293: dt=124.416000, rms=0.557 (0.081%), neg=0, invalid=4512 0294: dt=124.416000, rms=0.557 (0.059%), neg=0, invalid=4512 0295: dt=124.416000, rms=0.556 (0.042%), neg=0, invalid=4512 0296: dt=124.416000, rms=0.556 (0.074%), neg=0, invalid=4512 0297: dt=124.416000, rms=0.556 (0.045%), neg=0, invalid=4512 0298: dt=124.416000, rms=0.555 (0.057%), neg=0, invalid=4512 0299: dt=124.416000, rms=0.555 (0.040%), neg=0, invalid=4512 0300: dt=124.416000, rms=0.555 (0.044%), neg=0, invalid=4512 0301: dt=124.416000, rms=0.555 (0.045%), neg=0, invalid=4512 0302: dt=124.416000, rms=0.554 (0.061%), neg=0, invalid=4512 0303: dt=124.416000, rms=0.554 (0.037%), neg=0, invalid=4512 0304: dt=124.416000, rms=0.554 (-0.231%), neg=0, invalid=4512 0305: dt=36.288000, rms=0.554 (0.051%), neg=0, invalid=4512 0306: dt=103.680000, rms=0.554 (0.006%), neg=0, invalid=4512 0307: dt=103.680000, rms=0.554 (-0.001%), neg=0, invalid=4512 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.561, neg=0, invalid=4512 0308: dt=2.000000, rms=0.561 (0.137%), neg=0, invalid=4512 0309: dt=0.175000, rms=0.561 (0.003%), neg=0, invalid=4512 0310: dt=0.043750, rms=0.561 (0.000%), neg=0, invalid=4512 0311: dt=0.010937, rms=0.561 (0.000%), neg=0, invalid=4512 0312: dt=0.005469, rms=0.561 (0.000%), neg=0, invalid=4512 0313: dt=0.000684, rms=0.561 (0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.561, neg=0, invalid=4512 0314: dt=81.362599, rms=0.557 (0.749%), neg=0, invalid=4512 0315: dt=44.800000, rms=0.553 (0.697%), neg=0, invalid=4512 0316: dt=11.200000, rms=0.552 (0.152%), neg=0, invalid=4512 0317: dt=2.800000, rms=0.552 (0.037%), neg=0, invalid=4512 0318: dt=0.700000, rms=0.552 (0.007%), neg=0, invalid=4512 0319: dt=0.350000, rms=0.552 (0.003%), neg=0, invalid=4512 0320: dt=0.021875, rms=0.552 (0.000%), neg=0, invalid=4512 0321: dt=0.010937, rms=0.552 (0.000%), neg=0, invalid=4512 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.568, neg=0, invalid=4512 0322: dt=4.032000, rms=0.564 (0.797%), neg=0, invalid=4512 0323: dt=4.032000, rms=0.561 (0.516%), neg=0, invalid=4512 0324: dt=11.520000, rms=0.556 (0.940%), neg=0, invalid=4512 0325: dt=46.080000, rms=0.548 (1.380%), neg=0, invalid=4512 0326: dt=9.663366, rms=0.548 (0.091%), neg=0, invalid=4512 0327: dt=18.666667, rms=0.547 (0.097%), neg=0, invalid=4512 0328: dt=18.000000, rms=0.547 (0.080%), neg=0, invalid=4512 0329: dt=16.128000, rms=0.546 (0.102%), neg=0, invalid=4512 0330: dt=13.824000, rms=0.546 (0.094%), neg=0, invalid=4512 0331: dt=16.000000, rms=0.545 (0.068%), neg=0, invalid=4512 0332: dt=13.600000, rms=0.545 (0.065%), neg=0, invalid=4512 0333: dt=12.444444, rms=0.545 (0.053%), neg=0, invalid=4512 0334: dt=16.000000, rms=0.544 (0.052%), neg=0, invalid=4512 0335: dt=11.520000, rms=0.544 (0.040%), neg=0, invalid=4512 0336: dt=11.520000, rms=0.544 (0.042%), neg=0, invalid=4512 0337: dt=11.520000, rms=0.543 (0.072%), neg=0, invalid=4512 0338: dt=11.520000, rms=0.543 (0.077%), neg=0, invalid=4512 0339: dt=11.520000, rms=0.542 (0.092%), neg=0, invalid=4512 0340: dt=11.520000, rms=0.542 (0.105%), neg=0, invalid=4512 0341: dt=11.520000, rms=0.541 (0.113%), neg=0, invalid=4512 0342: dt=11.520000, rms=0.541 (0.076%), neg=0, invalid=4512 0343: dt=11.520000, rms=0.540 (0.078%), neg=0, invalid=4512 0344: dt=11.520000, rms=0.540 (0.093%), neg=0, invalid=4512 0345: dt=11.520000, rms=0.540 (0.082%), neg=0, invalid=4512 0346: dt=11.520000, rms=0.539 (0.055%), neg=0, invalid=4512 0347: dt=11.520000, rms=0.539 (0.050%), neg=0, invalid=4512 0348: dt=11.520000, rms=0.539 (0.061%), neg=0, invalid=4512 0349: dt=11.520000, rms=0.538 (0.054%), neg=0, invalid=4512 0350: dt=11.520000, rms=0.538 (0.029%), neg=0, invalid=4512 0351: dt=11.520000, rms=0.538 (0.031%), neg=0, invalid=4512 0352: dt=11.520000, rms=0.538 (0.018%), neg=0, invalid=4512 0353: dt=2.880000, rms=0.538 (-0.001%), neg=0, invalid=4512 0354: dt=2.880000, rms=0.538 (0.002%), neg=0, invalid=4512 0355: dt=0.252000, rms=0.538 (0.004%), neg=0, invalid=4512 0356: dt=0.252000, rms=0.538 (-0.001%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.538, neg=0, invalid=4512 0357: dt=0.252000, rms=0.538 (0.094%), neg=0, invalid=4512 0358: dt=0.180000, rms=0.538 (0.001%), neg=0, invalid=4512 0359: dt=0.002813, rms=0.538 (-0.000%), neg=0, invalid=4512 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.559, neg=0, invalid=4512 0360: dt=0.000000, rms=0.558 (0.087%), neg=0, invalid=4512 0361: dt=0.000000, rms=0.558 (0.000%), neg=0, invalid=4512 0362: dt=0.100000, rms=0.558 (-0.121%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.559, neg=0, invalid=4512 0363: dt=0.000000, rms=0.558 (0.087%), neg=0, invalid=4512 0364: dt=0.000000, rms=0.558 (0.000%), neg=0, invalid=4512 0365: dt=0.100000, rms=0.558 (-0.089%), neg=0, invalid=4512 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.524, neg=0, invalid=4512 0366: dt=0.448000, rms=0.508 (3.067%), neg=0, invalid=4512 0367: dt=0.448000, rms=0.505 (0.634%), neg=0, invalid=4512 0368: dt=0.448000, rms=0.503 (0.384%), neg=0, invalid=4512 0369: dt=0.448000, rms=0.502 (0.218%), neg=0, invalid=4512 0370: dt=0.448000, rms=0.501 (0.181%), neg=0, invalid=4512 0371: dt=0.448000, rms=0.501 (0.110%), neg=0, invalid=4512 0372: dt=0.448000, rms=0.500 (0.113%), neg=0, invalid=4512 0373: dt=0.448000, rms=0.500 (0.062%), neg=0, invalid=4512 0374: dt=0.448000, rms=0.499 (0.080%), neg=0, invalid=4512 0375: dt=0.448000, rms=0.499 (0.036%), neg=0, invalid=4512 0376: dt=0.448000, rms=0.499 (0.061%), neg=0, invalid=4512 0377: dt=0.448000, rms=0.498 (0.076%), neg=0, invalid=4512 0378: dt=0.224000, rms=0.498 (0.018%), neg=0, invalid=4512 0379: dt=0.224000, rms=0.498 (0.031%), neg=0, invalid=4512 0380: dt=0.224000, rms=0.498 (0.038%), neg=0, invalid=4512 0381: dt=0.224000, rms=0.498 (0.033%), neg=0, invalid=4512 0382: dt=0.224000, rms=0.498 (0.006%), neg=0, invalid=4512 0383: dt=0.224000, rms=0.498 (0.009%), neg=0, invalid=4512 0384: dt=0.224000, rms=0.498 (0.019%), neg=0, invalid=4512 0385: dt=0.224000, rms=0.498 (0.031%), neg=0, invalid=4512 0386: dt=0.224000, rms=0.497 (0.035%), neg=0, invalid=4512 0387: dt=0.224000, rms=0.497 (0.032%), neg=0, invalid=4512 0388: dt=0.224000, rms=0.497 (0.027%), neg=0, invalid=4512 0389: dt=0.224000, rms=0.497 (0.021%), neg=0, invalid=4512 0390: dt=0.224000, rms=0.497 (0.022%), neg=0, invalid=4512 0391: dt=0.224000, rms=0.497 (0.019%), neg=0, invalid=4512 0392: dt=0.028000, rms=0.497 (0.000%), neg=0, invalid=4512 0393: dt=0.028000, rms=0.497 (0.000%), neg=0, invalid=4512 0394: dt=0.028000, rms=0.497 (-0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.497, neg=0, invalid=4512 0395: dt=0.384000, rms=0.492 (1.028%), neg=0, invalid=4512 0396: dt=0.320000, rms=0.491 (0.171%), neg=0, invalid=4512 0397: dt=0.320000, rms=0.491 (0.073%), neg=0, invalid=4512 0398: dt=0.320000, rms=0.491 (0.027%), neg=0, invalid=4512 0399: dt=0.320000, rms=0.491 (0.016%), neg=0, invalid=4512 0400: dt=0.320000, rms=0.491 (0.017%), neg=0, invalid=4512 0401: dt=0.320000, rms=0.491 (0.010%), neg=0, invalid=4512 0402: dt=0.320000, rms=0.491 (-0.007%), neg=0, invalid=4512 label assignment complete, 0 changed (0.00%) ********************* ALLOWING NEGATIVE NODES IN DEFORMATION******************************** **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.489, neg=0, invalid=4512 0403: dt=0.000000, rms=0.489 (0.124%), neg=0, invalid=4512 0404: dt=0.000000, rms=0.489 (0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.489, neg=0, invalid=4512 0405: dt=129.472000, rms=0.488 (0.186%), neg=0, invalid=4512 0406: dt=92.480000, rms=0.488 (0.014%), neg=0, invalid=4512 0407: dt=92.480000, rms=0.488 (0.019%), neg=0, invalid=4512 0408: dt=92.480000, rms=0.488 (0.025%), neg=0, invalid=4512 0409: dt=92.480000, rms=0.488 (0.023%), neg=0, invalid=4512 0410: dt=92.480000, rms=0.488 (0.015%), neg=0, invalid=4512 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.488, neg=0, invalid=4512 0411: dt=9.072000, rms=0.488 (0.135%), neg=0, invalid=4512 0412: dt=9.072000, rms=0.488 (0.004%), neg=0, invalid=4512 0413: dt=9.072000, rms=0.488 (0.002%), neg=0, invalid=4512 0414: dt=9.072000, rms=0.488 (-0.004%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.488, neg=0, invalid=4512 0415: dt=145.152000, rms=0.486 (0.499%), neg=0, invalid=4512 0416: dt=31.104000, rms=0.486 (0.063%), neg=0, invalid=4512 0417: dt=31.104000, rms=0.485 (0.036%), neg=0, invalid=4512 0418: dt=31.104000, rms=0.485 (0.054%), neg=0, invalid=4512 0419: dt=31.104000, rms=0.485 (0.074%), neg=0, invalid=4512 0420: dt=31.104000, rms=0.484 (0.088%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0421: dt=31.104000, rms=0.484 (0.092%), neg=0, invalid=4512 0422: dt=31.104000, rms=0.483 (0.090%), neg=0, invalid=4512 0423: dt=31.104000, rms=0.483 (0.074%), neg=0, invalid=4512 0424: dt=36.288000, rms=0.483 (0.011%), neg=0, invalid=4512 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.484, neg=0, invalid=4512 iter 0, gcam->neg = 2 after 8 iterations, nbhd size=1, neg = 0 0425: dt=38.400000, rms=0.481 (0.677%), neg=0, invalid=4512 iter 0, gcam->neg = 22 after 10 iterations, nbhd size=1, neg = 0 0426: dt=78.417582, rms=0.477 (0.700%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 7 iterations, nbhd size=1, neg = 0 0427: dt=11.200000, rms=0.476 (0.249%), neg=0, invalid=4512 iter 0, gcam->neg = 3 after 12 iterations, nbhd size=1, neg = 0 0428: dt=11.200000, rms=0.476 (0.111%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0429: dt=11.200000, rms=0.475 (0.076%), neg=0, invalid=4512 iter 0, gcam->neg = 5 after 8 iterations, nbhd size=1, neg = 0 0430: dt=11.200000, rms=0.475 (0.090%), neg=0, invalid=4512 iter 0, gcam->neg = 7 after 11 iterations, nbhd size=1, neg = 0 0431: dt=11.200000, rms=0.474 (0.178%), neg=0, invalid=4512 iter 0, gcam->neg = 8 after 3 iterations, nbhd size=0, neg = 0 0432: dt=11.200000, rms=0.473 (0.234%), neg=0, invalid=4512 iter 0, gcam->neg = 4 after 7 iterations, nbhd size=1, neg = 0 0433: dt=11.200000, rms=0.472 (0.226%), neg=0, invalid=4512 iter 0, gcam->neg = 7 after 9 iterations, nbhd size=1, neg = 0 0434: dt=11.200000, rms=0.471 (0.175%), neg=0, invalid=4512 iter 0, gcam->neg = 9 after 9 iterations, nbhd size=1, neg = 0 0435: dt=11.200000, rms=0.470 (0.149%), neg=0, invalid=4512 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0436: dt=11.200000, rms=0.470 (0.126%), neg=0, invalid=4512 iter 0, gcam->neg = 8 after 12 iterations, nbhd size=1, neg = 0 0437: dt=11.200000, rms=0.469 (0.070%), neg=0, invalid=4512 iter 0, gcam->neg = 10 after 13 iterations, nbhd size=1, neg = 0 0438: dt=11.200000, rms=0.469 (0.090%), neg=0, invalid=4512 iter 0, gcam->neg = 16 after 10 iterations, nbhd size=1, neg = 0 0439: dt=11.200000, rms=0.468 (0.104%), neg=0, invalid=4512 iter 0, gcam->neg = 12 after 10 iterations, nbhd size=1, neg = 0 0440: dt=11.200000, rms=0.468 (0.116%), neg=0, invalid=4512 iter 0, gcam->neg = 15 after 2 iterations, nbhd size=0, neg = 0 0441: dt=11.200000, rms=0.467 (0.113%), neg=0, invalid=4512 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0442: dt=32.000000, rms=0.467 (0.050%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0443: dt=32.000000, rms=0.467 (0.040%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0444: dt=32.000000, rms=0.467 (0.078%), neg=0, invalid=4512 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0445: dt=32.000000, rms=0.467 (0.006%), neg=0, invalid=4512 iter 0, gcam->neg = 6 after 12 iterations, nbhd size=1, neg = 0 0446: dt=32.000000, rms=0.466 (0.105%), neg=0, invalid=4512 iter 0, gcam->neg = 6 after 1 iterations, nbhd size=0, neg = 0 0447: dt=32.000000, rms=0.466 (0.051%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.467, neg=0, invalid=4512 0448: dt=38.133333, rms=0.463 (0.759%), neg=0, invalid=4512 0449: dt=25.600000, rms=0.462 (0.321%), neg=0, invalid=4512 0450: dt=22.814815, rms=0.461 (0.147%), neg=0, invalid=4512 0451: dt=22.814815, rms=0.461 (0.092%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0452: dt=22.814815, rms=0.460 (0.187%), neg=0, invalid=4512 0453: dt=22.814815, rms=0.459 (0.135%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0454: dt=22.814815, rms=0.458 (0.155%), neg=0, invalid=4512 0455: dt=22.814815, rms=0.458 (0.097%), neg=0, invalid=4512 0456: dt=22.814815, rms=0.457 (0.127%), neg=0, invalid=4512 0457: dt=22.814815, rms=0.457 (0.038%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0458: dt=22.814815, rms=0.457 (0.104%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0459: dt=22.814815, rms=0.456 (0.066%), neg=0, invalid=4512 0460: dt=11.200000, rms=0.456 (0.063%), neg=0, invalid=4512 0461: dt=11.200000, rms=0.456 (0.025%), neg=0, invalid=4512 0462: dt=11.200000, rms=0.456 (0.028%), neg=0, invalid=4512 0463: dt=11.200000, rms=0.456 (0.034%), neg=0, invalid=4512 0464: dt=11.200000, rms=0.456 (0.032%), neg=0, invalid=4512 0465: dt=11.200000, rms=0.455 (0.033%), neg=0, invalid=4512 0466: dt=11.200000, rms=0.455 (0.021%), neg=0, invalid=4512 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.461, neg=0, invalid=4512 0467: dt=0.000000, rms=0.460 (0.148%), neg=0, invalid=4512 0468: dt=0.000000, rms=0.460 (0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.461, neg=0, invalid=4512 0469: dt=0.252000, rms=0.460 (0.149%), neg=0, invalid=4512 0470: dt=0.250000, rms=0.460 (0.000%), neg=0, invalid=4512 0471: dt=0.250000, rms=0.460 (-0.000%), neg=0, invalid=4512 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.471, neg=0, invalid=4512 0472: dt=1.024000, rms=0.470 (0.315%), neg=0, invalid=4512 0473: dt=0.256000, rms=0.470 (0.006%), neg=0, invalid=4512 0474: dt=0.256000, rms=0.470 (-0.001%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.470, neg=0, invalid=4512 0475: dt=1.280000, rms=0.469 (0.315%), neg=0, invalid=4512 0476: dt=0.448000, rms=0.469 (0.018%), neg=0, invalid=4512 0477: dt=0.448000, rms=0.469 (0.008%), neg=0, invalid=4512 0478: dt=0.448000, rms=0.469 (-0.020%), neg=0, invalid=4512 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.460, neg=0, invalid=4512 iter 0, gcam->neg = 1212 after 16 iterations, nbhd size=1, neg = 0 0479: dt=2.203815, rms=0.433 (5.967%), neg=0, invalid=4512 0480: dt=0.096000, rms=0.433 (0.091%), neg=0, invalid=4512 0481: dt=0.096000, rms=0.433 (-0.072%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.433, neg=0, invalid=4512 0482: dt=0.096000, rms=0.432 (0.223%), neg=0, invalid=4512 0483: dt=0.000000, rms=0.432 (0.005%), neg=0, invalid=4512 0484: dt=0.050000, rms=0.432 (-0.016%), neg=0, invalid=4512 label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.418, neg=0, invalid=4512 0485: dt=0.000000, rms=0.418 (0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.418, neg=0, invalid=4512 0486: dt=32.368000, rms=0.418 (0.006%), neg=0, invalid=4512 0487: dt=32.368000, rms=0.418 (0.001%), neg=0, invalid=4512 0488: dt=32.368000, rms=0.418 (0.001%), neg=0, invalid=4512 0489: dt=32.368000, rms=0.418 (-0.000%), neg=0, invalid=4512 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.418, neg=0, invalid=4512 0490: dt=0.000000, rms=0.418 (0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.418, neg=0, invalid=4512 0491: dt=36.288000, rms=0.418 (0.024%), neg=0, invalid=4512 0492: dt=82.944000, rms=0.418 (0.019%), neg=0, invalid=4512 0493: dt=82.944000, rms=0.418 (0.017%), neg=0, invalid=4512 0494: dt=82.944000, rms=0.418 (0.011%), neg=0, invalid=4512 0495: dt=82.944000, rms=0.418 (-0.005%), neg=0, invalid=4512 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.419, neg=0, invalid=4512 0496: dt=11.200000, rms=0.419 (0.057%), neg=0, invalid=4512 0497: dt=8.000000, rms=0.418 (0.015%), neg=0, invalid=4512 0498: dt=8.000000, rms=0.418 (0.005%), neg=0, invalid=4512 0499: dt=8.000000, rms=0.418 (-0.021%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.418, neg=0, invalid=4512 0500: dt=77.070423, rms=0.416 (0.603%), neg=0, invalid=4512 0501: dt=25.600000, rms=0.415 (0.292%), neg=0, invalid=4512 0502: dt=76.800000, rms=0.414 (0.182%), neg=0, invalid=4512 0503: dt=76.800000, rms=0.414 (-0.413%), neg=0, invalid=4512 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.417, neg=0, invalid=4512 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0504: dt=8.888889, rms=0.416 (0.198%), neg=0, invalid=4512 iter 0, gcam->neg = 3 after 9 iterations, nbhd size=1, neg = 0 0505: dt=13.161290, rms=0.416 (0.049%), neg=0, invalid=4512 iter 0, gcam->neg = 5 after 11 iterations, nbhd size=1, neg = 0 0506: dt=13.161290, rms=0.415 (0.026%), neg=0, invalid=4512 iter 0, gcam->neg = 13 after 2 iterations, nbhd size=0, neg = 0 0507: dt=13.161290, rms=0.415 (0.036%), neg=0, invalid=4512 iter 0, gcam->neg = 19 after 13 iterations, nbhd size=1, neg = 0 0508: dt=13.161290, rms=0.415 (-0.049%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.415, neg=0, invalid=4512 iter 0, gcam->neg = 1 after 7 iterations, nbhd size=1, neg = 0 0509: dt=19.267606, rms=0.412 (0.733%), neg=0, invalid=4512 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0510: dt=15.714286, rms=0.412 (0.184%), neg=0, invalid=4512 iter 0, gcam->neg = 32 after 10 iterations, nbhd size=1, neg = 0 0511: dt=15.714286, rms=0.411 (0.089%), neg=0, invalid=4512 iter 0, gcam->neg = 45 after 12 iterations, nbhd size=1, neg = 0 0512: dt=15.714286, rms=0.410 (0.175%), neg=0, invalid=4512 iter 0, gcam->neg = 35 after 12 iterations, nbhd size=1, neg = 0 0513: dt=15.714286, rms=0.410 (0.164%), neg=0, invalid=4512 iter 0, gcam->neg = 38 after 12 iterations, nbhd size=1, neg = 0 0514: dt=15.714286, rms=0.409 (0.142%), neg=0, invalid=4512 iter 0, gcam->neg = 51 after 12 iterations, nbhd size=1, neg = 0 0515: dt=15.714286, rms=0.409 (0.142%), neg=0, invalid=4512 iter 0, gcam->neg = 61 after 17 iterations, nbhd size=1, neg = 0 0516: dt=15.714286, rms=0.408 (0.136%), neg=0, invalid=4512 iter 0, gcam->neg = 71 after 17 iterations, nbhd size=1, neg = 0 0517: dt=15.714286, rms=0.408 (0.036%), neg=0, invalid=4512 iter 0, gcam->neg = 85 after 16 iterations, nbhd size=1, neg = 0 0518: dt=15.714286, rms=0.408 (0.039%), neg=0, invalid=4512 iter 0, gcam->neg = 94 after 16 iterations, nbhd size=1, neg = 0 0519: dt=15.714286, rms=0.408 (0.020%), neg=0, invalid=4512 iter 0, gcam->neg = 4 after 0 iterations, nbhd size=0, neg = 0 0520: dt=11.500000, rms=0.407 (0.056%), neg=0, invalid=4512 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0521: dt=16.128000, rms=0.407 (0.043%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0522: dt=16.128000, rms=0.407 (-0.026%), neg=0, invalid=4512 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.413, neg=0, invalid=4512 0523: dt=0.000050, rms=0.413 (0.000%), neg=0, invalid=4512 0524: dt=0.000000, rms=0.413 (0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.413, neg=0, invalid=4512 0525: dt=0.000000, rms=0.413 (0.000%), neg=0, invalid=4512 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.403, neg=0, invalid=4512 iter 0, gcam->neg = 693 after 15 iterations, nbhd size=1, neg = 0 0526: dt=1.418699, rms=0.395 (1.902%), neg=0, invalid=4512 0527: dt=0.000023, rms=0.395 (0.000%), neg=0, invalid=4512 0528: dt=0.000023, rms=0.395 (-0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.395, neg=0, invalid=4512 0529: dt=0.112000, rms=0.395 (0.081%), neg=0, invalid=4512 0530: dt=0.064000, rms=0.395 (0.015%), neg=0, invalid=4512 0531: dt=0.064000, rms=0.395 (0.004%), neg=0, invalid=4512 0532: dt=0.064000, rms=0.395 (-0.033%), neg=0, invalid=4512 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 1 hours, 57 minutes and 10 seconds. mri_ca_register utimesec 7013.653022 mri_ca_register stimesec 10.352598 mri_ca_register ru_maxrss 1340644 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 10002754 mri_ca_register ru_majflt 0 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 0 mri_ca_register ru_oublock 62744 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 5084 mri_ca_register ru_nivcsw 705621 FSRUNTIME@ mri_ca_register 1.9528 hours 1 threads #-------------------------------------- #@# SubCort Seg Fri Nov 13 15:53:32 EST 2020
mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/packages/freesurfer_v6.0.0/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz
sysname Linux hostname blade21.dhe.duke.edu machine x86_64
setenv SUBJECTS_DIR /mnt/munin/Morey/Lab/T1Duke/Freesurfer cd /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/packages/freesurfer_v6.0.0/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/packages/freesurfer_v6.0.0/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 6.63 Atlas used for the 3D morph was /usr/local/packages/freesurfer_v6.0.0/average/RB_all_2016-05-10.vc700.gca average std = 7.3 using min determinant for regularization = 5.3 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.16259 (20) mri peak = 0.10240 (12) Left_Lateral_Ventricle (4): linear fit = 0.50 x + 0.0 (994 voxels, overlap=0.296) Left_Lateral_Ventricle (4): linear fit = 0.50 x + 0.0 (994 voxels, peak = 10), gca=9.9 gca peak = 0.17677 (13) mri peak = 0.10927 ( 8) Right_Lateral_Ventricle (43): linear fit = 0.51 x + 0.0 (787 voxels, overlap=0.422) Right_Lateral_Ventricle (43): linear fit = 0.51 x + 0.0 (787 voxels, peak = 7), gca=6.7 gca peak = 0.28129 (95) mri peak = 0.08808 (95) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (737 voxels, overlap=1.019) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (737 voxels, peak = 96), gca=96.4 gca peak = 0.16930 (96) mri peak = 0.08212 (98) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (718 voxels, overlap=1.014) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (718 voxels, peak = 97), gca=97.4 gca peak = 0.24553 (55) mri peak = 0.08103 (67) Right_Hippocampus (53): linear fit = 1.17 x + 0.0 (1046 voxels, overlap=0.364) Right_Hippocampus (53): linear fit = 1.17 x + 0.0 (1046 voxels, peak = 65), gca=64.6 gca peak = 0.30264 (59) mri peak = 0.08401 (68) Left_Hippocampus (17): linear fit = 1.13 x + 0.0 (986 voxels, overlap=0.718) Left_Hippocampus (17): linear fit = 1.13 x + 0.0 (986 voxels, peak = 67), gca=67.0 gca peak = 0.07580 (103) mri peak = 0.08449 (105) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (48441 voxels, overlap=0.693) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (48441 voxels, peak = 107), gca=106.6 gca peak = 0.07714 (104) mri peak = 0.08577 (106) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (48057 voxels, overlap=0.612) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (48057 voxels, peak = 109), gca=108.7 gca peak = 0.09712 (58) mri peak = 0.03722 (62) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (23106 voxels, overlap=0.967) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (23106 voxels, peak = 59), gca=59.4 gca peak = 0.11620 (58) mri peak = 0.03928 (63) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (21773 voxels, overlap=0.960) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (21773 voxels, peak = 59), gca=59.4 gca peak = 0.30970 (66) mri peak = 0.09857 (67) Right_Caudate (50): linear fit = 0.99 x + 0.0 (941 voxels, overlap=1.007) Right_Caudate (50): linear fit = 0.99 x + 0.0 (941 voxels, peak = 65), gca=65.0 gca peak = 0.15280 (69) mri peak = 0.10000 (73) Left_Caudate (11): linear fit = 0.98 x + 0.0 (809 voxels, overlap=1.002) Left_Caudate (11): linear fit = 0.98 x + 0.0 (809 voxels, peak = 67), gca=67.3 gca peak = 0.13902 (56) mri peak = 0.05731 (60) Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (18820 voxels, overlap=0.956) Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (18820 voxels, peak = 59), gca=58.5 gca peak = 0.14777 (55) mri peak = 0.06443 (62) Right_Cerebellum_Cortex (47): linear fit = 1.12 x + 0.0 (20512 voxels, overlap=0.820) Right_Cerebellum_Cortex (47): linear fit = 1.12 x + 0.0 (20512 voxels, peak = 61), gca=61.3 gca peak = 0.16765 (84) mri peak = 0.09673 (85) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (5531 voxels, overlap=0.864) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (5531 voxels, peak = 86), gca=86.1 gca peak = 0.18739 (84) mri peak = 0.10392 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (5553 voxels, overlap=0.742) Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (5553 voxels, peak = 88), gca=87.8 gca peak = 0.29869 (57) mri peak = 0.11259 (67) Left_Amygdala (18): linear fit = 1.16 x + 0.0 (481 voxels, overlap=0.061) Left_Amygdala (18): linear fit = 1.16 x + 0.0 (481 voxels, peak = 66), gca=66.4 gca peak = 0.33601 (57) mri peak = 0.09178 (65) Right_Amygdala (54): linear fit = 1.13 x + 0.0 (523 voxels, overlap=0.046) Right_Amygdala (54): linear fit = 1.13 x + 0.0 (523 voxels, peak = 65), gca=64.7 gca peak = 0.11131 (90) mri peak = 0.06120 (87) Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (4636 voxels, overlap=0.912) Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (4636 voxels, peak = 92), gca=92.2 gca peak = 0.11793 (83) mri peak = 0.06246 (89) Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (4255 voxels, overlap=0.950) Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (4255 voxels, peak = 87), gca=86.7 gca peak = 0.08324 (81) mri peak = 0.07840 (80) Left_Putamen (12): linear fit = 1.02 x + 0.0 (1872 voxels, overlap=0.851) Left_Putamen (12): linear fit = 1.02 x + 0.0 (1872 voxels, peak = 83), gca=83.0 gca peak = 0.10360 (77) mri peak = 0.07779 (79) Right_Putamen (51): linear fit = 1.02 x + 0.0 (2295 voxels, overlap=0.881) Right_Putamen (51): linear fit = 1.02 x + 0.0 (2295 voxels, peak = 79), gca=78.9 gca peak = 0.08424 (78) mri peak = 0.08304 (83) Brain_Stem (16): linear fit = 1.07 x + 0.0 (12188 voxels, overlap=0.476) Brain_Stem (16): linear fit = 1.07 x + 0.0 (12188 voxels, peak = 83), gca=83.1 gca peak = 0.12631 (89) mri peak = 0.09097 (95) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1534 voxels, overlap=0.421) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1534 voxels, peak = 97), gca=97.5 gca peak = 0.14500 (87) mri peak = 0.08284 (95) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1457 voxels, overlap=0.330) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1457 voxels, peak = 94), gca=93.5 gca peak = 0.14975 (24) mri peak = 0.22222 (14) gca peak = 0.19357 (14) mri peak = 0.13762 (14) Fourth_Ventricle (15): linear fit = 0.93 x + 0.0 (110 voxels, overlap=0.782) Fourth_Ventricle (15): linear fit = 0.93 x + 0.0 (110 voxels, peak = 13), gca=12.9 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 1.00000 (94) gca peak Third_Ventricle = 0.14975 (24) gca peak CSF = 0.23379 (36) gca peak Left_Accumbens_area = 0.70037 (62) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.24655 (23) gca peak Right_Accumbens_area = 0.45042 (65) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.65475 (32) gca peak WM_hypointensities = 0.07854 (76) gca peak non_WM_hypointensities = 0.08491 (43) gca peak Optic_Chiasm = 0.71127 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.11 x + 0.0 estimating mean wm scale to be 1.04 x + 0.0 estimating mean csf scale to be 0.64 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.28812 (10) mri peak = 0.10240 (12) Left_Lateral_Ventricle (4): linear fit = 1.05 x + 0.0 (994 voxels, overlap=1.000) Left_Lateral_Ventricle (4): linear fit = 1.05 x + 0.0 (994 voxels, peak = 11), gca=10.5 gca peak = 0.30003 ( 7) mri peak = 0.10927 ( 8) Right_Lateral_Ventricle (43): linear fit = 1.08 x + 0.0 (787 voxels, overlap=0.964) Right_Lateral_Ventricle (43): linear fit = 1.08 x + 0.0 (787 voxels, peak = 8), gca=7.5 gca peak = 0.25980 (97) mri peak = 0.08808 (95) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (737 voxels, overlap=1.019) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (737 voxels, peak = 97), gca=96.5 gca peak = 0.18386 (98) mri peak = 0.08212 (98) Left_Pallidum (13): linear fit = 0.99 x + 0.0 (718 voxels, overlap=1.011) Left_Pallidum (13): linear fit = 0.99 x + 0.0 (718 voxels, peak = 97), gca=96.5 gca peak = 0.24758 (65) mri peak = 0.08103 (67) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1046 voxels, overlap=1.003) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1046 voxels, peak = 65), gca=65.0 gca peak = 0.27962 (67) mri peak = 0.08401 (68) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (986 voxels, overlap=1.009) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (986 voxels, peak = 67), gca=67.0 gca peak = 0.07501 (106) mri peak = 0.08449 (105) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (48441 voxels, overlap=0.825) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (48441 voxels, peak = 105), gca=105.5 gca peak = 0.07788 (109) mri peak = 0.08577 (106) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (48057 voxels, overlap=0.788) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (48057 voxels, peak = 108), gca=108.5 gca peak = 0.09502 (59) mri peak = 0.03722 (62) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (23106 voxels, overlap=0.981) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (23106 voxels, peak = 60), gca=60.5 gca peak = 0.11326 (59) mri peak = 0.03928 (63) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (21773 voxels, overlap=0.970) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (21773 voxels, peak = 60), gca=60.5 gca peak = 0.31027 (65) mri peak = 0.09857 (67) Right_Caudate (50): linear fit = 1.00 x + 0.0 (941 voxels, overlap=1.007) Right_Caudate (50): linear fit = 1.00 x + 0.0 (941 voxels, peak = 65), gca=65.0 gca peak = 0.13850 (68) mri peak = 0.10000 (73) Left_Caudate (11): linear fit = 1.00 x + 0.0 (809 voxels, overlap=1.000) Left_Caudate (11): linear fit = 1.00 x + 0.0 (809 voxels, peak = 68), gca=68.0 gca peak = 0.13268 (57) mri peak = 0.05731 (60) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (18820 voxels, overlap=0.995) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (18820 voxels, peak = 58), gca=58.4 gca peak = 0.14076 (61) mri peak = 0.06443 (62) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (20512 voxels, overlap=0.993) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (20512 voxels, peak = 61), gca=61.0 gca peak = 0.15819 (86) mri peak = 0.09673 (85) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5531 voxels, overlap=0.937) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5531 voxels, peak = 86), gca=86.0 gca peak = 0.16825 (88) mri peak = 0.10392 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5553 voxels, overlap=0.921) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5553 voxels, peak = 88), gca=87.6 gca peak = 0.26359 (66) mri peak = 0.11259 (67) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (481 voxels, overlap=1.016) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (481 voxels, peak = 66), gca=66.0 gca peak = 0.32369 (65) mri peak = 0.09178 (65) Right_Amygdala (54): linear fit = 1.02 x + 0.0 (523 voxels, overlap=0.999) Right_Amygdala (54): linear fit = 1.02 x + 0.0 (523 voxels, peak = 67), gca=66.6 gca peak = 0.10627 (92) mri peak = 0.06120 (87) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4636 voxels, overlap=0.971) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4636 voxels, peak = 92), gca=91.5 gca peak = 0.09389 (90) mri peak = 0.06246 (89) Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (4255 voxels, overlap=0.985) Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (4255 voxels, peak = 89), gca=88.7 gca peak = 0.09216 (77) mri peak = 0.07840 (80) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1872 voxels, overlap=0.899) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1872 voxels, peak = 77), gca=76.6 gca peak = 0.10144 (79) mri peak = 0.07779 (79) Right_Putamen (51): linear fit = 1.01 x + 0.0 (2295 voxels, overlap=0.974) Right_Putamen (51): linear fit = 1.01 x + 0.0 (2295 voxels, peak = 80), gca=80.2 gca peak = 0.07278 (83) mri peak = 0.08304 (83) Brain_Stem (16): linear fit = 1.02 x + 0.0 (12188 voxels, overlap=0.725) Brain_Stem (16): linear fit = 1.02 x + 0.0 (12188 voxels, peak = 85), gca=85.1 gca peak = 0.11830 (92) mri peak = 0.09097 (95) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1534 voxels, overlap=0.825) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1534 voxels, peak = 92), gca=91.5 gca peak = 0.16587 (92) mri peak = 0.08284 (95) Left_VentralDC (28): linear fit = 1.01 x + 0.0 (1457 voxels, overlap=0.863) Left_VentralDC (28): linear fit = 1.01 x + 0.0 (1457 voxels, peak = 93), gca=93.4 gca peak = 0.24282 (17) mri peak = 0.22222 (14) gca peak = 0.19357 (13) mri peak = 0.13762 (14) Fourth_Ventricle (15): linear fit = 1.03 x + 0.0 (110 voxels, overlap=0.803) Fourth_Ventricle (15): linear fit = 1.03 x + 0.0 (110 voxels, peak = 13), gca=13.5 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.15778 (30) gca peak Left_Thalamus = 0.64095 (104) gca peak Third_Ventricle = 0.24282 (17) gca peak CSF = 0.22373 (23) gca peak Left_Accumbens_area = 0.49175 (60) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75962 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.21739 (27) gca peak Right_Accumbens_area = 0.45113 (64) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.54101 (21) gca peak WM_hypointensities = 0.07274 (74) gca peak non_WM_hypointensities = 0.09744 (45) gca peak Optic_Chiasm = 0.71047 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.01 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.05 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 72124 voxels changed in iteration 0 of unlikely voxel relabeling 316 voxels changed in iteration 1 of unlikely voxel relabeling 13 voxels changed in iteration 2 of unlikely voxel relabeling 1 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 42470 gm and wm labels changed (%23 to gray, %77 to white out of all changed labels) 379 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 72517 changed. image ll: -2.116, PF=0.500 pass 2: 19854 changed. image ll: -2.116, PF=0.500 pass 3: 5873 changed. pass 4: 2009 changed. 44218 voxels changed in iteration 0 of unlikely voxel relabeling 234 voxels changed in iteration 1 of unlikely voxel relabeling 14 voxels changed in iteration 2 of unlikely voxel relabeling 3 voxels changed in iteration 3 of unlikely voxel relabeling 1 voxels changed in iteration 4 of unlikely voxel relabeling 7971 voxels changed in iteration 0 of unlikely voxel relabeling 87 voxels changed in iteration 1 of unlikely voxel relabeling 11 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 6796 voxels changed in iteration 0 of unlikely voxel relabeling 106 voxels changed in iteration 1 of unlikely voxel relabeling 3 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 4898 voxels changed in iteration 0 of unlikely voxel relabeling 16 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling MRItoUCHAR: min=0, max=85 MRItoUCHAR: converting to UCHAR writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 2448.509228 mri_ca_label stimesec 4.489627 mri_ca_label ru_maxrss 2105276 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 5508935 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 0 mri_ca_label ru_oublock 496 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 607 mri_ca_label ru_nivcsw 246119 auto-labeling took 40 minutes and 54 seconds.
mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri/transforms/cc_up.lta 13265
will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri/transforms/cc_up.lta reading aseg from /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri/aseg.auto_noCCseg.mgz reading norm from /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri/norm.mgz 26766 voxels in left wm, 59703 in right wm, xrange [122, 132] searching rotation angles z=[-9 5], y=[-8 6]
searching scale 1 Z rot -8.9 searching scale 1 Z rot -8.6 searching scale 1 Z rot -8.4 searching scale 1 Z rot -8.1 searching scale 1 Z rot -7.9 searching scale 1 Z rot -7.6 searching scale 1 Z rot -7.4 searching scale 1 Z rot -7.1 searching scale 1 Z rot -6.9 searching scale 1 Z rot -6.6 searching scale 1 Z rot -6.4 searching scale 1 Z rot -6.1 searching scale 1 Z rot -5.9 searching scale 1 Z rot -5.6 searching scale 1 Z rot -5.4 searching scale 1 Z rot -5.1 searching scale 1 Z rot -4.9 searching scale 1 Z rot -4.6 searching scale 1 Z rot -4.4 searching scale 1 Z rot -4.1 searching scale 1 Z rot -3.9 searching scale 1 Z rot -3.6 searching scale 1 Z rot -3.4 searching scale 1 Z rot -3.1 searching scale 1 Z rot -2.9 searching scale 1 Z rot -2.6 searching scale 1 Z rot -2.4 searching scale 1 Z rot -2.1 searching scale 1 Z rot -1.9 searching scale 1 Z rot -1.6 searching scale 1 Z rot -1.4 searching scale 1 Z rot -1.1 searching scale 1 Z rot -0.9 searching scale 1 Z rot -0.6 searching scale 1 Z rot -0.4 searching scale 1 Z rot -0.1 searching scale 1 Z rot 0.1 searching scale 1 Z rot 0.4 searching scale 1 Z rot 0.6 searching scale 1 Z rot 0.9 searching scale 1 Z rot 1.1 searching scale 1 Z rot 1.4 searching scale 1 Z rot 1.6 searching scale 1 Z rot 1.9 searching scale 1 Z rot 2.1 searching scale 1 Z rot 2.4 searching scale 1 Z rot 2.6 searching scale 1 Z rot 2.9 searching scale 1 Z rot 3.1 searching scale 1 Z rot 3.4 searching scale 1 Z rot 3.6 searching scale 1 Z rot 3.9 searching scale 1 Z rot 4.1 searching scale 1 Z rot 4.4 searching scale 1 Z rot 4.6 searching scale 1 Z rot 4.9 global minimum found at slice 128.1, rotations (-1.40, -1.90) final transformation (x=128.1, yr=-1.397, zr=-1.896): 0.99916 0.03309 -0.02436 -1.15506; -0.03308 0.99945 0.00081 12.21022; 0.02438 0.00000 0.99970 7.91111; 0.00000 0.00000 0.00000 1.00000; updating x range to be [126, 130] in xformed coordinates best xformed slice 129 cc center is found at 129 120 117 eigenvectors: -0.00088 -0.00200 1.00000; -0.03141 -0.99950 -0.00203; 0.99951 -0.03141 0.00081; error in mid anterior detected - correcting... writing aseg with callosum to /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri/aseg.auto.mgz... corpus callosum segmentation took 0.6 minutes #-------------------------------------- #@# Merge ASeg Fri Nov 13 16:35:01 EST 2020
cp aseg.auto.mgz aseg.presurf.mgz
#-------------------------------------------- #@# Intensity Normalization2 Fri Nov 13 16:35:01 EST 2020 /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri
mri_normalize -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz
assuming input volume is MGH (Van der Kouwe) MP-RAGE using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.presurf.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 1117 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8...
Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 109 gm peak at 66 (66), valley at 26 (26) csf peak at 34, 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 66 (66), valley at 39 (39) csf peak at 20, setting threshold to 50 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 2 minutes and 11 seconds. #-------------------------------------------- #@# Mask BFS Fri Nov 13 16:37:14 EST 2020 /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri
mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
threshold mask volume at 5 DoAbs = 0 Found 1551223 voxels in mask (pct= 9.25) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Fri Nov 13 16:37:15 EST 2020
mri_segment -mprage brain.mgz wm.seg.mgz
doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (104.0): 104.8 +- 5.5 [79.0 --> 125.0] GM (70.0) : 68.4 +- 10.3 [30.0 --> 95.0] setting bottom of white matter range to 78.7 setting top of gray matter range to 89.0 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels...
reclassifying voxels using Gaussian border classifier...
removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 10620 sparsely connected voxels removed... thickening thin strands.... 20 segments, 5174 filled 491 bright non-wm voxels segmented. 5009 diagonally connected voxels added... white matter segmentation took 1.2 minutes writing output to wm.seg.mgz... assuming input volume is MGH (Van der Kouwe) MP-RAGE
mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz
preserving editing changes in input volume... auto filling took 0.33 minutes reading wm segmentation from wm.seg.mgz... 167 voxels added to wm to prevent paths from MTL structures to cortex 3031 additional wm voxels added 0 additional wm voxels added SEG EDIT: 41184 voxels turned on, 45871 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 97 new 97 115,126,128 old 97 new 97 writing edited volume to wm.asegedit.mgz....
mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz
Iteration Number : 1 pass 1 (xy+): 28 found - 28 modified | TOTAL: 28 pass 2 (xy+): 0 found - 28 modified | TOTAL: 28 pass 1 (xy-): 29 found - 29 modified | TOTAL: 57 pass 2 (xy-): 0 found - 29 modified | TOTAL: 57 pass 1 (yz+): 43 found - 43 modified | TOTAL: 100 pass 2 (yz+): 0 found - 43 modified | TOTAL: 100 pass 1 (yz-): 21 found - 21 modified | TOTAL: 121 pass 2 (yz-): 0 found - 21 modified | TOTAL: 121 pass 1 (xz+): 24 found - 24 modified | TOTAL: 145 pass 2 (xz+): 0 found - 24 modified | TOTAL: 145 pass 1 (xz-): 33 found - 33 modified | TOTAL: 178 pass 2 (xz-): 0 found - 33 modified | TOTAL: 178 Iteration Number : 1 pass 1 (+++): 20 found - 20 modified | TOTAL: 20 pass 2 (+++): 0 found - 20 modified | TOTAL: 20 pass 1 (+++): 19 found - 19 modified | TOTAL: 39 pass 2 (+++): 0 found - 19 modified | TOTAL: 39 pass 1 (+++): 26 found - 26 modified | TOTAL: 65 pass 2 (+++): 0 found - 26 modified | TOTAL: 65 pass 1 (+++): 44 found - 44 modified | TOTAL: 109 pass 2 (+++): 0 found - 44 modified | TOTAL: 109 Iteration Number : 1 pass 1 (++): 116 found - 116 modified | TOTAL: 116 pass 2 (++): 0 found - 116 modified | TOTAL: 116 pass 1 (+-): 124 found - 124 modified | TOTAL: 240 pass 2 (+-): 0 found - 124 modified | TOTAL: 240 pass 1 (--): 109 found - 109 modified | TOTAL: 349 pass 2 (--): 0 found - 109 modified | TOTAL: 349 pass 1 (-+): 98 found - 98 modified | TOTAL: 447 pass 2 (-+): 0 found - 98 modified | TOTAL: 447 Iteration Number : 2 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 7 found - 7 modified | TOTAL: 10 pass 2 (xy-): 0 found - 7 modified | TOTAL: 10 pass 1 (yz+): 10 found - 10 modified | TOTAL: 20 pass 2 (yz+): 0 found - 10 modified | TOTAL: 20 pass 1 (yz-): 9 found - 9 modified | TOTAL: 29 pass 2 (yz-): 0 found - 9 modified | TOTAL: 29 pass 1 (xz+): 13 found - 13 modified | TOTAL: 42 pass 2 (xz+): 0 found - 13 modified | TOTAL: 42 pass 1 (xz-): 3 found - 3 modified | TOTAL: 45 pass 2 (xz-): 0 found - 3 modified | TOTAL: 45 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 6 found - 6 modified | TOTAL: 6 pass 2 (+++): 0 found - 6 modified | TOTAL: 6 pass 1 (+++): 0 found - 0 modified | TOTAL: 6 Iteration Number : 2 pass 1 (++): 2 found - 2 modified | TOTAL: 2 pass 2 (++): 0 found - 2 modified | TOTAL: 2 pass 1 (+-): 3 found - 3 modified | TOTAL: 5 pass 2 (+-): 0 found - 3 modified | TOTAL: 5 pass 1 (--): 4 found - 4 modified | TOTAL: 9 pass 2 (--): 0 found - 4 modified | TOTAL: 9 pass 1 (-+): 5 found - 5 modified | TOTAL: 14 pass 2 (-+): 0 found - 5 modified | TOTAL: 14 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 1 found - 1 modified | TOTAL: 2 pass 2 (xz-): 0 found - 1 modified | TOTAL: 2 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 1 found - 1 modified | TOTAL: 2 pass 2 (+-): 0 found - 1 modified | TOTAL: 2 pass 1 (--): 0 found - 0 modified | TOTAL: 2 pass 1 (-+): 0 found - 0 modified | TOTAL: 2 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 1 found - 1 modified | TOTAL: 1 pass 2 (--): 0 found - 1 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 5 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 5 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 5 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 6 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 6 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 6 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0
Total Number of Modified Voxels = 807 (out of 628620: 0.128376) binarizing input wm segmentation... Ambiguous edge configurations...
mri_pretess done
#-------------------------------------------- #@# Fill Fri Nov 13 16:38:53 EST 2020 /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri
mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz
logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.01897 0.00293 -0.01249 -3.88443; -0.00353 1.18189 0.13522 -51.24037; 0.00303 -0.14908 0.98486 7.08509; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.01897 0.00293 -0.01249 -3.88443; -0.00353 1.18189 0.13522 -51.24037; 0.00303 -0.14908 0.98486 7.08509; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1343 (min = 350, max = 1400), aspect = 0.44 (min = 0.10, max = 0.75) no need to search using seed (126, 125, 155), TAL = (2.0, 27.0, 3.0) talairach voxel to voxel transform 0.98134 -0.00085 0.01256 3.67955; 0.00322 0.83169 -0.11415 43.43768; -0.00253 0.12590 0.99806 -0.63025; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (126, 125, 155) --> (2.0, 27.0, 3.0) done. writing output to filled.mgz... filling took 0.4 minutes talairach cc position changed to (2.00, 27.00, 3.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, 27.00, 3.00) SRC: (111.51, 130.05, 169.53) search lh wm seed point around talairach space (-16.00, 27.00, 3.00), SRC: (146.83, 130.17, 169.44) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Fri Nov 13 16:39:18 EST 2020 /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/scripts
mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz
Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 1 found - 1 modified | TOTAL: 2 pass 2 (xy-): 0 found - 1 modified | TOTAL: 2 pass 1 (yz+): 2 found - 2 modified | TOTAL: 4 pass 2 (yz+): 0 found - 2 modified | TOTAL: 4 pass 1 (yz-): 1 found - 1 modified | TOTAL: 5 pass 2 (yz-): 0 found - 1 modified | TOTAL: 5 pass 1 (xz+): 2 found - 2 modified | TOTAL: 7 pass 2 (xz+): 0 found - 2 modified | TOTAL: 7 pass 1 (xz-): 1 found - 1 modified | TOTAL: 8 pass 2 (xz-): 0 found - 1 modified | TOTAL: 8 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 1 found - 1 modified | TOTAL: 2 pass 2 (-+): 0 found - 1 modified | TOTAL: 2 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 1 found - 1 modified | TOTAL: 2 pass 2 (yz+): 0 found - 1 modified | TOTAL: 2 pass 1 (yz-): 0 found - 0 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0
Total Number of Modified Voxels = 12 (out of 302658: 0.003965) Ambiguous edge configurations...
mri_pretess done
mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix
$Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.2 2016/10/27 22:25:31 zkaufman Exp $ slice 40: 320 vertices, 369 faces slice 50: 4914 vertices, 5129 faces slice 60: 13017 vertices, 13345 faces slice 70: 23220 vertices, 23626 faces slice 80: 34676 vertices, 35078 faces slice 90: 45749 vertices, 46119 faces slice 100: 57447 vertices, 57871 faces slice 110: 69450 vertices, 69873 faces slice 120: 81023 vertices, 81456 faces slice 130: 92290 vertices, 92754 faces slice 140: 103633 vertices, 104086 faces slice 150: 114137 vertices, 114579 faces slice 160: 122584 vertices, 122966 faces slice 170: 130075 vertices, 130451 faces slice 180: 136925 vertices, 137259 faces slice 190: 143097 vertices, 143423 faces slice 200: 147598 vertices, 147833 faces slice 210: 149688 vertices, 149798 faces slice 220: 149688 vertices, 149798 faces slice 230: 149688 vertices, 149798 faces slice 240: 149688 vertices, 149798 faces slice 250: 149688 vertices, 149798 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000;
rm -f ../mri/filled-pretess255.mgz
mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix
counting number of connected components... 149688 voxel in cpt #1: X=-110 [v=149688,e=449394,f=299596] located at (-27.733900, -12.186969, 0.766020) For the whole surface: X=-110 [v=149688,e=449394,f=299596] One single component has been found nothing to do done
#-------------------------------------------- #@# Tessellate rh Fri Nov 13 16:39:23 EST 2020 /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/scripts
mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz
Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 4 found - 4 modified | TOTAL: 5 pass 2 (yz+): 0 found - 4 modified | TOTAL: 5 pass 1 (yz-): 2 found - 2 modified | TOTAL: 7 pass 2 (yz-): 0 found - 2 modified | TOTAL: 7 pass 1 (xz+): 0 found - 0 modified | TOTAL: 7 pass 1 (xz-): 0 found - 0 modified | TOTAL: 7 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 1 found - 1 modified | TOTAL: 1 pass 2 (-+): 0 found - 1 modified | TOTAL: 1 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0
Total Number of Modified Voxels = 8 (out of 303935: 0.002632) Ambiguous edge configurations...
mri_pretess done
mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix
$Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.2 2016/10/27 22:25:31 zkaufman Exp $ slice 40: 98 vertices, 109 faces slice 50: 2558 vertices, 2713 faces slice 60: 9376 vertices, 9643 faces slice 70: 19153 vertices, 19531 faces slice 80: 29906 vertices, 30323 faces slice 90: 41551 vertices, 41925 faces slice 100: 52600 vertices, 52979 faces slice 110: 64965 vertices, 65413 faces slice 120: 76832 vertices, 77258 faces slice 130: 88443 vertices, 88898 faces slice 140: 100084 vertices, 100523 faces slice 150: 111567 vertices, 111998 faces slice 160: 120962 vertices, 121342 faces slice 170: 129096 vertices, 129454 faces slice 180: 136242 vertices, 136574 faces slice 190: 142637 vertices, 142957 faces slice 200: 147987 vertices, 148241 faces slice 210: 151122 vertices, 151237 faces slice 220: 151174 vertices, 151276 faces slice 230: 151174 vertices, 151276 faces slice 240: 151174 vertices, 151276 faces slice 250: 151174 vertices, 151276 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000;
rm -f ../mri/filled-pretess127.mgz
mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix
counting number of connected components... 151174 voxel in cpt #1: X=-102 [v=151174,e=453828,f=302552] located at (27.245796, -8.269947, 2.955535) For the whole surface: X=-102 [v=151174,e=453828,f=302552] One single component has been found nothing to do done
#-------------------------------------------- #@# Smooth1 lh Fri Nov 13 16:39:28 EST 2020 /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/scripts
mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix
setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Smooth1 rh Fri Nov 13 16:39:32 EST 2020 /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/scripts
mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix
setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Fri Nov 13 16:39:37 EST 2020 /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/scripts
mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix
Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 48.9 mm, total surface area = 78067 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.5 minutes
step 000: RMS=0.159 (target=0.015) step 005: RMS=0.120 (target=0.015) step 010: RMS=0.094 (target=0.015) step 015: RMS=0.082 (target=0.015) step 020: RMS=0.073 (target=0.015) step 025: RMS=0.066 (target=0.015) step 030: RMS=0.062 (target=0.015) step 035: RMS=0.058 (target=0.015) step 040: RMS=0.055 (target=0.015) step 045: RMS=0.052 (target=0.015) step 050: RMS=0.052 (target=0.015) step 055: RMS=0.051 (target=0.015) step 060: RMS=0.052 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 28.529071 mris_inflate stimesec 0.141826 mris_inflate ru_maxrss 191696 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 141654 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 10536 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 987 mris_inflate ru_nivcsw 2901 #-------------------------------------------- #@# Inflation1 rh Fri Nov 13 16:40:06 EST 2020 /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/scripts
mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix
Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 48.5 mm, total surface area = 78065 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.5 minutes
step 000: RMS=0.163 (target=0.015) step 005: RMS=0.122 (target=0.015) step 010: RMS=0.095 (target=0.015) step 015: RMS=0.083 (target=0.015) step 020: RMS=0.074 (target=0.015) step 025: RMS=0.067 (target=0.015) step 030: RMS=0.063 (target=0.015) step 035: RMS=0.058 (target=0.015) step 040: RMS=0.054 (target=0.015) step 045: RMS=0.053 (target=0.015) step 050: RMS=0.051 (target=0.015) step 055: RMS=0.051 (target=0.015) step 060: RMS=0.050 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 28.751984 mris_inflate stimesec 0.159916 mris_inflate ru_maxrss 193744 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 144745 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 10640 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 1009 mris_inflate ru_nivcsw 2921 #-------------------------------------------- #@# QSphere lh Fri Nov 13 16:40:35 EST 2020 /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/scripts
mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix
doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.2 2016/10/27 22:25:31 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.94 +- 0.57 (0.00-->6.88) (max @ vno 58291 --> 58292) face area 0.02 +- 0.03 (-0.12-->0.45)
== Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.293... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.200, avgs=0 005/300: dt: 0.9000, rms radial error=176.937, avgs=0 010/300: dt: 0.9000, rms radial error=176.374, avgs=0 015/300: dt: 0.9000, rms radial error=175.638, avgs=0 020/300: dt: 0.9000, rms radial error=174.801, avgs=0 025/300: dt: 0.9000, rms radial error=173.906, avgs=0 030/300: dt: 0.9000, rms radial error=172.979, avgs=0 035/300: dt: 0.9000, rms radial error=172.036, avgs=0 040/300: dt: 0.9000, rms radial error=171.085, avgs=0 045/300: dt: 0.9000, rms radial error=170.132, avgs=0 050/300: dt: 0.9000, rms radial error=169.178, avgs=0 055/300: dt: 0.9000, rms radial error=168.228, avgs=0 060/300: dt: 0.9000, rms radial error=167.281, avgs=0 065/300: dt: 0.9000, rms radial error=166.339, avgs=0 070/300: dt: 0.9000, rms radial error=165.401, avgs=0 075/300: dt: 0.9000, rms radial error=164.471, avgs=0 080/300: dt: 0.9000, rms radial error=163.547, avgs=0 085/300: dt: 0.9000, rms radial error=162.628, avgs=0 090/300: dt: 0.9000, rms radial error=161.714, avgs=0 095/300: dt: 0.9000, rms radial error=160.805, avgs=0 100/300: dt: 0.9000, rms radial error=159.901, avgs=0 105/300: dt: 0.9000, rms radial error=159.002, avgs=0 110/300: dt: 0.9000, rms radial error=158.108, avgs=0 115/300: dt: 0.9000, rms radial error=157.218, avgs=0 120/300: dt: 0.9000, rms radial error=156.334, avgs=0 125/300: dt: 0.9000, rms radial error=155.454, avgs=0 130/300: dt: 0.9000, rms radial error=154.579, avgs=0 135/300: dt: 0.9000, rms radial error=153.709, avgs=0 140/300: dt: 0.9000, rms radial error=152.844, avgs=0 145/300: dt: 0.9000, rms radial error=151.983, avgs=0 150/300: dt: 0.9000, rms radial error=151.128, avgs=0 155/300: dt: 0.9000, rms radial error=150.276, avgs=0 160/300: dt: 0.9000, rms radial error=149.430, avgs=0 165/300: dt: 0.9000, rms radial error=148.588, avgs=0 170/300: dt: 0.9000, rms radial error=147.751, avgs=0 175/300: dt: 0.9000, rms radial error=146.918, avgs=0 180/300: dt: 0.9000, rms radial error=146.090, avgs=0 185/300: dt: 0.9000, rms radial error=145.267, avgs=0 190/300: dt: 0.9000, rms radial error=144.449, avgs=0 195/300: dt: 0.9000, rms radial error=143.634, avgs=0 200/300: dt: 0.9000, rms radial error=142.825, avgs=0 205/300: dt: 0.9000, rms radial error=142.020, avgs=0 210/300: dt: 0.9000, rms radial error=141.219, avgs=0 215/300: dt: 0.9000, rms radial error=140.424, avgs=0 220/300: dt: 0.9000, rms radial error=139.632, avgs=0 225/300: dt: 0.9000, rms radial error=138.845, avgs=0 230/300: dt: 0.9000, rms radial error=138.062, avgs=0 235/300: dt: 0.9000, rms radial error=137.284, avgs=0 240/300: dt: 0.9000, rms radial error=136.510, avgs=0 245/300: dt: 0.9000, rms radial error=135.740, avgs=0 250/300: dt: 0.9000, rms radial error=134.974, avgs=0 255/300: dt: 0.9000, rms radial error=134.213, avgs=0 260/300: dt: 0.9000, rms radial error=133.456, avgs=0 265/300: dt: 0.9000, rms radial error=132.703, avgs=0 270/300: dt: 0.9000, rms radial error=131.954, avgs=0 275/300: dt: 0.9000, rms radial error=131.210, avgs=0 280/300: dt: 0.9000, rms radial error=130.469, avgs=0 285/300: dt: 0.9000, rms radial error=129.733, avgs=0 290/300: dt: 0.9000, rms radial error=129.001, avgs=0 295/300: dt: 0.9000, rms radial error=128.273, avgs=0 300/300: dt: 0.9000, rms radial error=127.549, avgs=0
spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 17888.35 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00015 epoch 2 (K=40.0), pass 1, starting sse = 3138.19 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00004 epoch 3 (K=160.0), pass 1, starting sse = 363.23 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/11 = 0.00674 epoch 4 (K=640.0), pass 1, starting sse = 30.27 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.12/16 = 0.00750 final distance error %28.05 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.06 hours mris_sphere utimesec 199.181623 mris_sphere stimesec 0.184917 mris_sphere ru_maxrss 191924 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 235380 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 10536 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 1049 mris_sphere ru_nivcsw 19979 FSRUNTIME@ mris_sphere 0.0555 hours 1 threads #-------------------------------------------- #@# QSphere rh Fri Nov 13 16:43:55 EST 2020 /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/scripts
mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix
doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.2 2016/10/27 22:25:31 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.94 +- 0.57 (0.00-->5.96) (max @ vno 109219 --> 110267) face area 0.02 +- 0.03 (-0.09-->0.49)
== Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.290... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.525, avgs=0 005/300: dt: 0.9000, rms radial error=177.263, avgs=0 010/300: dt: 0.9000, rms radial error=176.701, avgs=0 015/300: dt: 0.9000, rms radial error=175.962, avgs=0 020/300: dt: 0.9000, rms radial error=175.120, avgs=0 025/300: dt: 0.9000, rms radial error=174.223, avgs=0 030/300: dt: 0.9000, rms radial error=173.296, avgs=0 035/300: dt: 0.9000, rms radial error=172.352, avgs=0 040/300: dt: 0.9000, rms radial error=171.400, avgs=0 045/300: dt: 0.9000, rms radial error=170.445, avgs=0 050/300: dt: 0.9000, rms radial error=169.491, avgs=0 055/300: dt: 0.9000, rms radial error=168.539, avgs=0 060/300: dt: 0.9000, rms radial error=167.591, avgs=0 065/300: dt: 0.9000, rms radial error=166.648, avgs=0 070/300: dt: 0.9000, rms radial error=165.709, avgs=0 075/300: dt: 0.9000, rms radial error=164.774, avgs=0 080/300: dt: 0.9000, rms radial error=163.845, avgs=0 085/300: dt: 0.9000, rms radial error=162.922, avgs=0 090/300: dt: 0.9000, rms radial error=162.005, avgs=0 095/300: dt: 0.9000, rms radial error=161.093, avgs=0 100/300: dt: 0.9000, rms radial error=160.185, avgs=0 105/300: dt: 0.9000, rms radial error=159.283, avgs=0 110/300: dt: 0.9000, rms radial error=158.385, avgs=0 115/300: dt: 0.9000, rms radial error=157.492, avgs=0 120/300: dt: 0.9000, rms radial error=156.604, avgs=0 125/300: dt: 0.9000, rms radial error=155.721, avgs=0 130/300: dt: 0.9000, rms radial error=154.843, avgs=0 135/300: dt: 0.9000, rms radial error=153.969, avgs=0 140/300: dt: 0.9000, rms radial error=153.100, avgs=0 145/300: dt: 0.9000, rms radial error=152.236, avgs=0 150/300: dt: 0.9000, rms radial error=151.378, avgs=0 155/300: dt: 0.9000, rms radial error=150.525, avgs=0 160/300: dt: 0.9000, rms radial error=149.676, avgs=0 165/300: dt: 0.9000, rms radial error=148.832, avgs=0 170/300: dt: 0.9000, rms radial error=147.993, avgs=0 175/300: dt: 0.9000, rms radial error=147.159, avgs=0 180/300: dt: 0.9000, rms radial error=146.331, avgs=0 185/300: dt: 0.9000, rms radial error=145.508, avgs=0 190/300: dt: 0.9000, rms radial error=144.689, avgs=0 195/300: dt: 0.9000, rms radial error=143.875, avgs=0 200/300: dt: 0.9000, rms radial error=143.066, avgs=0 205/300: dt: 0.9000, rms radial error=142.261, avgs=0 210/300: dt: 0.9000, rms radial error=141.460, avgs=0 215/300: dt: 0.9000, rms radial error=140.664, avgs=0 220/300: dt: 0.9000, rms radial error=139.872, avgs=0 225/300: dt: 0.9000, rms radial error=139.085, avgs=0 230/300: dt: 0.9000, rms radial error=138.302, avgs=0 235/300: dt: 0.9000, rms radial error=137.523, avgs=0 240/300: dt: 0.9000, rms radial error=136.749, avgs=0 245/300: dt: 0.9000, rms radial error=135.979, avgs=0 250/300: dt: 0.9000, rms radial error=135.213, avgs=0 255/300: dt: 0.9000, rms radial error=134.452, avgs=0 260/300: dt: 0.9000, rms radial error=133.694, avgs=0 265/300: dt: 0.9000, rms radial error=132.941, avgs=0 270/300: dt: 0.9000, rms radial error=132.193, avgs=0 275/300: dt: 0.9000, rms radial error=131.448, avgs=0 280/300: dt: 0.9000, rms radial error=130.707, avgs=0 285/300: dt: 0.9000, rms radial error=129.971, avgs=0 290/300: dt: 0.9000, rms radial error=129.238, avgs=0 295/300: dt: 0.9000, rms radial error=128.510, avgs=0 300/300: dt: 0.9000, rms radial error=127.786, avgs=0
spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 18132.74 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00012 epoch 2 (K=40.0), pass 1, starting sse = 3189.58 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00003 epoch 3 (K=160.0), pass 1, starting sse = 364.83 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/11 = 0.00599 epoch 4 (K=640.0), pass 1, starting sse = 28.10 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.09/13 = 0.00674 final distance error %26.95 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.06 hours mris_sphere utimesec 202.889765 mris_sphere stimesec 0.210848 mris_sphere ru_maxrss 193960 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 240515 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 10640 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 1032 mris_sphere ru_nivcsw 20399 FSRUNTIME@ mris_sphere 0.0565 hours 1 threads Linux blade21.dhe.duke.edu 3.10.0-1160.2.2.el7.x86_64 #1 SMP Mon Oct 19 10:20:12 CDT 2020 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 13265 exited with ERRORS at Fri Nov 13 16:47:19 EST 2020
To report a problem, see http://secure-web.cisco.com/1uz1bY-u0QAoQtk-bC3TyIlhK_DXsEcYGzkXETONSDseH80H...
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Fischl, Bruce BFISCHL@mgh.harvard.edu Sent: Thursday, December 3, 2020 11:56 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all issues debugging
Hi Courtney
Can you send us the recon-all.log file and the full screen output from one job that failed?
Cheers
Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Courtney Haswell Sent: Thursday, December 3, 2020 9:52 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] recon-all issues debugging
External Email - Use Caution
I am trying to debug why all of our T1's are failing Freesurfer recon-all. It seems that most of the files are being created but it isn't getting to the stats steps to output those files. In the recon-all log it does say "recon-all -s 13265 exited with ERRORS."
I looked in the recon-all.error file and the only thing in that is "CMD mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix." Would this be the step where the error is happening?
I have checked the T1 thoroughly and it is good quality. What is the best way to debug why this is happening with our scans?
Hmmm, not sure what is going on as there are no errors reported there. Maybe you ran out of disk space? Or RAM?
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Courtney Haswell Sent: Thursday, December 3, 2020 1:34 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all issues debugging
External Email - Use Caution I could not attach but this is the log for recon-all.
Fri Nov 13 13:23:03 EST 2020
/mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265
/usr/local/packages/freesurfer_v6.0.0/bin/recon-all
-subjid 13265 -i /mnt/munin/Morey/Lab/T1Duke/T1s/13265.nii.gz -all
subjid 13265
setenv SUBJECTS_DIR /mnt/munin/Morey/Lab/T1Duke/Freesurfer
FREESURFER_HOME /usr/local/packages/freesurfer_v6.0.0
Actual FREESURFER_HOME /usr/local/packages/freesurfer_v6.0.0
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-4cfbf2a #freesurfer-Linux-centos6_x86_64-stable-v6-beta-20161028-4cfbf2a
Linux blade21.dhe.duke.edu 3.10.0-1160.2.2.el7.x86_64 #1 SMP Mon Oct 19 10:20:12 CDT 2020 x86_64 x86_64 x86_64 GNU/Linux
cputime unlimited
filesize unlimited
datasize unlimited
stacksize unlimited
coredumpsize unlimited
memoryuse unlimited
vmemoryuse unlimited
descriptors 1024
memorylocked 64 kbytes
maxproc 1024
maxlocks unlimited
maxsignal 514553
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buff/cache available
Mem: 131771700 11355116 105128156 220060 15288428 119570388
Swap: 0 0 0
########################################
program versions used
$Id: recon-all,v 1.580.2.13 2016/10/18 14:39:30 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: 2020/11/13-18:23:03-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
FLIRT version 5.5
$Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $
mri_convert.bin --version
stable6
ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:03-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:03-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/11/13-18:23:03-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mri_normalize.c,v 1.88.2.1 2016/07/29 22:20:35 zkaufman Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:03-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:03-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/11/13-18:23:04-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/11/13-18:23:04-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mri_label2label.c,v 1.48.2.1 2016/08/02 20:14:55 zkaufman Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/11/13-18:23:04-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/11/13-18:23:04-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/11/13-18:23:04-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/11/13-18:23:04-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:04-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:04-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/11/13-18:23:04-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:04-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:04-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:04-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:04-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:04-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:04-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/11/13-18:23:04-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:04-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:04-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:04-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:04-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mris_make_surfaces.c,v 1.164 2016/05/13 18:03:58 fischl Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:05-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:05-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mris_volmask.cpp,v 1.26 2014/11/06 03:40:22 nicks Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:05-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:05-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:05-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:05-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
$Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $
ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:05-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
$Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $
ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:05-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:05-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:05-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:05-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:05-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/11/13-18:23:05-GMT BuildTimeStamp: Oct 28 2016 10:36:27 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: ch186 Machine: blade21.dhe.duke.edu Platform: Linux PlatformVersion: 3.10.0-1160.2.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400
#######################################
GCADIR /usr/local/packages/freesurfer_v6.0.0/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/packages/freesurfer_v6.0.0/average
GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
#######################################
/mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265
mri_convert /mnt/munin/Morey/Lab/T1Duke/T1s/13265.nii.gz /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri/orig/001.mgz
mri_convert.bin /mnt/munin/Morey/Lab/T1Duke/T1s/13265.nii.gz /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri/orig/001.mgz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /mnt/munin/Morey/Lab/T1Duke/T1s/13265.nii.gz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
writing to /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Fri Nov 13 13:23:08 EST 2020
Found 1 runs
/mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/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 /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri/orig/001.mgz /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri/rawavg.mgz
/mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265
mri_convert /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri/rawavg.mgz /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri/orig.mgz --conform
mri_convert.bin /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri/rawavg.mgz /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri/orig.mgz --conform
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri/rawavg.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
changing data type from short to uchar (noscale = 0)...
MRIchangeType: Building histogram
Reslicing using trilinear interpolation
writing to /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri/orig.mgz...
mri_add_xform_to_header -c /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri/transforms/talairach.xfm /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri/orig.mgz /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri/orig.mgz
INFO: extension is mgz
#--------------------------------------------
#@# Talairach Fri Nov 13 13:23:18 EST 2020
/mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri
mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
/mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri
/usr/local/packages/freesurfer_v6.0.0/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 blade21.dhe.duke.edu 3.10.0-1160.2.2.el7.x86_64 #1 SMP Mon Oct 19 10:20:12 CDT 2020 x86_64 x86_64 x86_64 GNU/Linux
Fri Nov 13 13:23:18 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
/bin/bc
tmpdir is ./tmp.mri_nu_correct.mni.10582
/mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.10582/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.10582/nu0.mnc -odt float
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from orig.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.10582/nu0.mnc...
--------------------------------------------------------
Iteration 1 Fri Nov 13 13:23:21 EST 2020
nu_correct -clobber ./tmp.mri_nu_correct.mni.10582/nu0.mnc ./tmp.mri_nu_correct.mni.10582/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.10582/0/ -iterations 1000 -distance 50
[ch186@blade21.dhe.duke.edu:/mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri/] [2020-11-13 13:23:21] running:
/usr/local/packages/freesurfer_v6.0.0/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.10582/0/ ./tmp.mri_nu_correct.mni.10582/nu0.mnc ./tmp.mri_nu_correct.mni.10582/nu1.imp
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
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Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
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: 35
CV of field change: 0.000973337
mri_convert ./tmp.mri_nu_correct.mni.10582/nu1.mnc orig_nu.mgz --like orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.10582/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.10582/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...
Fri Nov 13 13:24:34 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 Fri Nov 13 13:24:35 EST 2020
Ended at Fri Nov 13 13:24:59 EST 2020
talairach_avi done
cp transforms/talairach.auto.xfm transforms/talairach.xfm
#--------------------------------------------
#@# Talairach Failure Detection Fri Nov 13 13:25:01 EST 2020
/mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7962, pval=0.8469 >= threshold=0.0050)
awk -f /usr/local/packages/freesurfer_v6.0.0/bin/extract_talairach_avi_QA.awk /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri/transforms/talairach_avi.log
tal_QC_AZS /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri/transforms/talairach_avi.log
TalAviQA: 0.97951
z-score: 0
#--------------------------------------------
#@# Nu Intensity Correction Fri Nov 13 13:25:01 EST 2020
mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2
/mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri
/usr/local/packages/freesurfer_v6.0.0/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 blade21.dhe.duke.edu 3.10.0-1160.2.2.el7.x86_64 #1 SMP Mon Oct 19 10:20:12 CDT 2020 x86_64 x86_64 x86_64 GNU/Linux
Fri Nov 13 13:25:01 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
/bin/bc
tmpdir is ./tmp.mri_nu_correct.mni.11553
/mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.11553/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.11553/nu0.mnc -odt float
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from orig.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.11553/nu0.mnc...
--------------------------------------------------------
Iteration 1 Fri Nov 13 13:25:04 EST 2020
nu_correct -clobber ./tmp.mri_nu_correct.mni.11553/nu0.mnc ./tmp.mri_nu_correct.mni.11553/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.11553/0/
[ch186@blade21.dhe.duke.edu:/mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri/] [2020-11-13 13:25:05] running:
/usr/local/packages/freesurfer_v6.0.0/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.11553/0/ ./tmp.mri_nu_correct.mni.11553/nu0.mnc ./tmp.mri_nu_correct.mni.11553/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
Number of iterations: 28
CV of field change: 0.000986668
--------------------------------------------------------
Iteration 2 Fri Nov 13 13:25:57 EST 2020
nu_correct -clobber ./tmp.mri_nu_correct.mni.11553/nu1.mnc ./tmp.mri_nu_correct.mni.11553/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.11553/1/
[ch186@blade21.dhe.duke.edu:/mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri/] [2020-11-13 13:25:57] running:
/usr/local/packages/freesurfer_v6.0.0/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.11553/1/ ./tmp.mri_nu_correct.mni.11553/nu1.mnc ./tmp.mri_nu_correct.mni.11553/nu2.imp
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Number of iterations: 20
CV of field change: 0.000971098
mri_binarize --i ./tmp.mri_nu_correct.mni.11553/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.11553/ones.mgz
$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri
cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.11553/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.11553/ones.mgz
sysname Linux
hostname blade21.dhe.duke.edu
machine x86_64
user ch186
input ./tmp.mri_nu_correct.mni.11553/nu2.mnc
frame 0
nErode3d 0
nErode2d 0
output ./tmp.mri_nu_correct.mni.11553/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.11553/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.11553/sum.junk --avgwf ./tmp.mri_nu_correct.mni.11553/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.11553/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.11553/sum.junk --avgwf ./tmp.mri_nu_correct.mni.11553/input.mean.dat
sysname Linux
hostname blade21.dhe.duke.edu
machine x86_64
user ch186
UseRobust 0
Loading ./tmp.mri_nu_correct.mni.11553/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.11553/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.11553/ones.mgz --i ./tmp.mri_nu_correct.mni.11553/nu2.mnc --sum ./tmp.mri_nu_correct.mni.11553/sum.junk --avgwf ./tmp.mri_nu_correct.mni.11553/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.11553/ones.mgz --i ./tmp.mri_nu_correct.mni.11553/nu2.mnc --sum ./tmp.mri_nu_correct.mni.11553/sum.junk --avgwf ./tmp.mri_nu_correct.mni.11553/output.mean.dat
sysname Linux
hostname blade21.dhe.duke.edu
machine x86_64
user ch186
UseRobust 0
Loading ./tmp.mri_nu_correct.mni.11553/ones.mgz
Loading ./tmp.mri_nu_correct.mni.11553/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.11553/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.11553/nu2.mnc ./tmp.mri_nu_correct.mni.11553/nu2.mnc mul 1.03361326205155151317
Saving result to './tmp.mri_nu_correct.mni.11553/nu2.mnc' (type = MINC ) [ ok ]
mri_convert ./tmp.mri_nu_correct.mni.11553/nu2.mnc nu.mgz --like orig.mgz
mri_convert.bin ./tmp.mri_nu_correct.mni.11553/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.11553/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 6 seconds.
mapping (15, 94) to ( 3, 110)
Fri Nov 13 13:27:15 EST 2020
mri_nu_correct.mni done
mri_add_xform_to_header -c /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri/transforms/talairach.xfm nu.mgz nu.mgz
INFO: extension is mgz
#--------------------------------------------
#@# Intensity Normalization Fri Nov 13 13:27:16 EST 2020
/mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/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
1.04893 0.01526 -0.00374 1.45294;
-0.04316 1.00886 0.18821 -51.03661;
-0.01136 -0.16057 1.13393 -0.98010;
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 109
gm peak at 66 (66), valley at 34 (34)
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 67 (67), valley at 32 (32)
csf peak at 34, setting threshold to 56
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to T1.mgz
3D bias adjustment took 1 minutes and 30 seconds.
#--------------------------------------------
#@# Skull Stripping Fri Nov 13 13:28:46 EST 2020
/mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri
mri_em_register -rusage /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /usr/local/packages/freesurfer_v6.0.0/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/packages/freesurfer_v6.0.0/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=14.0
skull bounding box = (43, 52, 20) --> (215, 205, 233)
using (100, 103, 127) as brain centroid...
mean wm in atlas = 108, using box (79,84,101) --> (121, 121,153) to find MRI wm
before smoothing, mri peak at 99
robust fit to distribution - 99 +- 7.9
after smoothing, mri peak at 99, scaling input intensities by 1.091
scaling channel 0 by 1.09091
initial log_p = -4.587
************************************************
First Search limited to translation only.
************************************************
max log p = -4.579605 @ (-9.091, -9.091, -9.091)
max log p = -4.428650 @ (4.545, -4.545, -4.545)
max log p = -4.397101 @ (2.273, 2.273, 2.273)
max log p = -4.382682 @ (-1.136, 1.136, -1.136)
max log p = -4.363797 @ (0.568, 0.568, -1.705)
max log p = -4.363797 @ (0.000, 0.000, 0.000)
Found translation: (-2.8, -9.7, -14.2): log p = -4.364
****************************************
Nine parameter search. iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.216, old_max_log_p =-4.364 (thresh=-4.4)
1.00000 0.00000 0.00000 -2.84091;
0.00000 1.15000 0.00000 -32.43408;
0.00000 0.00000 1.00000 -14.20455;
0.00000 0.00000 0.00000 1.00000;
****************************************
Nine parameter search. iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.216, old_max_log_p =-4.216 (thresh=-4.2)
1.00000 0.00000 0.00000 -2.84091;
0.00000 1.15000 0.00000 -32.43408;
0.00000 0.00000 1.00000 -14.20455;
0.00000 0.00000 0.00000 1.00000;
reducing scale to 0.2500
****************************************
Nine parameter search. iteration 2 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-4.129, old_max_log_p =-4.216 (thresh=-4.2)
1.03686 0.00528 -0.03487 -3.98750;
0.00000 1.20510 0.13796 -54.24200;
0.03149 -0.15004 0.99099 5.68060;
0.00000 0.00000 0.00000 1.00000;
****************************************
Nine parameter search. iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-4.129, old_max_log_p =-4.129 (thresh=-4.1)
1.03686 0.00528 -0.03487 -3.98750;
0.00000 1.20510 0.13796 -54.24200;
0.03149 -0.15004 0.99099 5.68060;
0.00000 0.00000 0.00000 1.00000;
reducing scale to 0.0625
****************************************
Nine parameter search. iteration 4 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-4.108, old_max_log_p =-4.129 (thresh=-4.1)
1.03533 0.04326 -0.02167 -11.08516;
-0.03334 1.20174 0.16292 -52.12689;
0.02321 -0.17869 0.98412 11.38717;
0.00000 0.00000 0.00000 1.00000;
****************************************
Nine parameter search. iteration 5 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-4.103, old_max_log_p =-4.108 (thresh=-4.1)
1.03533 0.04326 -0.02167 -11.08516;
-0.03353 1.20315 0.15489 -50.83923;
0.02286 -0.16824 0.98196 10.15241;
0.00000 0.00000 0.00000 1.00000;
****************************************
Nine parameter search. iteration 6 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-4.103, old_max_log_p =-4.103 (thresh=-4.1)
1.03533 0.04326 -0.02167 -11.08516;
-0.03353 1.20315 0.15489 -50.83923;
0.02286 -0.16824 0.98196 10.15241;
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
1.03533 0.04326 -0.02167 -11.08516;
-0.03353 1.20315 0.15489 -50.83923;
0.02286 -0.16824 0.98196 10.15241;
0.00000 0.00000 0.00000 1.00000;
nsamples 3243
Quasinewton: input matrix
1.03533 0.04326 -0.02167 -11.08516;
-0.03353 1.20315 0.15489 -50.83923;
0.02286 -0.16824 0.98196 10.15241;
0.00000 0.00000 0.00000 1.00000;
outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010
Resulting transform:
1.03533 0.04326 -0.02167 -11.08516;
-0.03353 1.20315 0.15489 -50.83923;
0.02286 -0.16824 0.98196 10.15241;
0.00000 0.00000 0.00000 1.00000;
pass 1, spacing 8: log(p) = -4.103 (old=-4.587)
transform before final EM align:
1.03533 0.04326 -0.02167 -11.08516;
-0.03353 1.20315 0.15489 -50.83923;
0.02286 -0.16824 0.98196 10.15241;
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
1.03533 0.04326 -0.02167 -11.08516;
-0.03353 1.20315 0.15489 -50.83923;
0.02286 -0.16824 0.98196 10.15241;
0.00000 0.00000 0.00000 1.00000;
nsamples 364799
Quasinewton: input matrix
1.03533 0.04326 -0.02167 -11.08516;
-0.03353 1.20315 0.15489 -50.83923;
0.02286 -0.16824 0.98196 10.15241;
0.00000 0.00000 0.00000 1.00000;
outof QuasiNewtonEMA: 011: -log(p) = 4.5 tol 0.000000
final transform:
1.03533 0.04326 -0.02167 -11.08516;
-0.03353 1.20315 0.15489 -50.83923;
0.02286 -0.16824 0.98196 10.15241;
0.00000 0.00000 0.00000 1.00000;
writing output transformation to transforms/talairach_with_skull.lta...
mri_em_register utimesec 846.321024
mri_em_register stimesec 2.335252
mri_em_register ru_maxrss 609856
mri_em_register ru_ixrss 0
mri_em_register ru_idrss 0
mri_em_register ru_isrss 0
mri_em_register ru_minflt 820113
mri_em_register ru_majflt 0
mri_em_register ru_nswap 0
mri_em_register ru_inblock 148912
mri_em_register ru_oublock 40
mri_em_register ru_msgsnd 0
mri_em_register ru_msgrcv 0
mri_em_register ru_nsignals 0
mri_em_register ru_nvcsw 484
mri_em_register ru_nivcsw 85111
registration took 14 minutes and 9 seconds.
mri_watershed -rusage /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/touch/rusage.mri_watershed.dat -T1 -brain_atlas /usr/local/packages/freesurfer_v6.0.0/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=129 y=125 z=123 r=75
first estimation of the main basin volume: 1796098 voxels
Looking for seedpoints
2 found in the cerebellum
18 found in the rest of the brain
global maximum in x=150, y=115, z=87, Imax=255
CSF=21, 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=502583624 voxels, voxel volume =1.000
= 502583624 mmm3 = 502583.616 cm3
done.
PostAnalyze...Basin Prior
77 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=132, z=119, r=9657 iterations
^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^
GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 45457
RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1035962766
LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1103986758
RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1077462120
LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1077264638
OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=23 , nb = 1070358796
Problem with the least square interpolation in GM_MIN calculation.
CSF_MAX TRANSITION GM_MIN GM
GLOBAL
before analyzing : 4, 6, 38, 63
after analyzing : 4, 27, 38, 36
RIGHT_CER
before analyzing : 4, 6, 41, 74
after analyzing : 4, 29, 41, 40
LEFT_CER
before analyzing : 4, 5, 32, 70
after analyzing : 4, 23, 32, 34
RIGHT_BRAIN
before analyzing : 4, 6, 37, 62
after analyzing : 4, 26, 37, 35
LEFT_BRAIN
before analyzing : 4, 6, 38, 63
after analyzing : 4, 27, 38, 36
OTHER
before analyzing : 23, 30, 45, 87
after analyzing : 23, 40, 45, 51
mri_strip_skull: done peeling brain
highly tesselated surface with 10242 vertices
matching...65 iterations
*********************VALIDATION*********************
curvature mean = -0.013, std = 0.010
curvature mean = 71.464, std = 8.269
No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
before rotation: sse = 1.98, sigma = 3.16
after rotation: sse = 1.98, sigma = 3.16
Localization of inacurate regions: Erosion-Dilation steps
the sse mean is 1.99, its var is 2.50
before Erosion-Dilatation 0.09% 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...36 iterations
mri_strip_skull: done peeling brain
Brain Size = 1628717 voxels, voxel volume = 1.000 mm3
= 1628717 mmm3 = 1628.717 cm3
******************************
Saving brainmask.auto.mgz
done
mri_watershed utimesec 14.860329
mri_watershed stimesec 0.584423
mri_watershed ru_maxrss 824448
mri_watershed ru_ixrss 0
mri_watershed ru_idrss 0
mri_watershed ru_isrss 0
mri_watershed ru_minflt 369932
mri_watershed ru_majflt 0
mri_watershed ru_nswap 0
mri_watershed ru_inblock 7960
mri_watershed ru_oublock 2608
mri_watershed ru_msgsnd 0
mri_watershed ru_msgrcv 0
mri_watershed ru_nsignals 0
mri_watershed ru_nvcsw 930
mri_watershed ru_nivcsw 1562
mri_watershed done
cp brainmask.auto.mgz brainmask.mgz
#-------------------------------------
#@# EM Registration Fri Nov 13 13:43:12 EST 2020
/mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri
mri_em_register -rusage /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /usr/local/packages/freesurfer_v6.0.0/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/packages/freesurfer_v6.0.0/average/RB_all_2016-05-10.vc700.gca'...
average std = 7.3 using min determinant for regularization = 5.3
0 singular and 841 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
freeing gibbs priors...done.
accounting for voxel sizes in initial transform
bounding unknown intensity as < 6.3 or > 503.7
total sample mean = 78.8 (1011 zeros)
************************************************
spacing=8, using 2830 sample points, tol=1.00e-05...
************************************************
register_mri: find_optimal_transform
find_optimal_transform: nsamples 2830, passno 0, spacing 8
resetting wm mean[0]: 98 --> 107
resetting gm mean[0]: 61 --> 61
input volume #1 is the most T1-like
using real data threshold=23.1
skull bounding box = (62, 70, 41) --> (194, 193, 210)
using (106, 111, 126) as brain centroid...
mean wm in atlas = 107, using box (90,96,105) --> (122, 126,146) to find MRI wm
before smoothing, mri peak at 100
robust fit to distribution - 100 +- 6.5
after smoothing, mri peak at 100, scaling input intensities by 1.070
scaling channel 0 by 1.07
initial log_p = -4.315
************************************************
First Search limited to translation only.
************************************************
max log p = -4.066327 @ (-9.091, -9.091, -9.091)
max log p = -3.894957 @ (4.545, -4.545, -4.545)
max log p = -3.818117 @ (2.273, 2.273, -2.273)
max log p = -3.815683 @ (1.136, -1.136, 1.136)
max log p = -3.770580 @ (0.568, 0.568, -0.568)
max log p = -3.770580 @ (0.000, 0.000, 0.000)
Found translation: (-0.6, -11.9, -15.3): log p = -3.771
****************************************
Nine parameter search. iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.692, old_max_log_p =-3.771 (thresh=-3.8)
1.00000 0.00000 0.00000 -0.56818;
0.00000 1.14016 0.13053 -46.08973;
0.00000 -0.15011 0.99144 5.38950;
0.00000 0.00000 0.00000 1.00000;
****************************************
Nine parameter search. iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.692, old_max_log_p =-3.692 (thresh=-3.7)
1.00000 0.00000 0.00000 -0.56818;
0.00000 1.14016 0.13053 -46.08973;
0.00000 -0.15011 0.99144 5.38950;
0.00000 0.00000 0.00000 1.00000;
reducing scale to 0.2500
****************************************
Nine parameter search. iteration 2 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.601, old_max_log_p =-3.692 (thresh=-3.7)
1.03718 0.00318 -0.00461 -6.79167;
-0.00210 1.16572 0.10116 -43.88010;
-0.00502 -0.10923 0.97631 4.42902;
0.00000 0.00000 0.00000 1.00000;
****************************************
Nine parameter search. iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.576, old_max_log_p =-3.601 (thresh=-3.6)
1.01711 0.04041 -0.00025 -9.55984;
-0.03687 1.18256 0.13563 -47.55101;
-0.00504 -0.15008 0.99071 8.02897;
0.00000 0.00000 0.00000 1.00000;
****************************************
Nine parameter search. iteration 4 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.576, old_max_log_p =-3.576 (thresh=-3.6)
1.01711 0.04041 -0.00025 -9.55984;
-0.03687 1.18256 0.13563 -47.55101;
-0.00504 -0.15008 0.99071 8.02897;
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=-3.569, old_max_log_p =-3.576 (thresh=-3.6)
1.01897 0.00293 -0.01249 -3.88443;
-0.00353 1.18189 0.13522 -51.24036;
0.00304 -0.14943 0.98717 6.85401;
0.00000 0.00000 0.00000 1.00000;
****************************************
Nine parameter search. iteration 6 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.568, old_max_log_p =-3.569 (thresh=-3.6)
1.01897 0.00293 -0.01249 -3.88443;
-0.00353 1.18189 0.13522 -51.24036;
0.00303 -0.14908 0.98486 7.08509;
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
1.01897 0.00293 -0.01249 -3.88443;
-0.00353 1.18189 0.13522 -51.24036;
0.00303 -0.14908 0.98486 7.08509;
0.00000 0.00000 0.00000 1.00000;
nsamples 2830
Quasinewton: input matrix
1.01897 0.00293 -0.01249 -3.88443;
-0.00353 1.18189 0.13522 -51.24036;
0.00303 -0.14908 0.98486 7.08509;
0.00000 0.00000 0.00000 1.00000;
outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010
Resulting transform:
1.01897 0.00293 -0.01249 -3.88443;
-0.00353 1.18189 0.13522 -51.24036;
0.00303 -0.14908 0.98486 7.08509;
0.00000 0.00000 0.00000 1.00000;
pass 1, spacing 8: log(p) = -3.568 (old=-4.315)
transform before final EM align:
1.01897 0.00293 -0.01249 -3.88443;
-0.00353 1.18189 0.13522 -51.24036;
0.00303 -0.14908 0.98486 7.08509;
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
1.01897 0.00293 -0.01249 -3.88443;
-0.00353 1.18189 0.13522 -51.24036;
0.00303 -0.14908 0.98486 7.08509;
0.00000 0.00000 0.00000 1.00000;
nsamples 315557
Quasinewton: input matrix
1.01897 0.00293 -0.01249 -3.88443;
-0.00353 1.18189 0.13522 -51.24036;
0.00303 -0.14908 0.98486 7.08509;
0.00000 0.00000 0.00000 1.00000;
outof QuasiNewtonEMA: 011: -log(p) = 4.0 tol 0.000000
final transform:
1.01897 0.00293 -0.01249 -3.88443;
-0.00353 1.18189 0.13522 -51.24036;
0.00303 -0.14908 0.98486 7.08509;
0.00000 0.00000 0.00000 1.00000;
writing output transformation to transforms/talairach.lta...
mri_em_register utimesec 716.320693
mri_em_register stimesec 2.339274
mri_em_register ru_maxrss 599164
mri_em_register ru_ixrss 0
mri_em_register ru_idrss 0
mri_em_register ru_isrss 0
mri_em_register ru_minflt 799686
mri_em_register ru_majflt 0
mri_em_register ru_nswap 0
mri_em_register ru_inblock 140152
mri_em_register ru_oublock 40
mri_em_register ru_msgsnd 0
mri_em_register ru_msgrcv 0
mri_em_register ru_nsignals 0
mri_em_register ru_nvcsw 655
mri_em_register ru_nivcsw 72101
registration took 11 minutes and 59 seconds.
#--------------------------------------
#@# CA Normalize Fri Nov 13 13:55:11 EST 2020
/mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri
mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/packages/freesurfer_v6.0.0/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/packages/freesurfer_v6.0.0/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=22.1
skull bounding box = (62, 69, 41) --> (194, 194, 210)
using (106, 111, 126) as brain centroid...
mean wm in atlas = 107, using box (90,96,105) --> (122, 126,146) to find MRI wm
before smoothing, mri peak at 100
robust fit to distribution - 100 +- 6.5
after smoothing, mri peak at 100, scaling input intensities by 1.070
scaling channel 0 by 1.07
using 246344 sample points...
INFO: compute sample coordinates transform
1.01897 0.00293 -0.01249 -3.88443;
-0.00353 1.18189 0.13522 -51.24036;
0.00303 -0.14908 0.98486 7.08509;
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 (128, 74, 41) --> (193, 173, 209)
Left_Cerebral_White_Matter: limiting intensities to 101.0 --> 132.0
1 of 169 (0.6%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (66, 76, 40) --> (131, 173, 209)
Right_Cerebral_White_Matter: limiting intensities to 104.0 --> 132.0
1 of 124 (0.8%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (130, 150, 67) --> (177, 186, 122)
Left_Cerebellum_White_Matter: limiting intensities to 121.0 --> 132.0
13 of 14 (92.9%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (85, 150, 65) --> (128, 185, 123)
Right_Cerebellum_White_Matter: limiting intensities to 108.0 --> 132.0
0 of 17 (0.0%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (113, 140, 104) --> (146, 200, 133)
Brain_Stem: limiting intensities to 100.0 --> 132.0
1 of 19 (5.3%) samples deleted
using 343 total control points for intensity normalization...
bias field = 0.872 +- 0.082
0 of 327 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (128, 74, 41) --> (193, 173, 209)
Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
0 of 363 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (66, 76, 40) --> (131, 173, 209)
Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
0 of 301 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (130, 150, 67) --> (177, 186, 122)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
48 of 70 (68.6%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (85, 150, 65) --> (128, 185, 123)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
20 of 79 (25.3%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (113, 140, 104) --> (146, 200, 133)
Brain_Stem: limiting intensities to 88.0 --> 132.0
72 of 117 (61.5%) samples deleted
using 930 total control points for intensity normalization...
bias field = 1.021 +- 0.063
0 of 785 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (128, 74, 41) --> (193, 173, 209)
Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
0 of 442 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (66, 76, 40) --> (131, 173, 209)
Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
0 of 418 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (130, 150, 67) --> (177, 186, 122)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
82 of 113 (72.6%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (85, 150, 65) --> (128, 185, 123)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
52 of 111 (46.8%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (113, 140, 104) --> (146, 200, 133)
Brain_Stem: limiting intensities to 88.0 --> 132.0
164 of 225 (72.9%) samples deleted
using 1309 total control points for intensity normalization...
bias field = 1.008 +- 0.054
1 of 986 control points discarded
writing normalized volume to norm.mgz...
writing control points to ctrl_pts.mgz
freeing GCA...done.
normalization took 1 minutes and 10 seconds.
#--------------------------------------
#@# CA Reg Fri Nov 13 13:56:21 EST 2020
/mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri
mri_ca_register -rusage /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /usr/local/packages/freesurfer_v6.0.0/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/packages/freesurfer_v6.0.0/average/RB_all_2016-05-10.vc700.gca'...
label assignment complete, 0 changed (0.00%)
det(m_affine) = 1.21 (predicted orig area = 6.6)
label assignment complete, 0 changed (0.00%)
freeing gibbs priors...done.
average std[0] = 5.0
**************** pass 1 of 1 ************************
enabling zero nodes
setting smoothness coefficient to 0.039
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.802, neg=0, invalid=4512
0001: dt=188.688327, rms=0.750 (6.513%), neg=0, invalid=4512
0002: dt=147.728155, rms=0.733 (2.209%), neg=0, invalid=4512
0003: dt=221.952000, rms=0.724 (1.206%), neg=0, invalid=4512
0004: dt=135.384615, rms=0.719 (0.662%), neg=0, invalid=4512
0005: dt=517.888000, rms=0.712 (1.016%), neg=0, invalid=4512
0006: dt=110.976000, rms=0.706 (0.787%), neg=0, invalid=4512
0007: dt=517.888000, rms=0.701 (0.820%), neg=0, invalid=4512
0008: dt=110.976000, rms=0.698 (0.328%), neg=0, invalid=4512
0009: dt=517.888000, rms=0.695 (0.455%), neg=0, invalid=4512
0010: dt=110.976000, rms=0.694 (0.120%), neg=0, invalid=4512
0011: dt=110.976000, rms=0.694 (0.071%), neg=0, invalid=4512
0012: dt=110.976000, rms=0.693 (0.114%), neg=0, invalid=4512
0013: dt=110.976000, rms=0.692 (0.136%), neg=0, invalid=4512
0014: dt=110.976000, rms=0.691 (0.155%), neg=0, invalid=4512
0015: dt=110.976000, rms=0.690 (0.164%), neg=0, invalid=4512
0016: dt=110.976000, rms=0.689 (0.165%), neg=0, invalid=4512
0017: dt=110.976000, rms=0.688 (0.154%), neg=0, invalid=4512
0018: dt=110.976000, rms=0.687 (0.143%), neg=0, invalid=4512
0019: dt=110.976000, rms=0.686 (0.131%), neg=0, invalid=4512
0020: dt=110.976000, rms=0.685 (0.137%), neg=0, invalid=4512
0021: dt=110.976000, rms=0.684 (0.134%), neg=0, invalid=4512
0022: dt=110.976000, rms=0.683 (0.121%), neg=0, invalid=4512
0023: dt=110.976000, rms=0.682 (0.106%), neg=0, invalid=4512
0024: dt=517.888000, rms=0.682 (0.062%), neg=0, invalid=4512
0025: dt=517.888000, rms=0.682 (-0.256%), neg=0, invalid=4512
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.682, neg=0, invalid=4512
0026: dt=129.472000, rms=0.681 (0.175%), neg=0, invalid=4512
0027: dt=517.888000, rms=0.680 (0.213%), neg=0, invalid=4512
0028: dt=110.976000, rms=0.680 (0.015%), neg=0, invalid=4512
0029: dt=110.976000, rms=0.679 (0.028%), neg=0, invalid=4512
0030: dt=110.976000, rms=0.679 (0.038%), neg=0, invalid=4512
0031: dt=110.976000, rms=0.679 (0.051%), neg=0, invalid=4512
0032: dt=110.976000, rms=0.678 (0.065%), neg=0, invalid=4512
0033: dt=110.976000, rms=0.678 (0.082%), neg=0, invalid=4512
0034: dt=110.976000, rms=0.677 (0.090%), neg=0, invalid=4512
0035: dt=110.976000, rms=0.677 (0.088%), neg=0, invalid=4512
0036: dt=110.976000, rms=0.676 (0.086%), neg=0, invalid=4512
setting smoothness coefficient to 0.154
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.679, neg=0, invalid=4512
0037: dt=202.524444, rms=0.670 (1.334%), neg=0, invalid=4512
0038: dt=133.719149, rms=0.662 (1.223%), neg=0, invalid=4512
0039: dt=63.780571, rms=0.658 (0.613%), neg=0, invalid=4512
0040: dt=145.152000, rms=0.655 (0.444%), neg=0, invalid=4512
0041: dt=73.612648, rms=0.652 (0.448%), neg=0, invalid=4512
0042: dt=79.078534, rms=0.651 (0.241%), neg=0, invalid=4512
0043: dt=79.078534, rms=0.648 (0.321%), neg=0, invalid=4512
0044: dt=79.078534, rms=0.646 (0.451%), neg=0, invalid=4512
0045: dt=79.078534, rms=0.642 (0.548%), neg=0, invalid=4512
0046: dt=79.078534, rms=0.638 (0.651%), neg=0, invalid=4512
0047: dt=79.078534, rms=0.633 (0.716%), neg=0, invalid=4512
0048: dt=79.078534, rms=0.629 (0.632%), neg=0, invalid=4512
0049: dt=79.078534, rms=0.626 (0.571%), neg=0, invalid=4512
0050: dt=79.078534, rms=0.622 (0.531%), neg=0, invalid=4512
0051: dt=79.078534, rms=0.619 (0.467%), neg=0, invalid=4512
0052: dt=79.078534, rms=0.617 (0.343%), neg=0, invalid=4512
0053: dt=79.078534, rms=0.616 (0.271%), neg=0, invalid=4512
0054: dt=79.078534, rms=0.614 (0.281%), neg=0, invalid=4512
0055: dt=79.078534, rms=0.613 (0.216%), neg=0, invalid=4512
0056: dt=79.078534, rms=0.612 (0.164%), neg=0, invalid=4512
0057: dt=79.078534, rms=0.611 (0.124%), neg=0, invalid=4512
0058: dt=79.078534, rms=0.610 (0.183%), neg=0, invalid=4512
0059: dt=79.078534, rms=0.609 (0.131%), neg=0, invalid=4512
0060: dt=79.078534, rms=0.608 (0.107%), neg=0, invalid=4512
0061: dt=79.078534, rms=0.608 (0.068%), neg=0, invalid=4512
0062: dt=62.208000, rms=0.607 (0.069%), neg=0, invalid=4512
0063: dt=31.104000, rms=0.607 (0.004%), neg=0, invalid=4512
0064: dt=31.104000, rms=0.607 (0.008%), neg=0, invalid=4512
0065: dt=31.104000, rms=0.607 (0.013%), neg=0, invalid=4512
0066: dt=31.104000, rms=0.607 (0.019%), neg=0, invalid=4512
0067: dt=31.104000, rms=0.607 (0.020%), neg=0, invalid=4512
0068: dt=31.104000, rms=0.607 (0.021%), neg=0, invalid=4512
0069: dt=31.104000, rms=0.607 (0.019%), neg=0, invalid=4512
0070: dt=31.104000, rms=0.607 (0.013%), neg=0, invalid=4512
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.607, neg=0, invalid=4512
0071: dt=145.152000, rms=0.605 (0.332%), neg=0, invalid=4512
0072: dt=103.680000, rms=0.605 (0.069%), neg=0, invalid=4512
0073: dt=103.680000, rms=0.605 (0.013%), neg=0, invalid=4512
0074: dt=103.680000, rms=0.605 (0.036%), neg=0, invalid=4512
0075: dt=103.680000, rms=0.604 (0.026%), neg=0, invalid=4512
0076: dt=103.680000, rms=0.604 (-0.001%), neg=0, invalid=4512
setting smoothness coefficient to 0.588
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.624, neg=0, invalid=4512
0077: dt=0.000000, rms=0.623 (0.090%), neg=0, invalid=4512
0078: dt=0.000000, rms=0.623 (0.000%), neg=0, invalid=4512
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.624, neg=0, invalid=4512
0079: dt=0.000000, rms=0.623 (0.090%), neg=0, invalid=4512
0080: dt=0.000000, rms=0.623 (0.000%), neg=0, invalid=4512
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.681, neg=0, invalid=4512
0081: dt=4.878049, rms=0.663 (2.572%), neg=0, invalid=4512
0082: dt=1.728000, rms=0.663 (0.064%), neg=0, invalid=4512
0083: dt=1.728000, rms=0.663 (-0.024%), neg=0, invalid=4512
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.663, neg=0, invalid=4512
0084: dt=0.000000, rms=0.663 (0.061%), neg=0, invalid=4512
0085: dt=0.000000, rms=0.663 (0.000%), neg=0, invalid=4512
setting smoothness coefficient to 5.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.719, neg=0, invalid=4512
0086: dt=1.317507, rms=0.714 (0.755%), neg=0, invalid=4512
0087: dt=1.792000, rms=0.710 (0.565%), neg=0, invalid=4512
0088: dt=0.448000, rms=0.709 (0.029%), neg=0, invalid=4512
0089: dt=0.448000, rms=0.709 (0.026%), neg=0, invalid=4512
0090: dt=0.448000, rms=0.709 (0.011%), neg=0, invalid=4512
0091: dt=0.448000, rms=0.709 (-0.051%), neg=0, invalid=4512
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.709, neg=0, invalid=4512
0092: dt=1.536000, rms=0.708 (0.220%), neg=0, invalid=4512
0093: dt=0.000000, rms=0.708 (-0.000%), neg=0, invalid=4512
resetting metric properties...
setting smoothness coefficient to 10.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.670, neg=0, invalid=4512
0094: dt=0.916276, rms=0.649 (3.188%), neg=0, invalid=4512
0095: dt=0.080000, rms=0.648 (0.163%), neg=0, invalid=4512
0096: dt=0.080000, rms=0.648 (-0.083%), neg=0, invalid=4512
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.648, neg=0, invalid=4512
0097: dt=0.028000, rms=0.648 (0.081%), neg=0, invalid=4512
0098: dt=0.007000, rms=0.648 (0.000%), neg=0, invalid=4512
0099: dt=0.007000, rms=0.648 (-0.000%), neg=0, invalid=4512
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.10027 (20)
mri peak = 0.12287 (11)
Left_Lateral_Ventricle (4): linear fit = 0.47 x + 0.0 (1254 voxels, overlap=0.360)
Left_Lateral_Ventricle (4): linear fit = 0.47 x + 0.0 (1254 voxels, peak = 10), gca=9.5
gca peak = 0.15565 (16)
mri peak = 0.08848 (10)
Right_Lateral_Ventricle (43): linear fit = 0.51 x + 0.0 (503 voxels, overlap=0.224)
Right_Lateral_Ventricle (43): linear fit = 0.51 x + 0.0 (503 voxels, peak = 8), gca=8.2
gca peak = 0.26829 (96)
mri peak = 0.07737 (95)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (773 voxels, overlap=1.005)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (773 voxels, peak = 96), gca=96.5
gca peak = 0.20183 (93)
mri peak = 0.05740 (87)
Left_Pallidum (13): linear fit = 0.89 x + 0.0 (712 voxels, overlap=1.021)
Left_Pallidum (13): linear fit = 0.89 x + 0.0 (712 voxels, peak = 83), gca=83.2
gca peak = 0.21683 (55)
mri peak = 0.08078 (67)
Right_Hippocampus (53): linear fit = 1.21 x + 0.0 (969 voxels, overlap=0.334)
Right_Hippocampus (53): linear fit = 1.21 x + 0.0 (969 voxels, peak = 66), gca=66.3
gca peak = 0.30730 (58)
mri peak = 0.08482 (69)
Left_Hippocampus (17): linear fit = 1.16 x + 0.0 (696 voxels, overlap=0.564)
Left_Hippocampus (17): linear fit = 1.16 x + 0.0 (696 voxels, peak = 68), gca=67.6
gca peak = 0.11430 (101)
mri peak = 0.08210 (105)
Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (64908 voxels, overlap=0.687)
Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (64908 voxels, peak = 107), gca=106.6
gca peak = 0.12076 (102)
mri peak = 0.08181 (106)
Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (61293 voxels, overlap=0.719)
Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (61293 voxels, peak = 108), gca=107.6
gca peak = 0.14995 (59)
mri peak = 0.03500 (56)
Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (18356 voxels, overlap=0.973)
Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (18356 voxels, peak = 60), gca=60.5
gca peak = 0.15082 (58)
mri peak = 0.03869 (56)
Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (20996 voxels, overlap=0.978)
Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (20996 voxels, peak = 59), gca=59.4
gca peak = 0.14161 (67)
mri peak = 0.11457 (67)
Right_Caudate (50): linear fit = 0.98 x + 0.0 (623 voxels, overlap=0.987)
Right_Caudate (50): linear fit = 0.98 x + 0.0 (623 voxels, peak = 65), gca=65.3
gca peak = 0.15243 (71)
mri peak = 0.08065 (73)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (944 voxels, overlap=0.987)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (944 voxels, peak = 71), gca=71.0
gca peak = 0.13336 (57)
mri peak = 0.05185 (56)
Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (19168 voxels, overlap=0.903)
Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (19168 voxels, peak = 60), gca=59.6
gca peak = 0.13252 (56)
mri peak = 0.05346 (63)
Right_Cerebellum_Cortex (47): linear fit = 1.12 x + 0.0 (22877 voxels, overlap=0.758)
Right_Cerebellum_Cortex (47): linear fit = 1.12 x + 0.0 (22877 voxels, peak = 62), gca=62.4
gca peak = 0.18181 (84)
mri peak = 0.07035 (85)
Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (8728 voxels, overlap=0.784)
Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (8728 voxels, peak = 87), gca=86.9
gca peak = 0.20573 (83)
mri peak = 0.07458 (88)
Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (8456 voxels, overlap=0.749)
Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (8456 voxels, peak = 88), gca=87.6
gca peak = 0.21969 (57)
mri peak = 0.09707 (66)
Left_Amygdala (18): linear fit = 1.18 x + 0.0 (490 voxels, overlap=0.183)
Left_Amygdala (18): linear fit = 1.18 x + 0.0 (490 voxels, peak = 68), gca=67.5
gca peak = 0.39313 (56)
mri peak = 0.11141 (65)
Right_Amygdala (54): linear fit = 1.13 x + 0.0 (551 voxels, overlap=0.300)
Right_Amygdala (54): linear fit = 1.13 x + 0.0 (551 voxels, peak = 64), gca=63.6
gca peak = 0.14181 (85)
mri peak = 0.04962 (99)
Left_Thalamus_Proper (10): linear fit = 1.09 x + 0.0 (5514 voxels, overlap=0.764)
Left_Thalamus_Proper (10): linear fit = 1.09 x + 0.0 (5514 voxels, peak = 92), gca=92.2
gca peak = 0.11978 (83)
mri peak = 0.05466 (89)
Right_Thalamus_Proper (49): linear fit = 1.07 x + 0.0 (4601 voxels, overlap=0.885)
Right_Thalamus_Proper (49): linear fit = 1.07 x + 0.0 (4601 voxels, peak = 88), gca=88.4
gca peak = 0.13399 (79)
mri peak = 0.06231 (84)
Left_Putamen (12): linear fit = 1.04 x + 0.0 (1923 voxels, overlap=0.986)
Left_Putamen (12): linear fit = 1.04 x + 0.0 (1923 voxels, peak = 83), gca=82.6
gca peak = 0.14159 (79)
mri peak = 0.07409 (79)
Right_Putamen (51): linear fit = 1.04 x + 0.0 (2385 voxels, overlap=0.998)
Right_Putamen (51): linear fit = 1.04 x + 0.0 (2385 voxels, peak = 83), gca=82.6
gca peak = 0.10025 (80)
mri peak = 0.08538 (82)
Brain_Stem (16): linear fit = 1.10 x + 0.0 (13178 voxels, overlap=0.402)
Brain_Stem (16): linear fit = 1.10 x + 0.0 (13178 voxels, peak = 88), gca=87.6
gca peak = 0.13281 (86)
mri peak = 0.07803 (94)
Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1335 voxels, overlap=0.391)
Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1335 voxels, peak = 93), gca=93.3
gca peak = 0.12801 (89)
mri peak = 0.09039 (95)
Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1400 voxels, overlap=0.291)
Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1400 voxels, peak = 97), gca=97.5
gca peak = 0.20494 (23)
uniform distribution in MR - rejecting arbitrary fit
gca peak = 0.15061 (21)
mri peak = 0.09801 (16)
Fourth_Ventricle (15): linear fit = 0.88 x + 0.0 (252 voxels, overlap=0.533)
Fourth_Ventricle (15): linear fit = 0.88 x + 0.0 (252 voxels, peak = 18), gca=18.4
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.18056 (32)
gca peak Left_Thalamus = 0.64095 (94)
gca peak Third_Ventricle = 0.20494 (23)
gca peak CSF = 0.20999 (34)
gca peak Left_Accumbens_area = 0.39030 (62)
gca peak Left_undetermined = 0.95280 (25)
gca peak Left_vessel = 0.67734 (53)
gca peak Left_choroid_plexus = 0.09433 (44)
gca peak Right_Inf_Lat_Vent = 0.23544 (26)
gca peak Right_Accumbens_area = 0.30312 (64)
gca peak Right_vessel = 0.46315 (51)
gca peak Right_choroid_plexus = 0.14086 (44)
gca peak Fifth_Ventricle = 0.51669 (36)
gca peak WM_hypointensities = 0.09722 (76)
gca peak non_WM_hypointensities = 0.11899 (47)
gca peak Optic_Chiasm = 0.39033 (72)
label assignment complete, 0 changed (0.00%)
not using caudate to estimate GM means
estimating mean gm scale to be 1.12 x + 0.0
estimating mean wm scale to be 1.05 x + 0.0
estimating mean csf scale to be 0.62 x + 0.0
saving intensity scales to talairach.label_intensities.txt
**************** pass 1 of 1 ************************
enabling zero nodes
setting smoothness coefficient to 0.008
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.663, neg=0, invalid=4512
0100: dt=129.472000, rms=0.659 (0.684%), neg=0, invalid=4512
0101: dt=369.920000, rms=0.655 (0.577%), neg=0, invalid=4512
0102: dt=92.480000, rms=0.654 (0.201%), neg=0, invalid=4512
0103: dt=295.936000, rms=0.653 (0.181%), neg=0, invalid=4512
0104: dt=110.976000, rms=0.652 (0.154%), neg=0, invalid=4512
0105: dt=129.472000, rms=0.651 (0.068%), neg=0, invalid=4512
0106: dt=129.472000, rms=0.651 (0.076%), neg=0, invalid=4512
0107: dt=129.472000, rms=0.650 (0.063%), neg=0, invalid=4512
0108: dt=129.472000, rms=0.650 (0.061%), neg=0, invalid=4512
0109: dt=221.952000, rms=0.649 (0.074%), neg=0, invalid=4512
0110: dt=92.480000, rms=0.649 (0.056%), neg=0, invalid=4512
0111: dt=369.920000, rms=0.648 (0.087%), neg=0, invalid=4512
0112: dt=73.984000, rms=0.648 (0.072%), neg=0, invalid=4512
0113: dt=1479.680000, rms=0.646 (0.247%), neg=0, invalid=4512
0114: dt=73.984000, rms=0.646 (0.109%), neg=0, invalid=4512
0115: dt=517.888000, rms=0.645 (0.060%), neg=0, invalid=4512
0116: dt=92.480000, rms=0.645 (0.029%), neg=0, invalid=4512
0117: dt=92.480000, rms=0.645 (0.017%), neg=0, invalid=4512
0118: dt=92.480000, rms=0.645 (0.029%), neg=0, invalid=4512
0119: dt=92.480000, rms=0.645 (0.038%), neg=0, invalid=4512
0120: dt=92.480000, rms=0.644 (0.041%), neg=0, invalid=4512
0121: dt=92.480000, rms=0.644 (0.042%), neg=0, invalid=4512
0122: dt=92.480000, rms=0.644 (0.047%), neg=0, invalid=4512
0123: dt=92.480000, rms=0.643 (0.047%), neg=0, invalid=4512
0124: dt=92.480000, rms=0.643 (0.049%), neg=0, invalid=4512
0125: dt=92.480000, rms=0.643 (0.053%), neg=0, invalid=4512
0126: dt=92.480000, rms=0.642 (0.056%), neg=0, invalid=4512
0127: dt=92.480000, rms=0.642 (0.059%), neg=0, invalid=4512
0128: dt=92.480000, rms=0.642 (0.056%), neg=0, invalid=4512
0129: dt=92.480000, rms=0.641 (0.051%), neg=0, invalid=4512
0130: dt=92.480000, rms=0.641 (0.047%), neg=0, invalid=4512
0131: dt=92.480000, rms=0.641 (0.046%), neg=0, invalid=4512
0132: dt=92.480000, rms=0.640 (0.048%), neg=0, invalid=4512
0133: dt=92.480000, rms=0.640 (0.044%), neg=0, invalid=4512
0134: dt=92.480000, rms=0.640 (0.041%), neg=0, invalid=4512
0135: dt=92.480000, rms=0.640 (0.043%), neg=0, invalid=4512
0136: dt=92.480000, rms=0.639 (0.042%), neg=0, invalid=4512
0137: dt=92.480000, rms=0.639 (0.043%), neg=0, invalid=4512
0138: dt=92.480000, rms=0.639 (0.043%), neg=0, invalid=4512
0139: dt=92.480000, rms=0.639 (0.040%), neg=0, invalid=4512
0140: dt=92.480000, rms=0.638 (0.041%), neg=0, invalid=4512
0141: dt=92.480000, rms=0.638 (0.040%), neg=0, invalid=4512
0142: dt=92.480000, rms=0.638 (0.038%), neg=0, invalid=4512
0143: dt=92.480000, rms=0.638 (0.037%), neg=0, invalid=4512
0144: dt=92.480000, rms=0.637 (0.037%), neg=0, invalid=4512
0145: dt=92.480000, rms=0.637 (0.036%), neg=0, invalid=4512
0146: dt=92.480000, rms=0.637 (0.035%), neg=0, invalid=4512
0147: dt=92.480000, rms=0.637 (0.032%), neg=0, invalid=4512
0148: dt=92.480000, rms=0.636 (0.030%), neg=0, invalid=4512
0149: dt=92.480000, rms=0.636 (0.030%), neg=0, invalid=4512
0150: dt=92.480000, rms=0.636 (0.029%), neg=0, invalid=4512
0151: dt=92.480000, rms=0.636 (0.030%), neg=0, invalid=4512
0152: dt=92.480000, rms=0.636 (0.028%), neg=0, invalid=4512
0153: dt=92.480000, rms=0.636 (0.028%), neg=0, invalid=4512
0154: dt=92.480000, rms=0.635 (0.028%), neg=0, invalid=4512
0155: dt=92.480000, rms=0.635 (0.028%), neg=0, invalid=4512
0156: dt=92.480000, rms=0.635 (0.026%), neg=0, invalid=4512
0157: dt=92.480000, rms=0.635 (0.022%), neg=0, invalid=4512
0158: dt=92.480000, rms=0.635 (0.023%), neg=0, invalid=4512
0159: dt=92.480000, rms=0.635 (0.023%), neg=0, invalid=4512
0160: dt=92.480000, rms=0.634 (0.022%), neg=0, invalid=4512
0161: dt=2071.552000, rms=0.634 (0.050%), neg=0, invalid=4512
0162: dt=32.368000, rms=0.634 (0.004%), neg=0, invalid=4512
0163: dt=32.368000, rms=0.634 (-0.001%), neg=0, invalid=4512
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.634, neg=0, invalid=4512
0164: dt=221.952000, rms=0.633 (0.189%), neg=0, invalid=4512
0165: dt=129.472000, rms=0.633 (0.042%), neg=0, invalid=4512
0166: dt=129.472000, rms=0.633 (0.036%), neg=0, invalid=4512
0167: dt=129.472000, rms=0.633 (0.043%), neg=0, invalid=4512
0168: dt=129.472000, rms=0.632 (0.042%), neg=0, invalid=4512
0169: dt=129.472000, rms=0.632 (0.035%), neg=0, invalid=4512
0170: dt=129.472000, rms=0.632 (0.052%), neg=0, invalid=4512
0171: dt=129.472000, rms=0.631 (0.036%), neg=0, invalid=4512
0172: dt=129.472000, rms=0.631 (0.019%), neg=0, invalid=4512
0173: dt=129.472000, rms=0.631 (0.009%), neg=0, invalid=4512
0174: dt=129.472000, rms=0.631 (0.026%), neg=0, invalid=4512
0175: dt=0.000000, rms=0.631 (-0.000%), neg=0, invalid=4512
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.632, neg=0, invalid=4512
0176: dt=119.118367, rms=0.628 (0.593%), neg=0, invalid=4512
0177: dt=124.416000, rms=0.624 (0.653%), neg=0, invalid=4512
0178: dt=58.566038, rms=0.622 (0.384%), neg=0, invalid=4512
0179: dt=98.818653, rms=0.620 (0.335%), neg=0, invalid=4512
0180: dt=36.288000, rms=0.618 (0.247%), neg=0, invalid=4512
0181: dt=580.608000, rms=0.610 (1.291%), neg=0, invalid=4512
0182: dt=36.288000, rms=0.609 (0.231%), neg=0, invalid=4512
0183: dt=331.776000, rms=0.607 (0.390%), neg=0, invalid=4512
0184: dt=36.288000, rms=0.605 (0.265%), neg=0, invalid=4512
0185: dt=145.152000, rms=0.604 (0.167%), neg=0, invalid=4512
0186: dt=78.315789, rms=0.603 (0.162%), neg=0, invalid=4512
0187: dt=82.944000, rms=0.602 (0.078%), neg=0, invalid=4512
0188: dt=124.416000, rms=0.602 (0.153%), neg=0, invalid=4512
0189: dt=36.288000, rms=0.601 (0.085%), neg=0, invalid=4512
0190: dt=580.608000, rms=0.599 (0.317%), neg=0, invalid=4512
0191: dt=36.288000, rms=0.597 (0.328%), neg=0, invalid=4512
0192: dt=124.416000, rms=0.597 (0.102%), neg=0, invalid=4512
0193: dt=36.288000, rms=0.596 (0.067%), neg=0, invalid=4512
0194: dt=580.608000, rms=0.594 (0.283%), neg=0, invalid=4512
0195: dt=36.288000, rms=0.593 (0.191%), neg=0, invalid=4512
0196: dt=124.416000, rms=0.593 (0.074%), neg=0, invalid=4512
0197: dt=62.208000, rms=0.593 (0.059%), neg=0, invalid=4512
0198: dt=145.152000, rms=0.592 (0.085%), neg=0, invalid=4512
0199: dt=36.288000, rms=0.592 (0.038%), neg=0, invalid=4512
0200: dt=36.288000, rms=0.592 (0.022%), neg=0, invalid=4512
0201: dt=36.288000, rms=0.591 (0.043%), neg=0, invalid=4512
0202: dt=36.288000, rms=0.591 (0.060%), neg=0, invalid=4512
0203: dt=36.288000, rms=0.591 (0.076%), neg=0, invalid=4512
0204: dt=36.288000, rms=0.590 (0.085%), neg=0, invalid=4512
0205: dt=36.288000, rms=0.590 (0.093%), neg=0, invalid=4512
0206: dt=36.288000, rms=0.589 (0.098%), neg=0, invalid=4512
0207: dt=36.288000, rms=0.588 (0.105%), neg=0, invalid=4512
0208: dt=36.288000, rms=0.588 (0.111%), neg=0, invalid=4512
0209: dt=36.288000, rms=0.587 (0.110%), neg=0, invalid=4512
0210: dt=36.288000, rms=0.586 (0.108%), neg=0, invalid=4512
0211: dt=36.288000, rms=0.586 (0.107%), neg=0, invalid=4512
0212: dt=36.288000, rms=0.585 (0.103%), neg=0, invalid=4512
0213: dt=36.288000, rms=0.585 (0.103%), neg=0, invalid=4512
0214: dt=36.288000, rms=0.584 (0.100%), neg=0, invalid=4512
0215: dt=36.288000, rms=0.583 (0.096%), neg=0, invalid=4512
0216: dt=36.288000, rms=0.583 (0.094%), neg=0, invalid=4512
0217: dt=36.288000, rms=0.582 (0.092%), neg=0, invalid=4512
0218: dt=36.288000, rms=0.582 (0.090%), neg=0, invalid=4512
0219: dt=36.288000, rms=0.581 (0.087%), neg=0, invalid=4512
0220: dt=36.288000, rms=0.581 (0.082%), neg=0, invalid=4512
0221: dt=36.288000, rms=0.580 (0.080%), neg=0, invalid=4512
0222: dt=36.288000, rms=0.580 (0.082%), neg=0, invalid=4512
0223: dt=36.288000, rms=0.579 (0.080%), neg=0, invalid=4512
0224: dt=36.288000, rms=0.579 (0.077%), neg=0, invalid=4512
0225: dt=36.288000, rms=0.579 (0.074%), neg=0, invalid=4512
0226: dt=36.288000, rms=0.578 (0.071%), neg=0, invalid=4512
0227: dt=36.288000, rms=0.578 (0.070%), neg=0, invalid=4512
0228: dt=36.288000, rms=0.577 (0.069%), neg=0, invalid=4512
0229: dt=36.288000, rms=0.577 (0.065%), neg=0, invalid=4512
0230: dt=36.288000, rms=0.577 (0.063%), neg=0, invalid=4512
0231: dt=36.288000, rms=0.576 (0.060%), neg=0, invalid=4512
0232: dt=36.288000, rms=0.576 (0.057%), neg=0, invalid=4512
0233: dt=36.288000, rms=0.576 (0.055%), neg=0, invalid=4512
0234: dt=36.288000, rms=0.575 (0.052%), neg=0, invalid=4512
0235: dt=36.288000, rms=0.575 (0.049%), neg=0, invalid=4512
0236: dt=36.288000, rms=0.575 (0.049%), neg=0, invalid=4512
0237: dt=36.288000, rms=0.574 (0.047%), neg=0, invalid=4512
0238: dt=36.288000, rms=0.574 (0.047%), neg=0, invalid=4512
0239: dt=36.288000, rms=0.574 (0.045%), neg=0, invalid=4512
0240: dt=36.288000, rms=0.574 (0.045%), neg=0, invalid=4512
0241: dt=36.288000, rms=0.573 (0.044%), neg=0, invalid=4512
0242: dt=36.288000, rms=0.573 (0.043%), neg=0, invalid=4512
0243: dt=36.288000, rms=0.573 (0.042%), neg=0, invalid=4512
0244: dt=36.288000, rms=0.573 (0.039%), neg=0, invalid=4512
0245: dt=36.288000, rms=0.573 (0.040%), neg=0, invalid=4512
0246: dt=36.288000, rms=0.572 (0.036%), neg=0, invalid=4512
0247: dt=36.288000, rms=0.572 (0.034%), neg=0, invalid=4512
0248: dt=36.288000, rms=0.572 (0.035%), neg=0, invalid=4512
0249: dt=36.288000, rms=0.572 (0.036%), neg=0, invalid=4512
0250: dt=36.288000, rms=0.572 (0.034%), neg=0, invalid=4512
0251: dt=36.288000, rms=0.571 (0.034%), neg=0, invalid=4512
0252: dt=36.288000, rms=0.571 (0.031%), neg=0, invalid=4512
0253: dt=36.288000, rms=0.571 (0.031%), neg=0, invalid=4512
0254: dt=36.288000, rms=0.571 (0.032%), neg=0, invalid=4512
0255: dt=36.288000, rms=0.571 (0.033%), neg=0, invalid=4512
0256: dt=36.288000, rms=0.570 (0.034%), neg=0, invalid=4512
0257: dt=36.288000, rms=0.570 (0.031%), neg=0, invalid=4512
0258: dt=36.288000, rms=0.570 (0.029%), neg=0, invalid=4512
0259: dt=36.288000, rms=0.570 (0.027%), neg=0, invalid=4512
0260: dt=36.288000, rms=0.570 (0.025%), neg=0, invalid=4512
0261: dt=36.288000, rms=0.570 (0.027%), neg=0, invalid=4512
0262: dt=36.288000, rms=0.569 (0.027%), neg=0, invalid=4512
0263: dt=36.288000, rms=0.569 (0.028%), neg=0, invalid=4512
0264: dt=36.288000, rms=0.569 (0.003%), neg=0, invalid=4512
0265: dt=36.288000, rms=0.569 (0.003%), neg=0, invalid=4512
0266: dt=9.072000, rms=0.569 (0.001%), neg=0, invalid=4512
0267: dt=9.072000, rms=0.569 (0.001%), neg=0, invalid=4512
0268: dt=1.134000, rms=0.569 (0.000%), neg=0, invalid=4512
0269: dt=0.283500, rms=0.569 (-0.000%), neg=0, invalid=4512
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.570, neg=0, invalid=4512
0270: dt=145.152000, rms=0.567 (0.507%), neg=0, invalid=4512
0271: dt=62.208000, rms=0.566 (0.105%), neg=0, invalid=4512
0272: dt=145.152000, rms=0.566 (0.084%), neg=0, invalid=4512
0273: dt=36.288000, rms=0.566 (0.059%), neg=0, invalid=4512
0274: dt=497.664000, rms=0.565 (0.172%), neg=0, invalid=4512
0275: dt=36.288000, rms=0.564 (0.071%), neg=0, invalid=4512
0276: dt=124.416000, rms=0.564 (0.023%), neg=0, invalid=4512
0277: dt=124.416000, rms=0.564 (0.032%), neg=0, invalid=4512
0278: dt=124.416000, rms=0.564 (0.050%), neg=0, invalid=4512
0279: dt=124.416000, rms=0.563 (0.090%), neg=0, invalid=4512
0280: dt=124.416000, rms=0.563 (0.088%), neg=0, invalid=4512
0281: dt=124.416000, rms=0.562 (0.074%), neg=0, invalid=4512
0282: dt=124.416000, rms=0.561 (0.133%), neg=0, invalid=4512
0283: dt=124.416000, rms=0.561 (0.083%), neg=0, invalid=4512
0284: dt=124.416000, rms=0.561 (0.057%), neg=0, invalid=4512
0285: dt=124.416000, rms=0.560 (0.105%), neg=0, invalid=4512
0286: dt=124.416000, rms=0.560 (0.084%), neg=0, invalid=4512
0287: dt=124.416000, rms=0.559 (0.065%), neg=0, invalid=4512
0288: dt=124.416000, rms=0.559 (0.083%), neg=0, invalid=4512
0289: dt=124.416000, rms=0.558 (0.075%), neg=0, invalid=4512
0290: dt=124.416000, rms=0.558 (0.054%), neg=0, invalid=4512
0291: dt=124.416000, rms=0.558 (0.072%), neg=0, invalid=4512
0292: dt=124.416000, rms=0.557 (0.053%), neg=0, invalid=4512
0293: dt=124.416000, rms=0.557 (0.081%), neg=0, invalid=4512
0294: dt=124.416000, rms=0.557 (0.059%), neg=0, invalid=4512
0295: dt=124.416000, rms=0.556 (0.042%), neg=0, invalid=4512
0296: dt=124.416000, rms=0.556 (0.074%), neg=0, invalid=4512
0297: dt=124.416000, rms=0.556 (0.045%), neg=0, invalid=4512
0298: dt=124.416000, rms=0.555 (0.057%), neg=0, invalid=4512
0299: dt=124.416000, rms=0.555 (0.040%), neg=0, invalid=4512
0300: dt=124.416000, rms=0.555 (0.044%), neg=0, invalid=4512
0301: dt=124.416000, rms=0.555 (0.045%), neg=0, invalid=4512
0302: dt=124.416000, rms=0.554 (0.061%), neg=0, invalid=4512
0303: dt=124.416000, rms=0.554 (0.037%), neg=0, invalid=4512
0304: dt=124.416000, rms=0.554 (-0.231%), neg=0, invalid=4512
0305: dt=36.288000, rms=0.554 (0.051%), neg=0, invalid=4512
0306: dt=103.680000, rms=0.554 (0.006%), neg=0, invalid=4512
0307: dt=103.680000, rms=0.554 (-0.001%), neg=0, invalid=4512
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.561, neg=0, invalid=4512
0308: dt=2.000000, rms=0.561 (0.137%), neg=0, invalid=4512
0309: dt=0.175000, rms=0.561 (0.003%), neg=0, invalid=4512
0310: dt=0.043750, rms=0.561 (0.000%), neg=0, invalid=4512
0311: dt=0.010937, rms=0.561 (0.000%), neg=0, invalid=4512
0312: dt=0.005469, rms=0.561 (0.000%), neg=0, invalid=4512
0313: dt=0.000684, rms=0.561 (0.000%), neg=0, invalid=4512
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.561, neg=0, invalid=4512
0314: dt=81.362599, rms=0.557 (0.749%), neg=0, invalid=4512
0315: dt=44.800000, rms=0.553 (0.697%), neg=0, invalid=4512
0316: dt=11.200000, rms=0.552 (0.152%), neg=0, invalid=4512
0317: dt=2.800000, rms=0.552 (0.037%), neg=0, invalid=4512
0318: dt=0.700000, rms=0.552 (0.007%), neg=0, invalid=4512
0319: dt=0.350000, rms=0.552 (0.003%), neg=0, invalid=4512
0320: dt=0.021875, rms=0.552 (0.000%), neg=0, invalid=4512
0321: dt=0.010937, rms=0.552 (0.000%), neg=0, invalid=4512
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.568, neg=0, invalid=4512
0322: dt=4.032000, rms=0.564 (0.797%), neg=0, invalid=4512
0323: dt=4.032000, rms=0.561 (0.516%), neg=0, invalid=4512
0324: dt=11.520000, rms=0.556 (0.940%), neg=0, invalid=4512
0325: dt=46.080000, rms=0.548 (1.380%), neg=0, invalid=4512
0326: dt=9.663366, rms=0.548 (0.091%), neg=0, invalid=4512
0327: dt=18.666667, rms=0.547 (0.097%), neg=0, invalid=4512
0328: dt=18.000000, rms=0.547 (0.080%), neg=0, invalid=4512
0329: dt=16.128000, rms=0.546 (0.102%), neg=0, invalid=4512
0330: dt=13.824000, rms=0.546 (0.094%), neg=0, invalid=4512
0331: dt=16.000000, rms=0.545 (0.068%), neg=0, invalid=4512
0332: dt=13.600000, rms=0.545 (0.065%), neg=0, invalid=4512
0333: dt=12.444444, rms=0.545 (0.053%), neg=0, invalid=4512
0334: dt=16.000000, rms=0.544 (0.052%), neg=0, invalid=4512
0335: dt=11.520000, rms=0.544 (0.040%), neg=0, invalid=4512
0336: dt=11.520000, rms=0.544 (0.042%), neg=0, invalid=4512
0337: dt=11.520000, rms=0.543 (0.072%), neg=0, invalid=4512
0338: dt=11.520000, rms=0.543 (0.077%), neg=0, invalid=4512
0339: dt=11.520000, rms=0.542 (0.092%), neg=0, invalid=4512
0340: dt=11.520000, rms=0.542 (0.105%), neg=0, invalid=4512
0341: dt=11.520000, rms=0.541 (0.113%), neg=0, invalid=4512
0342: dt=11.520000, rms=0.541 (0.076%), neg=0, invalid=4512
0343: dt=11.520000, rms=0.540 (0.078%), neg=0, invalid=4512
0344: dt=11.520000, rms=0.540 (0.093%), neg=0, invalid=4512
0345: dt=11.520000, rms=0.540 (0.082%), neg=0, invalid=4512
0346: dt=11.520000, rms=0.539 (0.055%), neg=0, invalid=4512
0347: dt=11.520000, rms=0.539 (0.050%), neg=0, invalid=4512
0348: dt=11.520000, rms=0.539 (0.061%), neg=0, invalid=4512
0349: dt=11.520000, rms=0.538 (0.054%), neg=0, invalid=4512
0350: dt=11.520000, rms=0.538 (0.029%), neg=0, invalid=4512
0351: dt=11.520000, rms=0.538 (0.031%), neg=0, invalid=4512
0352: dt=11.520000, rms=0.538 (0.018%), neg=0, invalid=4512
0353: dt=2.880000, rms=0.538 (-0.001%), neg=0, invalid=4512
0354: dt=2.880000, rms=0.538 (0.002%), neg=0, invalid=4512
0355: dt=0.252000, rms=0.538 (0.004%), neg=0, invalid=4512
0356: dt=0.252000, rms=0.538 (-0.001%), neg=0, invalid=4512
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.538, neg=0, invalid=4512
0357: dt=0.252000, rms=0.538 (0.094%), neg=0, invalid=4512
0358: dt=0.180000, rms=0.538 (0.001%), neg=0, invalid=4512
0359: dt=0.002813, rms=0.538 (-0.000%), neg=0, invalid=4512
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.559, neg=0, invalid=4512
0360: dt=0.000000, rms=0.558 (0.087%), neg=0, invalid=4512
0361: dt=0.000000, rms=0.558 (0.000%), neg=0, invalid=4512
0362: dt=0.100000, rms=0.558 (-0.121%), neg=0, invalid=4512
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.559, neg=0, invalid=4512
0363: dt=0.000000, rms=0.558 (0.087%), neg=0, invalid=4512
0364: dt=0.000000, rms=0.558 (0.000%), neg=0, invalid=4512
0365: dt=0.100000, rms=0.558 (-0.089%), neg=0, invalid=4512
resetting metric properties...
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.524, neg=0, invalid=4512
0366: dt=0.448000, rms=0.508 (3.067%), neg=0, invalid=4512
0367: dt=0.448000, rms=0.505 (0.634%), neg=0, invalid=4512
0368: dt=0.448000, rms=0.503 (0.384%), neg=0, invalid=4512
0369: dt=0.448000, rms=0.502 (0.218%), neg=0, invalid=4512
0370: dt=0.448000, rms=0.501 (0.181%), neg=0, invalid=4512
0371: dt=0.448000, rms=0.501 (0.110%), neg=0, invalid=4512
0372: dt=0.448000, rms=0.500 (0.113%), neg=0, invalid=4512
0373: dt=0.448000, rms=0.500 (0.062%), neg=0, invalid=4512
0374: dt=0.448000, rms=0.499 (0.080%), neg=0, invalid=4512
0375: dt=0.448000, rms=0.499 (0.036%), neg=0, invalid=4512
0376: dt=0.448000, rms=0.499 (0.061%), neg=0, invalid=4512
0377: dt=0.448000, rms=0.498 (0.076%), neg=0, invalid=4512
0378: dt=0.224000, rms=0.498 (0.018%), neg=0, invalid=4512
0379: dt=0.224000, rms=0.498 (0.031%), neg=0, invalid=4512
0380: dt=0.224000, rms=0.498 (0.038%), neg=0, invalid=4512
0381: dt=0.224000, rms=0.498 (0.033%), neg=0, invalid=4512
0382: dt=0.224000, rms=0.498 (0.006%), neg=0, invalid=4512
0383: dt=0.224000, rms=0.498 (0.009%), neg=0, invalid=4512
0384: dt=0.224000, rms=0.498 (0.019%), neg=0, invalid=4512
0385: dt=0.224000, rms=0.498 (0.031%), neg=0, invalid=4512
0386: dt=0.224000, rms=0.497 (0.035%), neg=0, invalid=4512
0387: dt=0.224000, rms=0.497 (0.032%), neg=0, invalid=4512
0388: dt=0.224000, rms=0.497 (0.027%), neg=0, invalid=4512
0389: dt=0.224000, rms=0.497 (0.021%), neg=0, invalid=4512
0390: dt=0.224000, rms=0.497 (0.022%), neg=0, invalid=4512
0391: dt=0.224000, rms=0.497 (0.019%), neg=0, invalid=4512
0392: dt=0.028000, rms=0.497 (0.000%), neg=0, invalid=4512
0393: dt=0.028000, rms=0.497 (0.000%), neg=0, invalid=4512
0394: dt=0.028000, rms=0.497 (-0.000%), neg=0, invalid=4512
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.497, neg=0, invalid=4512
0395: dt=0.384000, rms=0.492 (1.028%), neg=0, invalid=4512
0396: dt=0.320000, rms=0.491 (0.171%), neg=0, invalid=4512
0397: dt=0.320000, rms=0.491 (0.073%), neg=0, invalid=4512
0398: dt=0.320000, rms=0.491 (0.027%), neg=0, invalid=4512
0399: dt=0.320000, rms=0.491 (0.016%), neg=0, invalid=4512
0400: dt=0.320000, rms=0.491 (0.017%), neg=0, invalid=4512
0401: dt=0.320000, rms=0.491 (0.010%), neg=0, invalid=4512
0402: dt=0.320000, rms=0.491 (-0.007%), neg=0, invalid=4512
label assignment complete, 0 changed (0.00%)
********************* ALLOWING NEGATIVE NODES IN DEFORMATION********************************
**************** pass 1 of 1 ************************
enabling zero nodes
setting smoothness coefficient to 0.008
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.489, neg=0, invalid=4512
0403: dt=0.000000, rms=0.489 (0.124%), neg=0, invalid=4512
0404: dt=0.000000, rms=0.489 (0.000%), neg=0, invalid=4512
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.489, neg=0, invalid=4512
0405: dt=129.472000, rms=0.488 (0.186%), neg=0, invalid=4512
0406: dt=92.480000, rms=0.488 (0.014%), neg=0, invalid=4512
0407: dt=92.480000, rms=0.488 (0.019%), neg=0, invalid=4512
0408: dt=92.480000, rms=0.488 (0.025%), neg=0, invalid=4512
0409: dt=92.480000, rms=0.488 (0.023%), neg=0, invalid=4512
0410: dt=92.480000, rms=0.488 (0.015%), neg=0, invalid=4512
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.488, neg=0, invalid=4512
0411: dt=9.072000, rms=0.488 (0.135%), neg=0, invalid=4512
0412: dt=9.072000, rms=0.488 (0.004%), neg=0, invalid=4512
0413: dt=9.072000, rms=0.488 (0.002%), neg=0, invalid=4512
0414: dt=9.072000, rms=0.488 (-0.004%), neg=0, invalid=4512
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.488, neg=0, invalid=4512
0415: dt=145.152000, rms=0.486 (0.499%), neg=0, invalid=4512
0416: dt=31.104000, rms=0.486 (0.063%), neg=0, invalid=4512
0417: dt=31.104000, rms=0.485 (0.036%), neg=0, invalid=4512
0418: dt=31.104000, rms=0.485 (0.054%), neg=0, invalid=4512
0419: dt=31.104000, rms=0.485 (0.074%), neg=0, invalid=4512
0420: dt=31.104000, rms=0.484 (0.088%), neg=0, invalid=4512
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0421: dt=31.104000, rms=0.484 (0.092%), neg=0, invalid=4512
0422: dt=31.104000, rms=0.483 (0.090%), neg=0, invalid=4512
0423: dt=31.104000, rms=0.483 (0.074%), neg=0, invalid=4512
0424: dt=36.288000, rms=0.483 (0.011%), neg=0, invalid=4512
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.484, neg=0, invalid=4512
iter 0, gcam->neg = 2
after 8 iterations, nbhd size=1, neg = 0
0425: dt=38.400000, rms=0.481 (0.677%), neg=0, invalid=4512
iter 0, gcam->neg = 22
after 10 iterations, nbhd size=1, neg = 0
0426: dt=78.417582, rms=0.477 (0.700%), neg=0, invalid=4512
iter 0, gcam->neg = 1
after 7 iterations, nbhd size=1, neg = 0
0427: dt=11.200000, rms=0.476 (0.249%), neg=0, invalid=4512
iter 0, gcam->neg = 3
after 12 iterations, nbhd size=1, neg = 0
0428: dt=11.200000, rms=0.476 (0.111%), neg=0, invalid=4512
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0429: dt=11.200000, rms=0.475 (0.076%), neg=0, invalid=4512
iter 0, gcam->neg = 5
after 8 iterations, nbhd size=1, neg = 0
0430: dt=11.200000, rms=0.475 (0.090%), neg=0, invalid=4512
iter 0, gcam->neg = 7
after 11 iterations, nbhd size=1, neg = 0
0431: dt=11.200000, rms=0.474 (0.178%), neg=0, invalid=4512
iter 0, gcam->neg = 8
after 3 iterations, nbhd size=0, neg = 0
0432: dt=11.200000, rms=0.473 (0.234%), neg=0, invalid=4512
iter 0, gcam->neg = 4
after 7 iterations, nbhd size=1, neg = 0
0433: dt=11.200000, rms=0.472 (0.226%), neg=0, invalid=4512
iter 0, gcam->neg = 7
after 9 iterations, nbhd size=1, neg = 0
0434: dt=11.200000, rms=0.471 (0.175%), neg=0, invalid=4512
iter 0, gcam->neg = 9
after 9 iterations, nbhd size=1, neg = 0
0435: dt=11.200000, rms=0.470 (0.149%), neg=0, invalid=4512
iter 0, gcam->neg = 3
after 1 iterations, nbhd size=0, neg = 0
0436: dt=11.200000, rms=0.470 (0.126%), neg=0, invalid=4512
iter 0, gcam->neg = 8
after 12 iterations, nbhd size=1, neg = 0
0437: dt=11.200000, rms=0.469 (0.070%), neg=0, invalid=4512
iter 0, gcam->neg = 10
after 13 iterations, nbhd size=1, neg = 0
0438: dt=11.200000, rms=0.469 (0.090%), neg=0, invalid=4512
iter 0, gcam->neg = 16
after 10 iterations, nbhd size=1, neg = 0
0439: dt=11.200000, rms=0.468 (0.104%), neg=0, invalid=4512
iter 0, gcam->neg = 12
after 10 iterations, nbhd size=1, neg = 0
0440: dt=11.200000, rms=0.468 (0.116%), neg=0, invalid=4512
iter 0, gcam->neg = 15
after 2 iterations, nbhd size=0, neg = 0
0441: dt=11.200000, rms=0.467 (0.113%), neg=0, invalid=4512
iter 0, gcam->neg = 2
after 1 iterations, nbhd size=0, neg = 0
0442: dt=32.000000, rms=0.467 (0.050%), neg=0, invalid=4512
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0443: dt=32.000000, rms=0.467 (0.040%), neg=0, invalid=4512
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0444: dt=32.000000, rms=0.467 (0.078%), neg=0, invalid=4512
iter 0, gcam->neg = 2
after 2 iterations, nbhd size=0, neg = 0
0445: dt=32.000000, rms=0.467 (0.006%), neg=0, invalid=4512
iter 0, gcam->neg = 6
after 12 iterations, nbhd size=1, neg = 0
0446: dt=32.000000, rms=0.466 (0.105%), neg=0, invalid=4512
iter 0, gcam->neg = 6
after 1 iterations, nbhd size=0, neg = 0
0447: dt=32.000000, rms=0.466 (0.051%), neg=0, invalid=4512
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.467, neg=0, invalid=4512
0448: dt=38.133333, rms=0.463 (0.759%), neg=0, invalid=4512
0449: dt=25.600000, rms=0.462 (0.321%), neg=0, invalid=4512
0450: dt=22.814815, rms=0.461 (0.147%), neg=0, invalid=4512
0451: dt=22.814815, rms=0.461 (0.092%), neg=0, invalid=4512
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0452: dt=22.814815, rms=0.460 (0.187%), neg=0, invalid=4512
0453: dt=22.814815, rms=0.459 (0.135%), neg=0, invalid=4512
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0454: dt=22.814815, rms=0.458 (0.155%), neg=0, invalid=4512
0455: dt=22.814815, rms=0.458 (0.097%), neg=0, invalid=4512
0456: dt=22.814815, rms=0.457 (0.127%), neg=0, invalid=4512
0457: dt=22.814815, rms=0.457 (0.038%), neg=0, invalid=4512
iter 0, gcam->neg = 1
after 2 iterations, nbhd size=0, neg = 0
0458: dt=22.814815, rms=0.457 (0.104%), neg=0, invalid=4512
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0459: dt=22.814815, rms=0.456 (0.066%), neg=0, invalid=4512
0460: dt=11.200000, rms=0.456 (0.063%), neg=0, invalid=4512
0461: dt=11.200000, rms=0.456 (0.025%), neg=0, invalid=4512
0462: dt=11.200000, rms=0.456 (0.028%), neg=0, invalid=4512
0463: dt=11.200000, rms=0.456 (0.034%), neg=0, invalid=4512
0464: dt=11.200000, rms=0.456 (0.032%), neg=0, invalid=4512
0465: dt=11.200000, rms=0.455 (0.033%), neg=0, invalid=4512
0466: dt=11.200000, rms=0.455 (0.021%), neg=0, invalid=4512
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.461, neg=0, invalid=4512
0467: dt=0.000000, rms=0.460 (0.148%), neg=0, invalid=4512
0468: dt=0.000000, rms=0.460 (0.000%), neg=0, invalid=4512
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.461, neg=0, invalid=4512
0469: dt=0.252000, rms=0.460 (0.149%), neg=0, invalid=4512
0470: dt=0.250000, rms=0.460 (0.000%), neg=0, invalid=4512
0471: dt=0.250000, rms=0.460 (-0.000%), neg=0, invalid=4512
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.471, neg=0, invalid=4512
0472: dt=1.024000, rms=0.470 (0.315%), neg=0, invalid=4512
0473: dt=0.256000, rms=0.470 (0.006%), neg=0, invalid=4512
0474: dt=0.256000, rms=0.470 (-0.001%), neg=0, invalid=4512
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.470, neg=0, invalid=4512
0475: dt=1.280000, rms=0.469 (0.315%), neg=0, invalid=4512
0476: dt=0.448000, rms=0.469 (0.018%), neg=0, invalid=4512
0477: dt=0.448000, rms=0.469 (0.008%), neg=0, invalid=4512
0478: dt=0.448000, rms=0.469 (-0.020%), neg=0, invalid=4512
resetting metric properties...
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.460, neg=0, invalid=4512
iter 0, gcam->neg = 1212
after 16 iterations, nbhd size=1, neg = 0
0479: dt=2.203815, rms=0.433 (5.967%), neg=0, invalid=4512
0480: dt=0.096000, rms=0.433 (0.091%), neg=0, invalid=4512
0481: dt=0.096000, rms=0.433 (-0.072%), neg=0, invalid=4512
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.433, neg=0, invalid=4512
0482: dt=0.096000, rms=0.432 (0.223%), neg=0, invalid=4512
0483: dt=0.000000, rms=0.432 (0.005%), neg=0, invalid=4512
0484: dt=0.050000, rms=0.432 (-0.016%), neg=0, invalid=4512
label assignment complete, 0 changed (0.00%)
label assignment complete, 0 changed (0.00%)
***************** morphing with label term set to 0 *******************************
**************** pass 1 of 1 ************************
enabling zero nodes
setting smoothness coefficient to 0.008
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.418, neg=0, invalid=4512
0485: dt=0.000000, rms=0.418 (0.000%), neg=0, invalid=4512
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.418, neg=0, invalid=4512
0486: dt=32.368000, rms=0.418 (0.006%), neg=0, invalid=4512
0487: dt=32.368000, rms=0.418 (0.001%), neg=0, invalid=4512
0488: dt=32.368000, rms=0.418 (0.001%), neg=0, invalid=4512
0489: dt=32.368000, rms=0.418 (-0.000%), neg=0, invalid=4512
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.418, neg=0, invalid=4512
0490: dt=0.000000, rms=0.418 (0.000%), neg=0, invalid=4512
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.418, neg=0, invalid=4512
0491: dt=36.288000, rms=0.418 (0.024%), neg=0, invalid=4512
0492: dt=82.944000, rms=0.418 (0.019%), neg=0, invalid=4512
0493: dt=82.944000, rms=0.418 (0.017%), neg=0, invalid=4512
0494: dt=82.944000, rms=0.418 (0.011%), neg=0, invalid=4512
0495: dt=82.944000, rms=0.418 (-0.005%), neg=0, invalid=4512
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.419, neg=0, invalid=4512
0496: dt=11.200000, rms=0.419 (0.057%), neg=0, invalid=4512
0497: dt=8.000000, rms=0.418 (0.015%), neg=0, invalid=4512
0498: dt=8.000000, rms=0.418 (0.005%), neg=0, invalid=4512
0499: dt=8.000000, rms=0.418 (-0.021%), neg=0, invalid=4512
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.418, neg=0, invalid=4512
0500: dt=77.070423, rms=0.416 (0.603%), neg=0, invalid=4512
0501: dt=25.600000, rms=0.415 (0.292%), neg=0, invalid=4512
0502: dt=76.800000, rms=0.414 (0.182%), neg=0, invalid=4512
0503: dt=76.800000, rms=0.414 (-0.413%), neg=0, invalid=4512
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.417, neg=0, invalid=4512
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
0504: dt=8.888889, rms=0.416 (0.198%), neg=0, invalid=4512
iter 0, gcam->neg = 3
after 9 iterations, nbhd size=1, neg = 0
0505: dt=13.161290, rms=0.416 (0.049%), neg=0, invalid=4512
iter 0, gcam->neg = 5
after 11 iterations, nbhd size=1, neg = 0
0506: dt=13.161290, rms=0.415 (0.026%), neg=0, invalid=4512
iter 0, gcam->neg = 13
after 2 iterations, nbhd size=0, neg = 0
0507: dt=13.161290, rms=0.415 (0.036%), neg=0, invalid=4512
iter 0, gcam->neg = 19
after 13 iterations, nbhd size=1, neg = 0
0508: dt=13.161290, rms=0.415 (-0.049%), neg=0, invalid=4512
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.415, neg=0, invalid=4512
iter 0, gcam->neg = 1
after 7 iterations, nbhd size=1, neg = 0
0509: dt=19.267606, rms=0.412 (0.733%), neg=0, invalid=4512
iter 0, gcam->neg = 3
after 1 iterations, nbhd size=0, neg = 0
0510: dt=15.714286, rms=0.412 (0.184%), neg=0, invalid=4512
iter 0, gcam->neg = 32
after 10 iterations, nbhd size=1, neg = 0
0511: dt=15.714286, rms=0.411 (0.089%), neg=0, invalid=4512
iter 0, gcam->neg = 45
after 12 iterations, nbhd size=1, neg = 0
0512: dt=15.714286, rms=0.410 (0.175%), neg=0, invalid=4512
iter 0, gcam->neg = 35
after 12 iterations, nbhd size=1, neg = 0
0513: dt=15.714286, rms=0.410 (0.164%), neg=0, invalid=4512
iter 0, gcam->neg = 38
after 12 iterations, nbhd size=1, neg = 0
0514: dt=15.714286, rms=0.409 (0.142%), neg=0, invalid=4512
iter 0, gcam->neg = 51
after 12 iterations, nbhd size=1, neg = 0
0515: dt=15.714286, rms=0.409 (0.142%), neg=0, invalid=4512
iter 0, gcam->neg = 61
after 17 iterations, nbhd size=1, neg = 0
0516: dt=15.714286, rms=0.408 (0.136%), neg=0, invalid=4512
iter 0, gcam->neg = 71
after 17 iterations, nbhd size=1, neg = 0
0517: dt=15.714286, rms=0.408 (0.036%), neg=0, invalid=4512
iter 0, gcam->neg = 85
after 16 iterations, nbhd size=1, neg = 0
0518: dt=15.714286, rms=0.408 (0.039%), neg=0, invalid=4512
iter 0, gcam->neg = 94
after 16 iterations, nbhd size=1, neg = 0
0519: dt=15.714286, rms=0.408 (0.020%), neg=0, invalid=4512
iter 0, gcam->neg = 4
after 0 iterations, nbhd size=0, neg = 0
0520: dt=11.500000, rms=0.407 (0.056%), neg=0, invalid=4512
iter 0, gcam->neg = 2
after 2 iterations, nbhd size=0, neg = 0
0521: dt=16.128000, rms=0.407 (0.043%), neg=0, invalid=4512
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0522: dt=16.128000, rms=0.407 (-0.026%), neg=0, invalid=4512
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.413, neg=0, invalid=4512
0523: dt=0.000050, rms=0.413 (0.000%), neg=0, invalid=4512
0524: dt=0.000000, rms=0.413 (0.000%), neg=0, invalid=4512
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.413, neg=0, invalid=4512
0525: dt=0.000000, rms=0.413 (0.000%), neg=0, invalid=4512
resetting metric properties...
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.403, neg=0, invalid=4512
iter 0, gcam->neg = 693
after 15 iterations, nbhd size=1, neg = 0
0526: dt=1.418699, rms=0.395 (1.902%), neg=0, invalid=4512
0527: dt=0.000023, rms=0.395 (0.000%), neg=0, invalid=4512
0528: dt=0.000023, rms=0.395 (-0.000%), neg=0, invalid=4512
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.395, neg=0, invalid=4512
0529: dt=0.112000, rms=0.395 (0.081%), neg=0, invalid=4512
0530: dt=0.064000, rms=0.395 (0.015%), neg=0, invalid=4512
0531: dt=0.064000, rms=0.395 (0.004%), neg=0, invalid=4512
0532: dt=0.064000, rms=0.395 (-0.033%), neg=0, invalid=4512
writing output transformation to transforms/talairach.m3z...
GCAMwrite
mri_ca_register took 1 hours, 57 minutes and 10 seconds.
mri_ca_register utimesec 7013.653022
mri_ca_register stimesec 10.352598
mri_ca_register ru_maxrss 1340644
mri_ca_register ru_ixrss 0
mri_ca_register ru_idrss 0
mri_ca_register ru_isrss 0
mri_ca_register ru_minflt 10002754
mri_ca_register ru_majflt 0
mri_ca_register ru_nswap 0
mri_ca_register ru_inblock 0
mri_ca_register ru_oublock 62744
mri_ca_register ru_msgsnd 0
mri_ca_register ru_msgrcv 0
mri_ca_register ru_nsignals 0
mri_ca_register ru_nvcsw 5084
mri_ca_register ru_nivcsw 705621
FSRUNTIME@ mri_ca_register 1.9528 hours 1 threads
#--------------------------------------
#@# SubCort Seg Fri Nov 13 15:53:32 EST 2020
mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/packages/freesurfer_v6.0.0/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz
sysname Linux
hostname blade21.dhe.duke.edu
machine x86_64
setenv SUBJECTS_DIR /mnt/munin/Morey/Lab/T1Duke/Freesurfer
cd /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri
mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/packages/freesurfer_v6.0.0/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/packages/freesurfer_v6.0.0/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 6.63
Atlas used for the 3D morph was /usr/local/packages/freesurfer_v6.0.0/average/RB_all_2016-05-10.vc700.gca
average std = 7.3 using min determinant for regularization = 5.3
0 singular and 0 ill-conditioned covariance matrices regularized
labeling volume...
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.16259 (20)
mri peak = 0.10240 (12)
Left_Lateral_Ventricle (4): linear fit = 0.50 x + 0.0 (994 voxels, overlap=0.296)
Left_Lateral_Ventricle (4): linear fit = 0.50 x + 0.0 (994 voxels, peak = 10), gca=9.9
gca peak = 0.17677 (13)
mri peak = 0.10927 ( 8)
Right_Lateral_Ventricle (43): linear fit = 0.51 x + 0.0 (787 voxels, overlap=0.422)
Right_Lateral_Ventricle (43): linear fit = 0.51 x + 0.0 (787 voxels, peak = 7), gca=6.7
gca peak = 0.28129 (95)
mri peak = 0.08808 (95)
Right_Pallidum (52): linear fit = 1.01 x + 0.0 (737 voxels, overlap=1.019)
Right_Pallidum (52): linear fit = 1.01 x + 0.0 (737 voxels, peak = 96), gca=96.4
gca peak = 0.16930 (96)
mri peak = 0.08212 (98)
Left_Pallidum (13): linear fit = 1.01 x + 0.0 (718 voxels, overlap=1.014)
Left_Pallidum (13): linear fit = 1.01 x + 0.0 (718 voxels, peak = 97), gca=97.4
gca peak = 0.24553 (55)
mri peak = 0.08103 (67)
Right_Hippocampus (53): linear fit = 1.17 x + 0.0 (1046 voxels, overlap=0.364)
Right_Hippocampus (53): linear fit = 1.17 x + 0.0 (1046 voxels, peak = 65), gca=64.6
gca peak = 0.30264 (59)
mri peak = 0.08401 (68)
Left_Hippocampus (17): linear fit = 1.13 x + 0.0 (986 voxels, overlap=0.718)
Left_Hippocampus (17): linear fit = 1.13 x + 0.0 (986 voxels, peak = 67), gca=67.0
gca peak = 0.07580 (103)
mri peak = 0.08449 (105)
Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (48441 voxels, overlap=0.693)
Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (48441 voxels, peak = 107), gca=106.6
gca peak = 0.07714 (104)
mri peak = 0.08577 (106)
Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (48057 voxels, overlap=0.612)
Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (48057 voxels, peak = 109), gca=108.7
gca peak = 0.09712 (58)
mri peak = 0.03722 (62)
Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (23106 voxels, overlap=0.967)
Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (23106 voxels, peak = 59), gca=59.4
gca peak = 0.11620 (58)
mri peak = 0.03928 (63)
Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (21773 voxels, overlap=0.960)
Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (21773 voxels, peak = 59), gca=59.4
gca peak = 0.30970 (66)
mri peak = 0.09857 (67)
Right_Caudate (50): linear fit = 0.99 x + 0.0 (941 voxels, overlap=1.007)
Right_Caudate (50): linear fit = 0.99 x + 0.0 (941 voxels, peak = 65), gca=65.0
gca peak = 0.15280 (69)
mri peak = 0.10000 (73)
Left_Caudate (11): linear fit = 0.98 x + 0.0 (809 voxels, overlap=1.002)
Left_Caudate (11): linear fit = 0.98 x + 0.0 (809 voxels, peak = 67), gca=67.3
gca peak = 0.13902 (56)
mri peak = 0.05731 (60)
Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (18820 voxels, overlap=0.956)
Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (18820 voxels, peak = 59), gca=58.5
gca peak = 0.14777 (55)
mri peak = 0.06443 (62)
Right_Cerebellum_Cortex (47): linear fit = 1.12 x + 0.0 (20512 voxels, overlap=0.820)
Right_Cerebellum_Cortex (47): linear fit = 1.12 x + 0.0 (20512 voxels, peak = 61), gca=61.3
gca peak = 0.16765 (84)
mri peak = 0.09673 (85)
Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (5531 voxels, overlap=0.864)
Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (5531 voxels, peak = 86), gca=86.1
gca peak = 0.18739 (84)
mri peak = 0.10392 (88)
Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (5553 voxels, overlap=0.742)
Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (5553 voxels, peak = 88), gca=87.8
gca peak = 0.29869 (57)
mri peak = 0.11259 (67)
Left_Amygdala (18): linear fit = 1.16 x + 0.0 (481 voxels, overlap=0.061)
Left_Amygdala (18): linear fit = 1.16 x + 0.0 (481 voxels, peak = 66), gca=66.4
gca peak = 0.33601 (57)
mri peak = 0.09178 (65)
Right_Amygdala (54): linear fit = 1.13 x + 0.0 (523 voxels, overlap=0.046)
Right_Amygdala (54): linear fit = 1.13 x + 0.0 (523 voxels, peak = 65), gca=64.7
gca peak = 0.11131 (90)
mri peak = 0.06120 (87)
Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (4636 voxels, overlap=0.912)
Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (4636 voxels, peak = 92), gca=92.2
gca peak = 0.11793 (83)
mri peak = 0.06246 (89)
Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (4255 voxels, overlap=0.950)
Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (4255 voxels, peak = 87), gca=86.7
gca peak = 0.08324 (81)
mri peak = 0.07840 (80)
Left_Putamen (12): linear fit = 1.02 x + 0.0 (1872 voxels, overlap=0.851)
Left_Putamen (12): linear fit = 1.02 x + 0.0 (1872 voxels, peak = 83), gca=83.0
gca peak = 0.10360 (77)
mri peak = 0.07779 (79)
Right_Putamen (51): linear fit = 1.02 x + 0.0 (2295 voxels, overlap=0.881)
Right_Putamen (51): linear fit = 1.02 x + 0.0 (2295 voxels, peak = 79), gca=78.9
gca peak = 0.08424 (78)
mri peak = 0.08304 (83)
Brain_Stem (16): linear fit = 1.07 x + 0.0 (12188 voxels, overlap=0.476)
Brain_Stem (16): linear fit = 1.07 x + 0.0 (12188 voxels, peak = 83), gca=83.1
gca peak = 0.12631 (89)
mri peak = 0.09097 (95)
Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1534 voxels, overlap=0.421)
Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1534 voxels, peak = 97), gca=97.5
gca peak = 0.14500 (87)
mri peak = 0.08284 (95)
Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1457 voxels, overlap=0.330)
Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1457 voxels, peak = 94), gca=93.5
gca peak = 0.14975 (24)
mri peak = 0.22222 (14)
gca peak = 0.19357 (14)
mri peak = 0.13762 (14)
Fourth_Ventricle (15): linear fit = 0.93 x + 0.0 (110 voxels, overlap=0.782)
Fourth_Ventricle (15): linear fit = 0.93 x + 0.0 (110 voxels, peak = 13), gca=12.9
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.16825 (27)
gca peak Left_Thalamus = 1.00000 (94)
gca peak Third_Ventricle = 0.14975 (24)
gca peak CSF = 0.23379 (36)
gca peak Left_Accumbens_area = 0.70037 (62)
gca peak Left_undetermined = 1.00000 (26)
gca peak Left_vessel = 0.75997 (52)
gca peak Left_choroid_plexus = 0.12089 (35)
gca peak Right_Inf_Lat_Vent = 0.24655 (23)
gca peak Right_Accumbens_area = 0.45042 (65)
gca peak Right_vessel = 0.82168 (52)
gca peak Right_choroid_plexus = 0.14516 (37)
gca peak Fifth_Ventricle = 0.65475 (32)
gca peak WM_hypointensities = 0.07854 (76)
gca peak non_WM_hypointensities = 0.08491 (43)
gca peak Optic_Chiasm = 0.71127 (75)
not using caudate to estimate GM means
estimating mean gm scale to be 1.11 x + 0.0
estimating mean wm scale to be 1.04 x + 0.0
estimating mean csf scale to be 0.64 x + 0.0
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.28812 (10)
mri peak = 0.10240 (12)
Left_Lateral_Ventricle (4): linear fit = 1.05 x + 0.0 (994 voxels, overlap=1.000)
Left_Lateral_Ventricle (4): linear fit = 1.05 x + 0.0 (994 voxels, peak = 11), gca=10.5
gca peak = 0.30003 ( 7)
mri peak = 0.10927 ( 8)
Right_Lateral_Ventricle (43): linear fit = 1.08 x + 0.0 (787 voxels, overlap=0.964)
Right_Lateral_Ventricle (43): linear fit = 1.08 x + 0.0 (787 voxels, peak = 8), gca=7.5
gca peak = 0.25980 (97)
mri peak = 0.08808 (95)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (737 voxels, overlap=1.019)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (737 voxels, peak = 97), gca=96.5
gca peak = 0.18386 (98)
mri peak = 0.08212 (98)
Left_Pallidum (13): linear fit = 0.99 x + 0.0 (718 voxels, overlap=1.011)
Left_Pallidum (13): linear fit = 0.99 x + 0.0 (718 voxels, peak = 97), gca=96.5
gca peak = 0.24758 (65)
mri peak = 0.08103 (67)
Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1046 voxels, overlap=1.003)
Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1046 voxels, peak = 65), gca=65.0
gca peak = 0.27962 (67)
mri peak = 0.08401 (68)
Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (986 voxels, overlap=1.009)
Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (986 voxels, peak = 67), gca=67.0
gca peak = 0.07501 (106)
mri peak = 0.08449 (105)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (48441 voxels, overlap=0.825)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (48441 voxels, peak = 105), gca=105.5
gca peak = 0.07788 (109)
mri peak = 0.08577 (106)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (48057 voxels, overlap=0.788)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (48057 voxels, peak = 108), gca=108.5
gca peak = 0.09502 (59)
mri peak = 0.03722 (62)
Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (23106 voxels, overlap=0.981)
Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (23106 voxels, peak = 60), gca=60.5
gca peak = 0.11326 (59)
mri peak = 0.03928 (63)
Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (21773 voxels, overlap=0.970)
Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (21773 voxels, peak = 60), gca=60.5
gca peak = 0.31027 (65)
mri peak = 0.09857 (67)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (941 voxels, overlap=1.007)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (941 voxels, peak = 65), gca=65.0
gca peak = 0.13850 (68)
mri peak = 0.10000 (73)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (809 voxels, overlap=1.000)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (809 voxels, peak = 68), gca=68.0
gca peak = 0.13268 (57)
mri peak = 0.05731 (60)
Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (18820 voxels, overlap=0.995)
Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (18820 voxels, peak = 58), gca=58.4
gca peak = 0.14076 (61)
mri peak = 0.06443 (62)
Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (20512 voxels, overlap=0.993)
Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (20512 voxels, peak = 61), gca=61.0
gca peak = 0.15819 (86)
mri peak = 0.09673 (85)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5531 voxels, overlap=0.937)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5531 voxels, peak = 86), gca=86.0
gca peak = 0.16825 (88)
mri peak = 0.10392 (88)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5553 voxels, overlap=0.921)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5553 voxels, peak = 88), gca=87.6
gca peak = 0.26359 (66)
mri peak = 0.11259 (67)
Left_Amygdala (18): linear fit = 1.00 x + 0.0 (481 voxels, overlap=1.016)
Left_Amygdala (18): linear fit = 1.00 x + 0.0 (481 voxels, peak = 66), gca=66.0
gca peak = 0.32369 (65)
mri peak = 0.09178 (65)
Right_Amygdala (54): linear fit = 1.02 x + 0.0 (523 voxels, overlap=0.999)
Right_Amygdala (54): linear fit = 1.02 x + 0.0 (523 voxels, peak = 67), gca=66.6
gca peak = 0.10627 (92)
mri peak = 0.06120 (87)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4636 voxels, overlap=0.971)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4636 voxels, peak = 92), gca=91.5
gca peak = 0.09389 (90)
mri peak = 0.06246 (89)
Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (4255 voxels, overlap=0.985)
Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (4255 voxels, peak = 89), gca=88.7
gca peak = 0.09216 (77)
mri peak = 0.07840 (80)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (1872 voxels, overlap=0.899)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (1872 voxels, peak = 77), gca=76.6
gca peak = 0.10144 (79)
mri peak = 0.07779 (79)
Right_Putamen (51): linear fit = 1.01 x + 0.0 (2295 voxels, overlap=0.974)
Right_Putamen (51): linear fit = 1.01 x + 0.0 (2295 voxels, peak = 80), gca=80.2
gca peak = 0.07278 (83)
mri peak = 0.08304 (83)
Brain_Stem (16): linear fit = 1.02 x + 0.0 (12188 voxels, overlap=0.725)
Brain_Stem (16): linear fit = 1.02 x + 0.0 (12188 voxels, peak = 85), gca=85.1
gca peak = 0.11830 (92)
mri peak = 0.09097 (95)
Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1534 voxels, overlap=0.825)
Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1534 voxels, peak = 92), gca=91.5
gca peak = 0.16587 (92)
mri peak = 0.08284 (95)
Left_VentralDC (28): linear fit = 1.01 x + 0.0 (1457 voxels, overlap=0.863)
Left_VentralDC (28): linear fit = 1.01 x + 0.0 (1457 voxels, peak = 93), gca=93.4
gca peak = 0.24282 (17)
mri peak = 0.22222 (14)
gca peak = 0.19357 (13)
mri peak = 0.13762 (14)
Fourth_Ventricle (15): linear fit = 1.03 x + 0.0 (110 voxels, overlap=0.803)
Fourth_Ventricle (15): linear fit = 1.03 x + 0.0 (110 voxels, peak = 13), gca=13.5
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.15778 (30)
gca peak Left_Thalamus = 0.64095 (104)
gca peak Third_Ventricle = 0.24282 (17)
gca peak CSF = 0.22373 (23)
gca peak Left_Accumbens_area = 0.49175 (60)
gca peak Left_undetermined = 1.00000 (26)
gca peak Left_vessel = 0.75962 (52)
gca peak Left_choroid_plexus = 0.12089 (35)
gca peak Right_Inf_Lat_Vent = 0.21739 (27)
gca peak Right_Accumbens_area = 0.45113 (64)
gca peak Right_vessel = 0.82168 (52)
gca peak Right_choroid_plexus = 0.14516 (37)
gca peak Fifth_Ventricle = 0.54101 (21)
gca peak WM_hypointensities = 0.07274 (74)
gca peak non_WM_hypointensities = 0.09744 (45)
gca peak Optic_Chiasm = 0.71047 (75)
not using caudate to estimate GM means
estimating mean gm scale to be 1.01 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 1.05 x + 0.0
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt
72124 voxels changed in iteration 0 of unlikely voxel relabeling
316 voxels changed in iteration 1 of unlikely voxel relabeling
13 voxels changed in iteration 2 of unlikely voxel relabeling
1 voxels changed in iteration 3 of unlikely voxel relabeling
0 voxels changed in iteration 4 of unlikely voxel relabeling
42470 gm and wm labels changed (%23 to gray, %77 to white out of all changed labels)
379 hippocampal voxels changed.
0 amygdala voxels changed.
pass 1: 72517 changed. image ll: -2.116, PF=0.500
pass 2: 19854 changed. image ll: -2.116, PF=0.500
pass 3: 5873 changed.
pass 4: 2009 changed.
44218 voxels changed in iteration 0 of unlikely voxel relabeling
234 voxels changed in iteration 1 of unlikely voxel relabeling
14 voxels changed in iteration 2 of unlikely voxel relabeling
3 voxels changed in iteration 3 of unlikely voxel relabeling
1 voxels changed in iteration 4 of unlikely voxel relabeling
7971 voxels changed in iteration 0 of unlikely voxel relabeling
87 voxels changed in iteration 1 of unlikely voxel relabeling
11 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
6796 voxels changed in iteration 0 of unlikely voxel relabeling
106 voxels changed in iteration 1 of unlikely voxel relabeling
3 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
4898 voxels changed in iteration 0 of unlikely voxel relabeling
16 voxels changed in iteration 1 of unlikely voxel relabeling
0 voxels changed in iteration 2 of unlikely voxel relabeling
MRItoUCHAR: min=0, max=85
MRItoUCHAR: converting to UCHAR
writing labeled volume to aseg.auto_noCCseg.mgz
mri_ca_label utimesec 2448.509228
mri_ca_label stimesec 4.489627
mri_ca_label ru_maxrss 2105276
mri_ca_label ru_ixrss 0
mri_ca_label ru_idrss 0
mri_ca_label ru_isrss 0
mri_ca_label ru_minflt 5508935
mri_ca_label ru_majflt 0
mri_ca_label ru_nswap 0
mri_ca_label ru_inblock 0
mri_ca_label ru_oublock 496
mri_ca_label ru_msgsnd 0
mri_ca_label ru_msgrcv 0
mri_ca_label ru_nsignals 0
mri_ca_label ru_nvcsw 607
mri_ca_label ru_nivcsw 246119
auto-labeling took 40 minutes and 54 seconds.
mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri/transforms/cc_up.lta 13265
will read input aseg from aseg.auto_noCCseg.mgz
writing aseg with cc labels to aseg.auto.mgz
will write lta as /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri/transforms/cc_up.lta
reading aseg from /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri/aseg.auto_noCCseg.mgz
reading norm from /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri/norm.mgz
26766 voxels in left wm, 59703 in right wm, xrange [122, 132]
searching rotation angles z=[-9 5], y=[-8 6]
searching scale 1 Z rot -8.9
searching scale 1 Z rot -8.6
searching scale 1 Z rot -8.4
searching scale 1 Z rot -8.1
searching scale 1 Z rot -7.9
searching scale 1 Z rot -7.6
searching scale 1 Z rot -7.4
searching scale 1 Z rot -7.1
searching scale 1 Z rot -6.9
searching scale 1 Z rot -6.6
searching scale 1 Z rot -6.4
searching scale 1 Z rot -6.1
searching scale 1 Z rot -5.9
searching scale 1 Z rot -5.6
searching scale 1 Z rot -5.4
searching scale 1 Z rot -5.1
searching scale 1 Z rot -4.9
searching scale 1 Z rot -4.6
searching scale 1 Z rot -4.4
searching scale 1 Z rot -4.1
searching scale 1 Z rot -3.9
searching scale 1 Z rot -3.6
searching scale 1 Z rot -3.4
searching scale 1 Z rot -3.1
searching scale 1 Z rot -2.9
searching scale 1 Z rot -2.6
searching scale 1 Z rot -2.4
searching scale 1 Z rot -2.1
searching scale 1 Z rot -1.9
searching scale 1 Z rot -1.6
searching scale 1 Z rot -1.4
searching scale 1 Z rot -1.1
searching scale 1 Z rot -0.9
searching scale 1 Z rot -0.6
searching scale 1 Z rot -0.4
searching scale 1 Z rot -0.1
searching scale 1 Z rot 0.1
searching scale 1 Z rot 0.4
searching scale 1 Z rot 0.6
searching scale 1 Z rot 0.9
searching scale 1 Z rot 1.1
searching scale 1 Z rot 1.4
searching scale 1 Z rot 1.6
searching scale 1 Z rot 1.9
searching scale 1 Z rot 2.1
searching scale 1 Z rot 2.4
searching scale 1 Z rot 2.6
searching scale 1 Z rot 2.9
searching scale 1 Z rot 3.1
searching scale 1 Z rot 3.4
searching scale 1 Z rot 3.6
searching scale 1 Z rot 3.9
searching scale 1 Z rot 4.1
searching scale 1 Z rot 4.4
searching scale 1 Z rot 4.6
searching scale 1 Z rot 4.9 global minimum found at slice 128.1, rotations (-1.40, -1.90)
final transformation (x=128.1, yr=-1.397, zr=-1.896):
0.99916 0.03309 -0.02436 -1.15506;
-0.03308 0.99945 0.00081 12.21022;
0.02438 0.00000 0.99970 7.91111;
0.00000 0.00000 0.00000 1.00000;
updating x range to be [126, 130] in xformed coordinates
best xformed slice 129
cc center is found at 129 120 117
eigenvectors:
-0.00088 -0.00200 1.00000;
-0.03141 -0.99950 -0.00203;
0.99951 -0.03141 0.00081;
error in mid anterior detected - correcting...
writing aseg with callosum to /mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri/aseg.auto.mgz...
corpus callosum segmentation took 0.6 minutes
#--------------------------------------
#@# Merge ASeg Fri Nov 13 16:35:01 EST 2020
cp aseg.auto.mgz aseg.presurf.mgz
#--------------------------------------------
#@# Intensity Normalization2 Fri Nov 13 16:35:01 EST 2020
/mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri
mri_normalize -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz
assuming input volume is MGH (Van der Kouwe) MP-RAGE
using segmentation for initial intensity normalization
using MR volume brainmask.mgz to mask input volume...
reading from norm.mgz...
Reading aseg aseg.presurf.mgz
normalizing image...
processing with aseg
removing outliers in the aseg WM...
1117 control points removed
Building bias image
building Voronoi diagram...
performing soap bubble smoothing, sigma = 0...
Smoothing with sigma 8
Applying bias correction
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 110
white matter peak found at 109
gm peak at 66 (66), valley at 26 (26)
csf peak at 34, 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 66 (66), valley at 39 (39)
csf peak at 20, setting threshold to 50
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 2 minutes and 11 seconds.
#--------------------------------------------
#@# Mask BFS Fri Nov 13 16:37:14 EST 2020
/mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri
mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
threshold mask volume at 5
DoAbs = 0
Found 1551223 voxels in mask (pct= 9.25)
Writing masked volume to brain.finalsurfs.mgz...done.
#--------------------------------------------
#@# WM Segmentation Fri Nov 13 16:37:15 EST 2020
mri_segment -mprage brain.mgz wm.seg.mgz
doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
computing class statistics for intensity windows...
WM (104.0): 104.8 +- 5.5 [79.0 --> 125.0]
GM (70.0) : 68.4 +- 10.3 [30.0 --> 95.0]
setting bottom of white matter range to 78.7
setting top of gray matter range to 89.0
doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
using local geometry to label remaining ambiguous voxels...
reclassifying voxels using Gaussian border classifier...
removing voxels with positive offset direction...
smoothing T1 volume with sigma = 0.250
removing 1-dimensional structures...
10620 sparsely connected voxels removed...
thickening thin strands....
20 segments, 5174 filled
491 bright non-wm voxels segmented.
5009 diagonally connected voxels added...
white matter segmentation took 1.2 minutes
writing output to wm.seg.mgz...
assuming input volume is MGH (Van der Kouwe) MP-RAGE
mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz
preserving editing changes in input volume...
auto filling took 0.33 minutes
reading wm segmentation from wm.seg.mgz...
167 voxels added to wm to prevent paths from MTL structures to cortex
3031 additional wm voxels added
0 additional wm voxels added
SEG EDIT: 41184 voxels turned on, 45871 voxels turned off.
propagating editing to output volume from wm.seg.mgz
115,126,128 old 97 new 97
115,126,128 old 97 new 97
writing edited volume to wm.asegedit.mgz....
mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz
Iteration Number : 1
pass 1 (xy+): 28 found - 28 modified | TOTAL: 28
pass 2 (xy+): 0 found - 28 modified | TOTAL: 28
pass 1 (xy-): 29 found - 29 modified | TOTAL: 57
pass 2 (xy-): 0 found - 29 modified | TOTAL: 57
pass 1 (yz+): 43 found - 43 modified | TOTAL: 100
pass 2 (yz+): 0 found - 43 modified | TOTAL: 100
pass 1 (yz-): 21 found - 21 modified | TOTAL: 121
pass 2 (yz-): 0 found - 21 modified | TOTAL: 121
pass 1 (xz+): 24 found - 24 modified | TOTAL: 145
pass 2 (xz+): 0 found - 24 modified | TOTAL: 145
pass 1 (xz-): 33 found - 33 modified | TOTAL: 178
pass 2 (xz-): 0 found - 33 modified | TOTAL: 178
Iteration Number : 1
pass 1 (+++): 20 found - 20 modified | TOTAL: 20
pass 2 (+++): 0 found - 20 modified | TOTAL: 20
pass 1 (+++): 19 found - 19 modified | TOTAL: 39
pass 2 (+++): 0 found - 19 modified | TOTAL: 39
pass 1 (+++): 26 found - 26 modified | TOTAL: 65
pass 2 (+++): 0 found - 26 modified | TOTAL: 65
pass 1 (+++): 44 found - 44 modified | TOTAL: 109
pass 2 (+++): 0 found - 44 modified | TOTAL: 109
Iteration Number : 1
pass 1 (++): 116 found - 116 modified | TOTAL: 116
pass 2 (++): 0 found - 116 modified | TOTAL: 116
pass 1 (+-): 124 found - 124 modified | TOTAL: 240
pass 2 (+-): 0 found - 124 modified | TOTAL: 240
pass 1 (--): 109 found - 109 modified | TOTAL: 349
pass 2 (--): 0 found - 109 modified | TOTAL: 349
pass 1 (-+): 98 found - 98 modified | TOTAL: 447
pass 2 (-+): 0 found - 98 modified | TOTAL: 447
Iteration Number : 2
pass 1 (xy+): 3 found - 3 modified | TOTAL: 3
pass 2 (xy+): 0 found - 3 modified | TOTAL: 3
pass 1 (xy-): 7 found - 7 modified | TOTAL: 10
pass 2 (xy-): 0 found - 7 modified | TOTAL: 10
pass 1 (yz+): 10 found - 10 modified | TOTAL: 20
pass 2 (yz+): 0 found - 10 modified | TOTAL: 20
pass 1 (yz-): 9 found - 9 modified | TOTAL: 29
pass 2 (yz-): 0 found - 9 modified | TOTAL: 29
pass 1 (xz+): 13 found - 13 modified | TOTAL: 42
pass 2 (xz+): 0 found - 13 modified | TOTAL: 42
pass 1 (xz-): 3 found - 3 modified | TOTAL: 45
pass 2 (xz-): 0 found - 3 modified | TOTAL: 45
Iteration Number : 2
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 6 found - 6 modified | TOTAL: 6
pass 2 (+++): 0 found - 6 modified | TOTAL: 6
pass 1 (+++): 0 found - 0 modified | TOTAL: 6
Iteration Number : 2
pass 1 (++): 2 found - 2 modified | TOTAL: 2
pass 2 (++): 0 found - 2 modified | TOTAL: 2
pass 1 (+-): 3 found - 3 modified | TOTAL: 5
pass 2 (+-): 0 found - 3 modified | TOTAL: 5
pass 1 (--): 4 found - 4 modified | TOTAL: 9
pass 2 (--): 0 found - 4 modified | TOTAL: 9
pass 1 (-+): 5 found - 5 modified | TOTAL: 14
pass 2 (-+): 0 found - 5 modified | TOTAL: 14
Iteration Number : 3
pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
pass 1 (yz+): 1 found - 1 modified | TOTAL: 1
pass 2 (yz+): 0 found - 1 modified | TOTAL: 1
pass 1 (yz-): 0 found - 0 modified | TOTAL: 1
pass 1 (xz+): 0 found - 0 modified | TOTAL: 1
pass 1 (xz-): 1 found - 1 modified | TOTAL: 2
pass 2 (xz-): 0 found - 1 modified | TOTAL: 2
Iteration Number : 3
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
Iteration Number : 3
pass 1 (++): 1 found - 1 modified | TOTAL: 1
pass 2 (++): 0 found - 1 modified | TOTAL: 1
pass 1 (+-): 1 found - 1 modified | TOTAL: 2
pass 2 (+-): 0 found - 1 modified | TOTAL: 2
pass 1 (--): 0 found - 0 modified | TOTAL: 2
pass 1 (-+): 0 found - 0 modified | TOTAL: 2
Iteration Number : 4
pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
Iteration Number : 4
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 2 found - 2 modified | TOTAL: 2
pass 2 (+++): 0 found - 2 modified | TOTAL: 2
pass 1 (+++): 0 found - 0 modified | TOTAL: 2
pass 1 (+++): 0 found - 0 modified | TOTAL: 2
Iteration Number : 4
pass 1 (++): 0 found - 0 modified | TOTAL: 0
pass 1 (+-): 0 found - 0 modified | TOTAL: 0
pass 1 (--): 1 found - 1 modified | TOTAL: 1
pass 2 (--): 0 found - 1 modified | TOTAL: 1
pass 1 (-+): 0 found - 0 modified | TOTAL: 1
Iteration Number : 5
pass 1 (xy+): 1 found - 1 modified | TOTAL: 1
pass 2 (xy+): 0 found - 1 modified | TOTAL: 1
pass 1 (xy-): 0 found - 0 modified | TOTAL: 1
pass 1 (yz+): 0 found - 0 modified | TOTAL: 1
pass 1 (yz-): 0 found - 0 modified | TOTAL: 1
pass 1 (xz+): 0 found - 0 modified | TOTAL: 1
pass 1 (xz-): 0 found - 0 modified | TOTAL: 1
Iteration Number : 5
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
Iteration Number : 5
pass 1 (++): 0 found - 0 modified | TOTAL: 0
pass 1 (+-): 0 found - 0 modified | TOTAL: 0
pass 1 (--): 0 found - 0 modified | TOTAL: 0
pass 1 (-+): 0 found - 0 modified | TOTAL: 0
Iteration Number : 6
pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
Iteration Number : 6
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
Iteration Number : 6
pass 1 (++): 0 found - 0 modified | TOTAL: 0
pass 1 (+-): 0 found - 0 modified | TOTAL: 0
pass 1 (--): 0 found - 0 modified | TOTAL: 0
pass 1 (-+): 0 found - 0 modified | TOTAL: 0
Total Number of Modified Voxels = 807 (out of 628620: 0.128376)
binarizing input wm segmentation...
Ambiguous edge configurations...
mri_pretess done
#--------------------------------------------
#@# Fill Fri Nov 13 16:38:53 EST 2020
/mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/mri
mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz
logging cutting plane coordinates to ../scripts/ponscc.cut.log...
INFO: Using transforms/talairach.lta and its offset for Talairach volume ...
using segmentation aseg.auto_noCCseg.mgz...
reading input volume...done.
searching for cutting planes...voxel to talairach voxel transform
1.01897 0.00293 -0.01249 -3.88443;
-0.00353 1.18189 0.13522 -51.24037;
0.00303 -0.14908 0.98486 7.08509;
0.00000 0.00000 0.00000 1.00000;
voxel to talairach voxel transform
1.01897 0.00293 -0.01249 -3.88443;
-0.00353 1.18189 0.13522 -51.24037;
0.00303 -0.14908 0.98486 7.08509;
0.00000 0.00000 0.00000 1.00000;
reading segmented volume aseg.auto_noCCseg.mgz...
Looking for area (min, max) = (350, 1400)
area[0] = 1343 (min = 350, max = 1400), aspect = 0.44 (min = 0.10, max = 0.75)
no need to search
using seed (126, 125, 155), TAL = (2.0, 27.0, 3.0)
talairach voxel to voxel transform
0.98134 -0.00085 0.01256 3.67955;
0.00322 0.83169 -0.11415 43.43768;
-0.00253 0.12590 0.99806 -0.63025;
0.00000 0.00000 0.00000 1.00000;
segmentation indicates cc at (126, 125, 155) --> (2.0, 27.0, 3.0)
done.
writing output to filled.mgz...
filling took 0.4 minutes
talairach cc position changed to (2.00, 27.00, 3.00)
Erasing brainstem...done.
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(20.00, 27.00, 3.00) SRC: (111.51, 130.05, 169.53)
search lh wm seed point around talairach space (-16.00, 27.00, 3.00), SRC: (146.83, 130.17, 169.44)
compute mri_fill using aseg
Erasing Brain Stem and Cerebellum ...
Define left and right masks using aseg:
Building Voronoi diagram ...
Using the Voronoi diagram to separate WM into two hemispheres ...
Find the largest connected component for each hemisphere ...
#--------------------------------------------
#@# Tessellate lh Fri Nov 13 16:39:18 EST 2020
/mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/scripts
mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz
Iteration Number : 1
pass 1 (xy+): 1 found - 1 modified | TOTAL: 1
pass 2 (xy+): 0 found - 1 modified | TOTAL: 1
pass 1 (xy-): 1 found - 1 modified | TOTAL: 2
pass 2 (xy-): 0 found - 1 modified | TOTAL: 2
pass 1 (yz+): 2 found - 2 modified | TOTAL: 4
pass 2 (yz+): 0 found - 2 modified | TOTAL: 4
pass 1 (yz-): 1 found - 1 modified | TOTAL: 5
pass 2 (yz-): 0 found - 1 modified | TOTAL: 5
pass 1 (xz+): 2 found - 2 modified | TOTAL: 7
pass 2 (xz+): 0 found - 2 modified | TOTAL: 7
pass 1 (xz-): 1 found - 1 modified | TOTAL: 8
pass 2 (xz-): 0 found - 1 modified | TOTAL: 8
Iteration Number : 1
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
Iteration Number : 1
pass 1 (++): 0 found - 0 modified | TOTAL: 0
pass 1 (+-): 1 found - 1 modified | TOTAL: 1
pass 2 (+-): 0 found - 1 modified | TOTAL: 1
pass 1 (--): 0 found - 0 modified | TOTAL: 1
pass 1 (-+): 1 found - 1 modified | TOTAL: 2
pass 2 (-+): 0 found - 1 modified | TOTAL: 2
Iteration Number : 2
pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
pass 1 (xy-): 1 found - 1 modified | TOTAL: 1
pass 2 (xy-): 0 found - 1 modified | TOTAL: 1
pass 1 (yz+): 1 found - 1 modified | TOTAL: 2
pass 2 (yz+): 0 found - 1 modified | TOTAL: 2
pass 1 (yz-): 0 found - 0 modified | TOTAL: 2
pass 1 (xz+): 0 found - 0 modified | TOTAL: 2
pass 1 (xz-): 0 found - 0 modified | TOTAL: 2
Iteration Number : 2
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
Iteration Number : 2
pass 1 (++): 0 found - 0 modified | TOTAL: 0
pass 1 (+-): 0 found - 0 modified | TOTAL: 0
pass 1 (--): 0 found - 0 modified | TOTAL: 0
pass 1 (-+): 0 found - 0 modified | TOTAL: 0
Iteration Number : 3
pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
Iteration Number : 3
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
Iteration Number : 3
pass 1 (++): 0 found - 0 modified | TOTAL: 0
pass 1 (+-): 0 found - 0 modified | TOTAL: 0
pass 1 (--): 0 found - 0 modified | TOTAL: 0
pass 1 (-+): 0 found - 0 modified | TOTAL: 0
Total Number of Modified Voxels = 12 (out of 302658: 0.003965)
Ambiguous edge configurations...
mri_pretess done
mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix
$Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $
$Id: mrisurf.c,v 1.781.2.2 2016/10/27 22:25:31 zkaufman Exp $
slice 40: 320 vertices, 369 faces
slice 50: 4914 vertices, 5129 faces
slice 60: 13017 vertices, 13345 faces
slice 70: 23220 vertices, 23626 faces
slice 80: 34676 vertices, 35078 faces
slice 90: 45749 vertices, 46119 faces
slice 100: 57447 vertices, 57871 faces
slice 110: 69450 vertices, 69873 faces
slice 120: 81023 vertices, 81456 faces
slice 130: 92290 vertices, 92754 faces
slice 140: 103633 vertices, 104086 faces
slice 150: 114137 vertices, 114579 faces
slice 160: 122584 vertices, 122966 faces
slice 170: 130075 vertices, 130451 faces
slice 180: 136925 vertices, 137259 faces
slice 190: 143097 vertices, 143423 faces
slice 200: 147598 vertices, 147833 faces
slice 210: 149688 vertices, 149798 faces
slice 220: 149688 vertices, 149798 faces
slice 230: 149688 vertices, 149798 faces
slice 240: 149688 vertices, 149798 faces
slice 250: 149688 vertices, 149798 faces
using the conformed surface RAS to save vertex points...
writing ../surf/lh.orig.nofix
using vox2ras matrix:
-1.00000 0.00000 0.00000 128.00000;
0.00000 0.00000 1.00000 -128.00000;
0.00000 -1.00000 0.00000 128.00000;
0.00000 0.00000 0.00000 1.00000;
rm -f ../mri/filled-pretess255.mgz
mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix
counting number of connected components...
149688 voxel in cpt #1: X=-110 [v=149688,e=449394,f=299596] located at (-27.733900, -12.186969, 0.766020)
For the whole surface: X=-110 [v=149688,e=449394,f=299596]
One single component has been found
nothing to do
done
#--------------------------------------------
#@# Tessellate rh Fri Nov 13 16:39:23 EST 2020
/mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/scripts
mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz
Iteration Number : 1
pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
pass 1 (xy-): 1 found - 1 modified | TOTAL: 1
pass 2 (xy-): 0 found - 1 modified | TOTAL: 1
pass 1 (yz+): 4 found - 4 modified | TOTAL: 5
pass 2 (yz+): 0 found - 4 modified | TOTAL: 5
pass 1 (yz-): 2 found - 2 modified | TOTAL: 7
pass 2 (yz-): 0 found - 2 modified | TOTAL: 7
pass 1 (xz+): 0 found - 0 modified | TOTAL: 7
pass 1 (xz-): 0 found - 0 modified | TOTAL: 7
Iteration Number : 1
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
Iteration Number : 1
pass 1 (++): 0 found - 0 modified | TOTAL: 0
pass 1 (+-): 0 found - 0 modified | TOTAL: 0
pass 1 (--): 0 found - 0 modified | TOTAL: 0
pass 1 (-+): 1 found - 1 modified | TOTAL: 1
pass 2 (-+): 0 found - 1 modified | TOTAL: 1
Iteration Number : 2
pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
Iteration Number : 2
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
Iteration Number : 2
pass 1 (++): 0 found - 0 modified | TOTAL: 0
pass 1 (+-): 0 found - 0 modified | TOTAL: 0
pass 1 (--): 0 found - 0 modified | TOTAL: 0
pass 1 (-+): 0 found - 0 modified | TOTAL: 0
Total Number of Modified Voxels = 8 (out of 303935: 0.002632)
Ambiguous edge configurations...
mri_pretess done
mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix
$Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $
$Id: mrisurf.c,v 1.781.2.2 2016/10/27 22:25:31 zkaufman Exp $
slice 40: 98 vertices, 109 faces
slice 50: 2558 vertices, 2713 faces
slice 60: 9376 vertices, 9643 faces
slice 70: 19153 vertices, 19531 faces
slice 80: 29906 vertices, 30323 faces
slice 90: 41551 vertices, 41925 faces
slice 100: 52600 vertices, 52979 faces
slice 110: 64965 vertices, 65413 faces
slice 120: 76832 vertices, 77258 faces
slice 130: 88443 vertices, 88898 faces
slice 140: 100084 vertices, 100523 faces
slice 150: 111567 vertices, 111998 faces
slice 160: 120962 vertices, 121342 faces
slice 170: 129096 vertices, 129454 faces
slice 180: 136242 vertices, 136574 faces
slice 190: 142637 vertices, 142957 faces
slice 200: 147987 vertices, 148241 faces
slice 210: 151122 vertices, 151237 faces
slice 220: 151174 vertices, 151276 faces
slice 230: 151174 vertices, 151276 faces
slice 240: 151174 vertices, 151276 faces
slice 250: 151174 vertices, 151276 faces
using the conformed surface RAS to save vertex points...
writing ../surf/rh.orig.nofix
using vox2ras matrix:
-1.00000 0.00000 0.00000 128.00000;
0.00000 0.00000 1.00000 -128.00000;
0.00000 -1.00000 0.00000 128.00000;
0.00000 0.00000 0.00000 1.00000;
rm -f ../mri/filled-pretess127.mgz
mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix
counting number of connected components...
151174 voxel in cpt #1: X=-102 [v=151174,e=453828,f=302552] located at (27.245796, -8.269947, 2.955535)
For the whole surface: X=-102 [v=151174,e=453828,f=302552]
One single component has been found
nothing to do
done
#--------------------------------------------
#@# Smooth1 lh Fri Nov 13 16:39:28 EST 2020
/mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/scripts
mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix
setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
#--------------------------------------------
#@# Smooth1 rh Fri Nov 13 16:39:32 EST 2020
/mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/scripts
mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix
setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
#--------------------------------------------
#@# Inflation1 lh Fri Nov 13 16:39:37 EST 2020
/mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/scripts
mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix
Not saving sulc
Reading ../surf/lh.smoothwm.nofix
avg radius = 48.9 mm, total surface area = 78067 mm^2
writing inflated surface to ../surf/lh.inflated.nofix
inflation took 0.5 minutes
step 000: RMS=0.159 (target=0.015)
step 005: RMS=0.120 (target=0.015)
step 010: RMS=0.094 (target=0.015)
step 015: RMS=0.082 (target=0.015)
step 020: RMS=0.073 (target=0.015)
step 025: RMS=0.066 (target=0.015)
step 030: RMS=0.062 (target=0.015)
step 035: RMS=0.058 (target=0.015)
step 040: RMS=0.055 (target=0.015)
step 045: RMS=0.052 (target=0.015)
step 050: RMS=0.052 (target=0.015)
step 055: RMS=0.051 (target=0.015)
step 060: RMS=0.052 (target=0.015)
inflation complete.
Not saving sulc
mris_inflate utimesec 28.529071
mris_inflate stimesec 0.141826
mris_inflate ru_maxrss 191696
mris_inflate ru_ixrss 0
mris_inflate ru_idrss 0
mris_inflate ru_isrss 0
mris_inflate ru_minflt 141654
mris_inflate ru_majflt 0
mris_inflate ru_nswap 0
mris_inflate ru_inblock 0
mris_inflate ru_oublock 10536
mris_inflate ru_msgsnd 0
mris_inflate ru_msgrcv 0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw 987
mris_inflate ru_nivcsw 2901
#--------------------------------------------
#@# Inflation1 rh Fri Nov 13 16:40:06 EST 2020
/mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/scripts
mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix
Not saving sulc
Reading ../surf/rh.smoothwm.nofix
avg radius = 48.5 mm, total surface area = 78065 mm^2
writing inflated surface to ../surf/rh.inflated.nofix
inflation took 0.5 minutes
step 000: RMS=0.163 (target=0.015)
step 005: RMS=0.122 (target=0.015)
step 010: RMS=0.095 (target=0.015)
step 015: RMS=0.083 (target=0.015)
step 020: RMS=0.074 (target=0.015)
step 025: RMS=0.067 (target=0.015)
step 030: RMS=0.063 (target=0.015)
step 035: RMS=0.058 (target=0.015)
step 040: RMS=0.054 (target=0.015)
step 045: RMS=0.053 (target=0.015)
step 050: RMS=0.051 (target=0.015)
step 055: RMS=0.051 (target=0.015)
step 060: RMS=0.050 (target=0.015)
inflation complete.
Not saving sulc
mris_inflate utimesec 28.751984
mris_inflate stimesec 0.159916
mris_inflate ru_maxrss 193744
mris_inflate ru_ixrss 0
mris_inflate ru_idrss 0
mris_inflate ru_isrss 0
mris_inflate ru_minflt 144745
mris_inflate ru_majflt 0
mris_inflate ru_nswap 0
mris_inflate ru_inblock 0
mris_inflate ru_oublock 10640
mris_inflate ru_msgsnd 0
mris_inflate ru_msgrcv 0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw 1009
mris_inflate ru_nivcsw 2921
#--------------------------------------------
#@# QSphere lh Fri Nov 13 16:40:35 EST 2020
/mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/scripts
mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix
doing quick spherical unfolding.
setting seed for random number genererator to 1234
$Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $
$Id: mrisurf.c,v 1.781.2.2 2016/10/27 22:25:31 zkaufman Exp $
reading original vertex positions...
unfolding cortex into spherical form...
surface projected - minimizing metric distortion...
vertex spacing 0.94 +- 0.57 (0.00-->6.88) (max @ vno 58291 --> 58292)
face area 0.02 +- 0.03 (-0.12-->0.45)
== Number of threads available to mris_sphere for OpenMP = 1 ==
scaling brain by 0.293...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=177.200, avgs=0
005/300: dt: 0.9000, rms radial error=176.937, avgs=0
010/300: dt: 0.9000, rms radial error=176.374, avgs=0
015/300: dt: 0.9000, rms radial error=175.638, avgs=0
020/300: dt: 0.9000, rms radial error=174.801, avgs=0
025/300: dt: 0.9000, rms radial error=173.906, avgs=0
030/300: dt: 0.9000, rms radial error=172.979, avgs=0
035/300: dt: 0.9000, rms radial error=172.036, avgs=0
040/300: dt: 0.9000, rms radial error=171.085, avgs=0
045/300: dt: 0.9000, rms radial error=170.132, avgs=0
050/300: dt: 0.9000, rms radial error=169.178, avgs=0
055/300: dt: 0.9000, rms radial error=168.228, avgs=0
060/300: dt: 0.9000, rms radial error=167.281, avgs=0
065/300: dt: 0.9000, rms radial error=166.339, avgs=0
070/300: dt: 0.9000, rms radial error=165.401, avgs=0
075/300: dt: 0.9000, rms radial error=164.471, avgs=0
080/300: dt: 0.9000, rms radial error=163.547, avgs=0
085/300: dt: 0.9000, rms radial error=162.628, avgs=0
090/300: dt: 0.9000, rms radial error=161.714, avgs=0
095/300: dt: 0.9000, rms radial error=160.805, avgs=0
100/300: dt: 0.9000, rms radial error=159.901, avgs=0
105/300: dt: 0.9000, rms radial error=159.002, avgs=0
110/300: dt: 0.9000, rms radial error=158.108, avgs=0
115/300: dt: 0.9000, rms radial error=157.218, avgs=0
120/300: dt: 0.9000, rms radial error=156.334, avgs=0
125/300: dt: 0.9000, rms radial error=155.454, avgs=0
130/300: dt: 0.9000, rms radial error=154.579, avgs=0
135/300: dt: 0.9000, rms radial error=153.709, avgs=0
140/300: dt: 0.9000, rms radial error=152.844, avgs=0
145/300: dt: 0.9000, rms radial error=151.983, avgs=0
150/300: dt: 0.9000, rms radial error=151.128, avgs=0
155/300: dt: 0.9000, rms radial error=150.276, avgs=0
160/300: dt: 0.9000, rms radial error=149.430, avgs=0
165/300: dt: 0.9000, rms radial error=148.588, avgs=0
170/300: dt: 0.9000, rms radial error=147.751, avgs=0
175/300: dt: 0.9000, rms radial error=146.918, avgs=0
180/300: dt: 0.9000, rms radial error=146.090, avgs=0
185/300: dt: 0.9000, rms radial error=145.267, avgs=0
190/300: dt: 0.9000, rms radial error=144.449, avgs=0
195/300: dt: 0.9000, rms radial error=143.634, avgs=0
200/300: dt: 0.9000, rms radial error=142.825, avgs=0
205/300: dt: 0.9000, rms radial error=142.020, avgs=0
210/300: dt: 0.9000, rms radial error=141.219, avgs=0
215/300: dt: 0.9000, rms radial error=140.424, avgs=0
220/300: dt: 0.9000, rms radial error=139.632, avgs=0
225/300: dt: 0.9000, rms radial error=138.845, avgs=0
230/300: dt: 0.9000, rms radial error=138.062, avgs=0
235/300: dt: 0.9000, rms radial error=137.284, avgs=0
240/300: dt: 0.9000, rms radial error=136.510, avgs=0
245/300: dt: 0.9000, rms radial error=135.740, avgs=0
250/300: dt: 0.9000, rms radial error=134.974, avgs=0
255/300: dt: 0.9000, rms radial error=134.213, avgs=0
260/300: dt: 0.9000, rms radial error=133.456, avgs=0
265/300: dt: 0.9000, rms radial error=132.703, avgs=0
270/300: dt: 0.9000, rms radial error=131.954, avgs=0
275/300: dt: 0.9000, rms radial error=131.210, avgs=0
280/300: dt: 0.9000, rms radial error=130.469, avgs=0
285/300: dt: 0.9000, rms radial error=129.733, avgs=0
290/300: dt: 0.9000, rms radial error=129.001, avgs=0
295/300: dt: 0.9000, rms radial error=128.273, avgs=0
300/300: dt: 0.9000, rms radial error=127.549, avgs=0
spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 17888.35
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00015
epoch 2 (K=40.0), pass 1, starting sse = 3138.19
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00004
epoch 3 (K=160.0), pass 1, starting sse = 363.23
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.07/11 = 0.00674
epoch 4 (K=640.0), pass 1, starting sse = 30.27
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.12/16 = 0.00750
final distance error %28.05
writing spherical brain to ../surf/lh.qsphere.nofix
spherical transformation took 0.06 hours
mris_sphere utimesec 199.181623
mris_sphere stimesec 0.184917
mris_sphere ru_maxrss 191924
mris_sphere ru_ixrss 0
mris_sphere ru_idrss 0
mris_sphere ru_isrss 0
mris_sphere ru_minflt 235380
mris_sphere ru_majflt 0
mris_sphere ru_nswap 0
mris_sphere ru_inblock 0
mris_sphere ru_oublock 10536
mris_sphere ru_msgsnd 0
mris_sphere ru_msgrcv 0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw 1049
mris_sphere ru_nivcsw 19979
FSRUNTIME@ mris_sphere 0.0555 hours 1 threads
#--------------------------------------------
#@# QSphere rh Fri Nov 13 16:43:55 EST 2020
/mnt/munin/Morey/Lab/T1Duke/Freesurfer/13265/scripts
mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix
doing quick spherical unfolding.
setting seed for random number genererator to 1234
$Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $
$Id: mrisurf.c,v 1.781.2.2 2016/10/27 22:25:31 zkaufman Exp $
reading original vertex positions...
unfolding cortex into spherical form...
surface projected - minimizing metric distortion...
vertex spacing 0.94 +- 0.57 (0.00-->5.96) (max @ vno 109219 --> 110267)
face area 0.02 +- 0.03 (-0.09-->0.49)
== Number of threads available to mris_sphere for OpenMP = 1 ==
scaling brain by 0.290...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=177.525, avgs=0
005/300: dt: 0.9000, rms radial error=177.263, avgs=0
010/300: dt: 0.9000, rms radial error=176.701, avgs=0
015/300: dt: 0.9000, rms radial error=175.962, avgs=0
020/300: dt: 0.9000, rms radial error=175.120, avgs=0
025/300: dt: 0.9000, rms radial error=174.223, avgs=0
030/300: dt: 0.9000, rms radial error=173.296, avgs=0
035/300: dt: 0.9000, rms radial error=172.352, avgs=0
040/300: dt: 0.9000, rms radial error=171.400, avgs=0
045/300: dt: 0.9000, rms radial error=170.445, avgs=0
050/300: dt: 0.9000, rms radial error=169.491, avgs=0
055/300: dt: 0.9000, rms radial error=168.539, avgs=0
060/300: dt: 0.9000, rms radial error=167.591, avgs=0
065/300: dt: 0.9000, rms radial error=166.648, avgs=0
070/300: dt: 0.9000, rms radial error=165.709, avgs=0
075/300: dt: 0.9000, rms radial error=164.774, avgs=0
080/300: dt: 0.9000, rms radial error=163.845, avgs=0
085/300: dt: 0.9000, rms radial error=162.922, avgs=0
090/300: dt: 0.9000, rms radial error=162.005, avgs=0
095/300: dt: 0.9000, rms radial error=161.093, avgs=0
100/300: dt: 0.9000, rms radial error=160.185, avgs=0
105/300: dt: 0.9000, rms radial error=159.283, avgs=0
110/300: dt: 0.9000, rms radial error=158.385, avgs=0
115/300: dt: 0.9000, rms radial error=157.492, avgs=0
120/300: dt: 0.9000, rms radial error=156.604, avgs=0
125/300: dt: 0.9000, rms radial error=155.721, avgs=0
130/300: dt: 0.9000, rms radial error=154.843, avgs=0
135/300: dt: 0.9000, rms radial error=153.969, avgs=0
140/300: dt: 0.9000, rms radial error=153.100, avgs=0
145/300: dt: 0.9000, rms radial error=152.236, avgs=0
150/300: dt: 0.9000, rms radial error=151.378, avgs=0
155/300: dt: 0.9000, rms radial error=150.525, avgs=0
160/300: dt: 0.9000, rms radial error=149.676, avgs=0
165/300: dt: 0.9000, rms radial error=148.832, avgs=0
170/300: dt: 0.9000, rms radial error=147.993, avgs=0
175/300: dt: 0.9000, rms radial error=147.159, avgs=0
180/300: dt: 0.9000, rms radial error=146.331, avgs=0
185/300: dt: 0.9000, rms radial error=145.508, avgs=0
190/300: dt: 0.9000, rms radial error=144.689, avgs=0
195/300: dt: 0.9000, rms radial error=143.875, avgs=0
200/300: dt: 0.9000, rms radial error=143.066, avgs=0
205/300: dt: 0.9000, rms radial error=142.261, avgs=0
210/300: dt: 0.9000, rms radial error=141.460, avgs=0
215/300: dt: 0.9000, rms radial error=140.664, avgs=0
220/300: dt: 0.9000, rms radial error=139.872, avgs=0
225/300: dt: 0.9000, rms radial error=139.085, avgs=0
230/300: dt: 0.9000, rms radial error=138.302, avgs=0
235/300: dt: 0.9000, rms radial error=137.523, avgs=0
240/300: dt: 0.9000, rms radial error=136.749, avgs=0
245/300: dt: 0.9000, rms radial error=135.979, avgs=0
250/300: dt: 0.9000, rms radial error=135.213, avgs=0
255/300: dt: 0.9000, rms radial error=134.452, avgs=0
260/300: dt: 0.9000, rms radial error=133.694, avgs=0
265/300: dt: 0.9000, rms radial error=132.941, avgs=0
270/300: dt: 0.9000, rms radial error=132.193, avgs=0
275/300: dt: 0.9000, rms radial error=131.448, avgs=0
280/300: dt: 0.9000, rms radial error=130.707, avgs=0
285/300: dt: 0.9000, rms radial error=129.971, avgs=0
290/300: dt: 0.9000, rms radial error=129.238, avgs=0
295/300: dt: 0.9000, rms radial error=128.510, avgs=0
300/300: dt: 0.9000, rms radial error=127.786, avgs=0
spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 18132.74
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00012
epoch 2 (K=40.0), pass 1, starting sse = 3189.58
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00003
epoch 3 (K=160.0), pass 1, starting sse = 364.83
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.07/11 = 0.00599
epoch 4 (K=640.0), pass 1, starting sse = 28.10
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.09/13 = 0.00674
final distance error %26.95
writing spherical brain to ../surf/rh.qsphere.nofix
spherical transformation took 0.06 hours
mris_sphere utimesec 202.889765
mris_sphere stimesec 0.210848
mris_sphere ru_maxrss 193960
mris_sphere ru_ixrss 0
mris_sphere ru_idrss 0
mris_sphere ru_isrss 0
mris_sphere ru_minflt 240515
mris_sphere ru_majflt 0
mris_sphere ru_nswap 0
mris_sphere ru_inblock 0
mris_sphere ru_oublock 10640
mris_sphere ru_msgsnd 0
mris_sphere ru_msgrcv 0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw 1032
mris_sphere ru_nivcsw 20399
FSRUNTIME@ mris_sphere 0.0565 hours 1 threads
Linux blade21.dhe.duke.edu 3.10.0-1160.2.2.el7.x86_64 #1 SMP Mon Oct 19 10:20:12 CDT 2020 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 13265 exited with ERRORS at Fri Nov 13 16:47:19 EST 2020
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Fischl, Bruce BFISCHL@mgh.harvard.edu Sent: Thursday, December 3, 2020 11:56 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all issues debugging
Hi Courtney
Can you send us the recon-all.log file and the full screen output from one job that failed?
Cheers
Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Courtney Haswell Sent: Thursday, December 3, 2020 9:52 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] recon-all issues debugging
External Email - Use Caution
I am trying to debug why all of our T1's are failing Freesurfer recon-all. It seems that most of the files are being created but it isn't getting to the stats steps to output those files. In the recon-all log it does say "recon-all -s 13265 exited with ERRORS."
I looked in the recon-all.error file and the only thing in that is "CMD mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix." Would this be the step where the error is happening?
I have checked the T1 thoroughly and it is good quality. What is the best way to debug why this is happening with our scans?
freesurfer@nmr.mgh.harvard.edu
-
Courtney Haswell -
Fischl, Bruce