Thu Sep 2 05:18:49 UTC 2021 /out/freesurfer/sub-M1215054 /opt/freesurfer/bin/recon-all -autorecon1 -i /data/sub-M1215054/anat/sub-M1215054_T1w.nii.gz -noskullstrip -openmp 3 -subjid sub-M1215054 -sd /out/freesurfer subjid sub-M1215054 setenv SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /opt/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a Linux 9e1e1df09144 5.4.72-microsoft-standard-WSL2 #1 SMP Wed Oct 28 23:40:43 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1048576 memorylocked 82000 kbytes maxproc unlimited maxlocks unlimited maxsignal 23036 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 5902064 1387216 2259112 194532 2255736 4004312 Swap: 2097152 307968 1789184 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-05:18:49-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-05:18:49-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-05:18:49-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-05:18:49-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-05:18:49-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-05:18:49-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-05:18:49-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-05:18:49-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-05:18:49-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-05:18:49-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-05:18:49-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-05:18:49-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-05:18:49-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-05:18:49-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-05:18:49-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-05:18:49-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-05:18:49-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-05:18:49-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-05:18:49-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-05:18:49-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-05:18:49-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-05:18:49-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-05:18:49-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-05:18:49-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-05:18:49-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-05:18:49-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-05:18:49-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-05:18:49-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-05:18:49-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-05:18:50-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-05:18:50-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-05:18:50-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-05:18:50-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-05:18:50-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-05:18:50-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-05:18:50-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-05:18:50-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-05:18:50-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-05:18:50-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /opt/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /opt/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /out/freesurfer/sub-M1215054 mri_convert /data/sub-M1215054/anat/sub-M1215054_T1w.nii.gz /out/freesurfer/sub-M1215054/mri/orig/001.mgz mri_convert.bin /data/sub-M1215054/anat/sub-M1215054_T1w.nii.gz /out/freesurfer/sub-M1215054/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /data/sub-M1215054/anat/sub-M1215054_T1w.nii.gz... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.999609, 0.00366895, -0.0277018) j_ras = (4.64859e-08, 0.991343, 0.131299) k_ras = (0.0279437, -0.131248, 0.990956) writing to /out/freesurfer/sub-M1215054/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Thu Sep 2 05:18:54 UTC 2021 Found 1 runs /out/freesurfer/sub-M1215054/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /out/freesurfer/sub-M1215054/mri/orig/001.mgz /out/freesurfer/sub-M1215054/mri/rawavg.mgz /out/freesurfer/sub-M1215054 mri_convert /out/freesurfer/sub-M1215054/mri/rawavg.mgz /out/freesurfer/sub-M1215054/mri/orig.mgz --conform mri_convert.bin /out/freesurfer/sub-M1215054/mri/rawavg.mgz /out/freesurfer/sub-M1215054/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /out/freesurfer/sub-M1215054/mri/rawavg.mgz... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.999609, 0.00366895, -0.0277018) j_ras = (4.64859e-08, 0.991343, 0.131299) k_ras = (0.0279437, -0.131248, 0.990956) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /out/freesurfer/sub-M1215054/mri/orig.mgz... mri_add_xform_to_header -c /out/freesurfer/sub-M1215054/mri/transforms/talairach.xfm /out/freesurfer/sub-M1215054/mri/orig.mgz /out/freesurfer/sub-M1215054/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Sep 2 05:19:03 UTC 2021 /out/freesurfer/sub-M1215054/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /out/freesurfer/sub-M1215054/mri /opt/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux 9e1e1df09144 5.4.72-microsoft-standard-WSL2 #1 SMP Wed Oct 28 23:40:43 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux Thu Sep 2 05:19:03 UTC 2021 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.8245 /out/freesurfer/sub-M1215054/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.8245/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.8245/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.32831e-10, 3.72529e-09) j_ras = (0, 0, -1) k_ras = (-2.32831e-10, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.8245/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Sep 2 05:19:08 UTC 2021 nu_correct -clobber ./tmp.mri_nu_correct.mni.8245/nu0.mnc ./tmp.mri_nu_correct.mni.8245/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.8245/0/ -iterations 1000 -distance 50 [root@9e1e1df09144:/out/freesurfer/sub-M1215054/mri/] [2021-09-02 05:19:09] running: /opt/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.8245/0/ ./tmp.mri_nu_correct.mni.8245/nu0.mnc ./tmp.mri_nu_correct.mni.8245/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 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Processing:.................................................................Done Number of iterations: 50 CV of field change: 0.000991737 mri_convert ./tmp.mri_nu_correct.mni.8245/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.8245/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.8245/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.32831e-10, 3.72529e-09) j_ras = (0, 0, -1) k_ras = (-2.32831e-10, 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... Thu Sep 2 05:20:58 UTC 2021 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at Thu Sep 2 05:20:58 UTC 2021 Ended at Thu Sep 2 05:21:26 UTC 2021 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Thu Sep 2 05:21:28 UTC 2021 /out/freesurfer/sub-M1215054/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7858, pval=0.8469 >= threshold=0.0050) awk -f /opt/freesurfer/bin/extract_talairach_avi_QA.awk /out/freesurfer/sub-M1215054/mri/transforms/talairach_avi.log tal_QC_AZS /out/freesurfer/sub-M1215054/mri/transforms/talairach_avi.log TalAviQA: 0.98401 z-score: 1 #-------------------------------------------- #@# Nu Intensity Correction Thu Sep 2 05:21:28 UTC 2021 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /out/freesurfer/sub-M1215054/mri /opt/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux 9e1e1df09144 5.4.72-microsoft-standard-WSL2 #1 SMP Wed Oct 28 23:40:43 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux Thu Sep 2 05:21:28 UTC 2021 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.9082 /out/freesurfer/sub-M1215054/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.9082/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.9082/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.32831e-10, 3.72529e-09) j_ras = (0, 0, -1) k_ras = (-2.32831e-10, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.9082/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Sep 2 05:21:34 UTC 2021 nu_correct -clobber ./tmp.mri_nu_correct.mni.9082/nu0.mnc ./tmp.mri_nu_correct.mni.9082/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.9082/0/ [root@9e1e1df09144:/out/freesurfer/sub-M1215054/mri/] [2021-09-02 05:21:34] running: /opt/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.9082/0/ ./tmp.mri_nu_correct.mni.9082/nu0.mnc ./tmp.mri_nu_correct.mni.9082/nu1.imp Processing:.................................................................Done 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Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 49 CV of field change: 0.00098091 -------------------------------------------------------- Iteration 2 Thu Sep 2 05:53:19 UTC 2021 nu_correct -clobber ./tmp.mri_nu_correct.mni.9082/nu1.mnc ./tmp.mri_nu_correct.mni.9082/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.9082/1/ [root@9e1e1df09144:/out/freesurfer/sub-M1215054/mri/] [2021-09-02 05:53:19] running: /opt/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.9082/1/ ./tmp.mri_nu_correct.mni.9082/nu1.mnc ./tmp.mri_nu_correct.mni.9082/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done 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: 40 CV of field change: 0.000989254 mri_binarize --i ./tmp.mri_nu_correct.mni.9082/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.9082/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /out/freesurfer/sub-M1215054/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.9082/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.9082/ones.mgz sysname Linux hostname 9e1e1df09144 machine x86_64 user root input ./tmp.mri_nu_correct.mni.9082/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.9082/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.9082/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.9082/sum.junk --avgwf ./tmp.mri_nu_correct.mni.9082/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.9082/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.9082/sum.junk --avgwf ./tmp.mri_nu_correct.mni.9082/input.mean.dat sysname Linux hostname 9e1e1df09144 machine x86_64 user root UseRobust 0 Loading ./tmp.mri_nu_correct.mni.9082/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.9082/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.9082/ones.mgz --i ./tmp.mri_nu_correct.mni.9082/nu2.mnc --sum ./tmp.mri_nu_correct.mni.9082/sum.junk --avgwf ./tmp.mri_nu_correct.mni.9082/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.9082/ones.mgz --i ./tmp.mri_nu_correct.mni.9082/nu2.mnc --sum ./tmp.mri_nu_correct.mni.9082/sum.junk --avgwf ./tmp.mri_nu_correct.mni.9082/output.mean.dat sysname Linux hostname 9e1e1df09144 machine x86_64 user root UseRobust 0 Loading ./tmp.mri_nu_correct.mni.9082/ones.mgz Loading ./tmp.mri_nu_correct.mni.9082/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.9082/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.9082/nu2.mnc ./tmp.mri_nu_correct.mni.9082/nu2.mnc mul .92000893060326928896 Saving result to './tmp.mri_nu_correct.mni.9082/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.9082/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.9082/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.9082/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.32831e-10, 3.72529e-09) j_ras = (0, 0, -1) k_ras = (-2.32831e-10, 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 ( 9, 127) to ( 3, 110) Thu Sep 2 05:55:17 UTC 2021 mri_nu_correct.mni done mri_add_xform_to_header -c /out/freesurfer/sub-M1215054/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Thu Sep 2 05:55:18 UTC 2021 /out/freesurfer/sub-M1215054/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 1.09889 -0.02375 -0.01857 4.32556; 0.01958 0.98813 0.18304 -24.30977; 0.00002 -0.15388 1.09345 -25.11205; 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 = 14 Starting OpenSpline(): npoints = 14 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 73 (73), valley at 39 (39) csf peak at 28, setting threshold to 58 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 74 (74), valley at 39 (39) csf peak at 27, setting threshold to 58 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 6 seconds. Started at Thu Sep 2 05:18:49 UTC 2021 Ended at Thu Sep 2 05:56:25 UTC 2021 #@#%# recon-all-run-time-hours 0.627 recon-all -s sub-M1215054 finished without error at Thu Sep 2 05:56:26 UTC 2021 New invocation of recon-all Thu Sep 2 08:11:49 UTC 2021 /out/freesurfer/sub-M1215054 /opt/freesurfer/bin/recon-all -autorecon2-volonly -openmp 3 -subjid sub-M1215054 -sd /out/freesurfer subjid sub-M1215054 setenv SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /opt/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a Linux 9e1e1df09144 5.4.72-microsoft-standard-WSL2 #1 SMP Wed Oct 28 23:40:43 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1048576 memorylocked 82000 kbytes maxproc unlimited maxlocks unlimited maxsignal 23036 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 5902064 1684484 2293084 189624 1924496 3710788 Swap: 2097152 332544 1764608 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-08:11:49-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-08:11:49-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-08:11:49-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-08:11:49-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-08:11:49-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-08:11:49-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-08:11:49-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-08:11:49-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-08:11:49-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-08:11:49-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-08:11:49-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-08:11:49-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-08:11:49-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-08:11:49-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-08:11:49-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-08:11:50-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-08:11:50-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-08:11:50-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-08:11:50-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-08:11:50-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-08:11:50-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-08:11:50-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-08:11:50-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-08:11:50-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-08:11:50-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-08:11:50-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-08:11:50-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-08:11:50-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-08:11:50-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-08:11:50-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-08:11:50-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-08:11:50-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-08:11:50-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-08:11:50-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-08:11:50-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-08:11:50-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-08:11:50-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-08:11:50-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-08:11:50-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /opt/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /opt/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #------------------------------------- #@# EM Registration Thu Sep 2 08:11:51 UTC 2021 /out/freesurfer/sub-M1215054/mri mri_em_register -rusage /out/freesurfer/sub-M1215054/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 3 == reading 1 input volumes... logging results to talairach.log reading '/opt/freesurfer/average/RB_all_2016-05-10.vc700.gca'... average std = 7.3 using min determinant for regularization = 5.3 0 singular and 841 ill-conditioned covariance matrices regularized reading 'nu.mgz'... INFO: MRImask() using MRImaskDifferentGeometry() INFO: MRImask() using MRImaskDifferentGeometry() INFO: MRImask() using MRImaskDifferentGeometry() INFO: MRImask() using MRImaskDifferentGeometry() INFO: MRImask() using MRImaskDifferentGeometry() freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 6.3 or > 503.7 total sample mean = 78.8 (1011 zeros) ************************************************ spacing=8, using 2830 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2830, passno 0, spacing 8 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=26.1 skull bounding box = (66, 74, 38) --> (197, 195, 206) using (110, 114, 122) as brain centroid... mean wm in atlas = 107, using box (94,99,101) --> (126, 128,142) to find MRI wm before smoothing, mri peak at 110 robust fit to distribution - 109 +- 4.1 after smoothing, mri peak at 109, scaling input intensities by 0.982 scaling channel 0 by 0.981651 initial log_p = -4.218 ************************************************ First Search limited to translation only. ************************************************ max log p = -3.737406 @ (-9.091, -9.091, -9.091) max log p = -3.724951 @ (4.545, -4.545, 4.545) max log p = -3.650114 @ (-2.273, 2.273, -6.818) max log p = -3.639049 @ (3.409, 1.136, 3.409) max log p = -3.608399 @ (-0.568, -1.705, -1.705) max log p = -3.608399 @ (0.000, 0.000, 0.000) Found translation: (-4.0, -11.9, -9.7): log p = -3.608 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.484, old_max_log_p =-3.608 (thresh=-3.6) 1.07500 0.00000 0.00000 -13.78086; 0.00000 1.14016 0.13053 -45.34810; 0.00000 -0.15011 0.99144 11.02271; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.484, old_max_log_p =-3.484 (thresh=-3.5) 1.07500 0.00000 0.00000 -13.78086; 0.00000 1.14016 0.13053 -45.34810; 0.00000 -0.15011 0.99144 11.02271; 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=-3.335, old_max_log_p =-3.484 (thresh=-3.5) 1.07385 -0.04203 0.02694 -12.96794; 0.03450 1.11803 0.12901 -46.77516; -0.03517 -0.14440 0.95375 22.95778; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.335, old_max_log_p =-3.335 (thresh=-3.3) 1.07385 -0.04203 0.02694 -12.96794; 0.03450 1.11803 0.12901 -46.77516; -0.03517 -0.14440 0.95375 22.95778; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.308, old_max_log_p =-3.335 (thresh=-3.3) 1.07831 -0.03063 0.01236 -12.49754; 0.02583 1.11947 0.12112 -44.46910; -0.01725 -0.13542 0.95174 18.69021; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.304, old_max_log_p =-3.308 (thresh=-3.3) 1.08084 -0.03070 0.01239 -12.82388; 0.02586 1.12078 0.12127 -44.66100; -0.01729 -0.13573 0.95397 18.48687; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.304, old_max_log_p =-3.304 (thresh=-3.3) 1.08084 -0.03070 0.01239 -12.82388; 0.02586 1.12078 0.12127 -44.66100; -0.01729 -0.13573 0.95397 18.48687; 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 1.08084 -0.03070 0.01239 -12.82388; 0.02586 1.12078 0.12127 -44.66100; -0.01729 -0.13573 0.95397 18.48687; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.08084 -0.03070 0.01239 -12.82388; 0.02586 1.12078 0.12127 -44.66100; -0.01729 -0.13573 0.95397 18.48687; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.08084 -0.03070 0.01239 -12.82388; 0.02586 1.12078 0.12127 -44.66100; -0.01729 -0.13573 0.95397 18.48687; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.304 (old=-4.218) transform before final EM align: 1.08084 -0.03070 0.01239 -12.82388; 0.02586 1.12078 0.12127 -44.66100; -0.01729 -0.13573 0.95397 18.48687; 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 1.08084 -0.03070 0.01239 -12.82388; 0.02586 1.12078 0.12127 -44.66100; -0.01729 -0.13573 0.95397 18.48687; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 1.08084 -0.03070 0.01239 -12.82388; 0.02586 1.12078 0.12127 -44.66100; -0.01729 -0.13573 0.95397 18.48687; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = 3.8 tol 0.000000 final transform: 1.08084 -0.03070 0.01239 -12.82388; 0.02586 1.12078 0.12127 -44.66100; -0.01729 -0.13573 0.95397 18.48687; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 910.666587 mri_em_register stimesec 3.667678 mri_em_register ru_maxrss 604672 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 162625 mri_em_register ru_majflt 6 mri_em_register ru_nswap 0 mri_em_register ru_inblock 75624 mri_em_register ru_oublock 0 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 1328 mri_em_register ru_nivcsw 704 registration took 5 minutes and 29 seconds. #-------------------------------------- #@# CA Normalize Thu Sep 2 08:17:20 UTC 2021 /out/freesurfer/sub-M1215054/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/opt/freesurfer/average/RB_all_2016-05-10.vc700.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... INFO: MRImask() using MRImaskDifferentGeometry() resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=25.9 skull bounding box = (66, 74, 37) --> (197, 195, 206) using (110, 114, 122) as brain centroid... mean wm in atlas = 107, using box (94,99,101) --> (126, 128,142) to find MRI wm before smoothing, mri peak at 110 robust fit to distribution - 109 +- 4.1 after smoothing, mri peak at 109, scaling input intensities by 0.982 scaling channel 0 by 0.981651 using 246344 sample points... INFO: compute sample coordinates transform 1.08084 -0.03070 0.01239 -12.82388; 0.02586 1.12078 0.12127 -44.66100; -0.01729 -0.13573 0.95397 18.48687; 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 (132, 71, 31) --> (193, 174, 205) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0 3 of 7408 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (71, 73, 30) --> (132, 176, 205) Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0 4 of 6982 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (134, 151, 58) --> (179, 188, 115) Left_Cerebellum_White_Matter: limiting intensities to 94.0 --> 132.0 0 of 173 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (92, 151, 55) --> (132, 188, 116) Right_Cerebellum_White_Matter: limiting intensities to 95.0 --> 132.0 0 of 246 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (117, 141, 96) --> (149, 204, 127) Brain_Stem: limiting intensities to 88.0 --> 132.0 0 of 693 (0.0%) samples deleted using 15502 total control points for intensity normalization... bias field = 0.968 +- 0.058 128 of 15495 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (132, 71, 31) --> (193, 174, 205) Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 3 of 7765 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (71, 73, 30) --> (132, 176, 205) Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 9 of 7410 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (134, 151, 58) --> (179, 188, 115) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 23 of 275 (8.4%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (92, 151, 55) --> (132, 188, 116) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 58 of 331 (17.5%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (117, 141, 96) --> (149, 204, 127) Brain_Stem: limiting intensities to 88.0 --> 132.0 261 of 881 (29.6%) samples deleted using 16662 total control points for intensity normalization... bias field = 1.031 +- 0.044 105 of 16178 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (132, 71, 31) --> (193, 174, 205) Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 132.0 3 of 7648 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (71, 73, 30) --> (132, 176, 205) Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 7 of 7449 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (134, 151, 58) --> (179, 188, 115) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 152 of 339 (44.8%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (92, 151, 55) --> (132, 188, 116) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 229 of 371 (61.7%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (117, 141, 96) --> (149, 204, 127) Brain_Stem: limiting intensities to 88.0 --> 132.0 659 of 930 (70.9%) samples deleted using 16737 total control points for intensity normalization... bias field = 1.028 +- 0.032 31 of 15501 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 1 seconds. #-------------------------------------- #@# CA Reg Thu Sep 2 08:18:21 UTC 2021 /out/freesurfer/sub-M1215054/mri mri_ca_register -rusage /out/freesurfer/sub-M1215054/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_ca_register for OpenMP = 3 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... INFO: MRImask() using MRImaskDifferentGeometry() INFO: MRImask() using MRImaskDifferentGeometry() INFO: MRImask() using MRImaskDifferentGeometry() INFO: MRImask() using MRImaskDifferentGeometry() INFO: MRImask() using MRImaskDifferentGeometry() reading GCA '/opt/freesurfer/average/RB_all_2016-05-10.vc700.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.17 (predicted orig area = 6.8) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.800, neg=0, invalid=762 0001: dt=237.461129, rms=0.736 (7.944%), neg=0, invalid=762 0002: dt=132.769231, rms=0.722 (1.978%), neg=0, invalid=762 0003: dt=369.920000, rms=0.710 (1.594%), neg=0, invalid=762 0004: dt=111.838384, rms=0.705 (0.699%), neg=0, invalid=762 0005: dt=517.888000, rms=0.700 (0.782%), neg=0, invalid=762 0006: dt=129.472000, rms=0.698 (0.319%), neg=0, invalid=762 0007: dt=369.920000, rms=0.696 (0.291%), neg=0, invalid=762 0008: dt=129.472000, rms=0.694 (0.222%), neg=0, invalid=762 0009: dt=129.472000, rms=0.693 (0.104%), neg=0, invalid=762 0010: dt=129.472000, rms=0.692 (0.170%), neg=0, invalid=762 0011: dt=129.472000, rms=0.690 (0.257%), neg=0, invalid=762 0012: dt=129.472000, rms=0.688 (0.284%), neg=0, invalid=762 0013: dt=129.472000, rms=0.687 (0.278%), neg=0, invalid=762 0014: dt=129.472000, rms=0.685 (0.266%), neg=0, invalid=762 0015: dt=129.472000, rms=0.683 (0.233%), neg=0, invalid=762 0016: dt=129.472000, rms=0.682 (0.201%), neg=0, invalid=762 0017: dt=129.472000, rms=0.681 (0.158%), neg=0, invalid=762 0018: dt=129.472000, rms=0.680 (0.153%), neg=0, invalid=762 0019: dt=129.472000, rms=0.679 (0.123%), neg=0, invalid=762 0020: dt=129.472000, rms=0.678 (0.097%), neg=0, invalid=762 0021: dt=295.936000, rms=0.678 (0.057%), neg=0, invalid=762 0022: dt=295.936000, rms=0.678 (-0.098%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.678, neg=0, invalid=762 0023: dt=295.936000, rms=0.674 (0.653%), neg=0, invalid=762 0024: dt=92.480000, rms=0.673 (0.110%), neg=0, invalid=762 0025: dt=92.480000, rms=0.673 (0.033%), neg=0, invalid=762 0026: dt=92.480000, rms=0.673 (0.039%), neg=0, invalid=762 0027: dt=92.480000, rms=0.672 (0.077%), neg=0, invalid=762 0028: dt=92.480000, rms=0.671 (0.110%), neg=0, invalid=762 0029: dt=92.480000, rms=0.670 (0.134%), neg=0, invalid=762 0030: dt=92.480000, rms=0.670 (0.119%), neg=0, invalid=762 0031: dt=92.480000, rms=0.669 (0.101%), neg=0, invalid=762 0032: dt=92.480000, rms=0.669 (0.006%), neg=0, invalid=762 0033: dt=92.480000, rms=0.669 (0.004%), neg=0, invalid=762 0034: dt=92.480000, rms=0.669 (0.012%), neg=0, invalid=762 0035: dt=92.480000, rms=0.669 (0.018%), neg=0, invalid=762 0036: dt=92.480000, rms=0.668 (0.030%), neg=0, invalid=762 0037: dt=92.480000, rms=0.668 (0.036%), neg=0, invalid=762 0038: dt=92.480000, rms=0.668 (0.045%), neg=0, invalid=762 0039: dt=92.480000, rms=0.668 (0.051%), neg=0, invalid=762 0040: dt=92.480000, rms=0.667 (0.056%), neg=0, invalid=762 0041: dt=92.480000, rms=0.667 (0.059%), neg=0, invalid=762 0042: dt=92.480000, rms=0.666 (0.058%), neg=0, invalid=762 0043: dt=92.480000, rms=0.666 (0.057%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.670, neg=0, invalid=762 0044: dt=36.288000, rms=0.669 (0.243%), neg=0, invalid=762 0045: dt=124.416000, rms=0.666 (0.393%), neg=0, invalid=762 0046: dt=404.795042, rms=0.646 (2.976%), neg=0, invalid=762 0047: dt=25.920000, rms=0.644 (0.326%), neg=0, invalid=762 0048: dt=6.480000, rms=0.644 (0.004%), neg=0, invalid=762 0049: dt=6.480000, rms=0.644 (0.002%), neg=0, invalid=762 0050: dt=6.480000, rms=0.644 (-0.020%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.645, neg=0, invalid=762 0051: dt=145.152000, rms=0.640 (0.716%), neg=0, invalid=762 0052: dt=248.832000, rms=0.636 (0.652%), neg=0, invalid=762 0053: dt=36.288000, rms=0.635 (0.188%), neg=0, invalid=762 0054: dt=36.288000, rms=0.634 (0.075%), neg=0, invalid=762 0055: dt=36.288000, rms=0.634 (0.082%), neg=0, invalid=762 0056: dt=36.288000, rms=0.633 (0.107%), neg=0, invalid=762 0057: dt=36.288000, rms=0.632 (0.205%), neg=0, invalid=762 0058: dt=36.288000, rms=0.630 (0.291%), neg=0, invalid=762 0059: dt=36.288000, rms=0.628 (0.307%), neg=0, invalid=762 0060: dt=36.288000, rms=0.626 (0.284%), neg=0, invalid=762 0061: dt=36.288000, rms=0.624 (0.268%), neg=0, invalid=762 0062: dt=36.288000, rms=0.623 (0.245%), neg=0, invalid=762 0063: dt=36.288000, rms=0.622 (0.211%), neg=0, invalid=762 0064: dt=36.288000, rms=0.620 (0.197%), neg=0, invalid=762 0065: dt=36.288000, rms=0.619 (0.211%), neg=0, invalid=762 0066: dt=36.288000, rms=0.618 (0.233%), neg=0, invalid=762 0067: dt=36.288000, rms=0.616 (0.223%), neg=0, invalid=762 0068: dt=36.288000, rms=0.615 (0.199%), neg=0, invalid=762 0069: dt=36.288000, rms=0.614 (0.173%), neg=0, invalid=762 0070: dt=36.288000, rms=0.613 (0.150%), neg=0, invalid=762 0071: dt=36.288000, rms=0.612 (0.139%), neg=0, invalid=762 0072: dt=36.288000, rms=0.611 (0.131%), neg=0, invalid=762 0073: dt=36.288000, rms=0.611 (0.132%), neg=0, invalid=762 0074: dt=36.288000, rms=0.610 (0.133%), neg=0, invalid=762 0075: dt=36.288000, rms=0.609 (0.128%), neg=0, invalid=762 0076: dt=36.288000, rms=0.608 (0.114%), neg=0, invalid=762 0077: dt=36.288000, rms=0.608 (0.104%), neg=0, invalid=762 0078: dt=36.288000, rms=0.608 (0.006%), neg=0, invalid=762 0079: dt=36.288000, rms=0.608 (0.002%), neg=0, invalid=762 0080: dt=36.288000, rms=0.608 (0.008%), neg=0, invalid=762 0081: dt=36.288000, rms=0.607 (0.012%), neg=0, invalid=762 0082: dt=36.288000, rms=0.607 (0.015%), neg=0, invalid=762 0083: dt=36.288000, rms=0.607 (0.025%), neg=0, invalid=762 0084: dt=36.288000, rms=0.607 (0.022%), neg=0, invalid=762 0085: dt=36.288000, rms=0.607 (0.028%), neg=0, invalid=762 0086: dt=36.288000, rms=0.607 (0.027%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.627, neg=0, invalid=762 0087: dt=0.175000, rms=0.627 (0.094%), neg=0, invalid=762 0088: dt=0.125000, rms=0.627 (0.000%), neg=0, invalid=762 0089: dt=0.125000, rms=0.627 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.627, neg=0, invalid=762 0090: dt=0.700000, rms=0.627 (0.095%), neg=0, invalid=762 0091: dt=0.300000, rms=0.627 (0.000%), neg=0, invalid=762 0092: dt=0.300000, rms=0.627 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.688, neg=0, invalid=762 0093: dt=5.620339, rms=0.669 (2.706%), neg=0, invalid=762 0094: dt=3.422222, rms=0.668 (0.140%), neg=0, invalid=762 0095: dt=3.422222, rms=0.668 (-0.047%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.668, neg=0, invalid=762 0096: dt=0.000000, rms=0.668 (0.075%), neg=0, invalid=762 0097: dt=0.000000, rms=0.668 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.726, neg=0, invalid=762 0098: dt=1.024000, rms=0.723 (0.350%), neg=0, invalid=762 0099: dt=2.034188, rms=0.718 (0.651%), neg=0, invalid=762 0100: dt=1.024000, rms=0.718 (0.092%), neg=0, invalid=762 0101: dt=1.024000, rms=0.716 (0.215%), neg=0, invalid=762 0102: dt=1.024000, rms=0.715 (0.166%), neg=0, invalid=762 0103: dt=1.024000, rms=0.715 (-0.045%), neg=0, invalid=762 0104: dt=0.192000, rms=0.715 (0.001%), neg=0, invalid=762 0105: dt=0.448000, rms=0.715 (0.007%), neg=0, invalid=762 0106: dt=1.792000, rms=0.715 (0.043%), neg=0, invalid=762 0107: dt=4.096000, rms=0.714 (0.122%), neg=0, invalid=762 0108: dt=0.000000, rms=0.714 (-0.003%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.714, neg=0, invalid=762 0109: dt=0.448000, rms=0.714 (0.081%), neg=0, invalid=762 0110: dt=0.096000, rms=0.714 (0.003%), neg=0, invalid=762 0111: dt=0.096000, rms=0.714 (-0.000%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.684, neg=0, invalid=762 0112: dt=0.861799, rms=0.666 (2.629%), neg=0, invalid=762 0113: dt=0.080000, rms=0.665 (0.137%), neg=0, invalid=762 0114: dt=0.080000, rms=0.665 (-0.074%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.666, neg=0, invalid=762 0115: dt=0.028000, rms=0.665 (0.085%), neg=0, invalid=762 0116: dt=0.000013, rms=0.665 (0.001%), neg=0, invalid=762 0117: dt=0.000013, rms=0.665 (-0.000%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.14300 (25) Left_Lateral_Ventricle (4): linear fit = 1.27 x + 0.0 (1281 voxels, overlap=0.509) Left_Lateral_Ventricle (4): linear fit = 1.27 x + 0.0 (1281 voxels, peak = 26), gca=25.5 gca peak = 0.15565 (16) mri peak = 0.10431 (23) Right_Lateral_Ventricle (43): linear fit = 1.39 x + 0.0 (878 voxels, overlap=0.410) Right_Lateral_Ventricle (43): linear fit = 1.39 x + 0.0 (878 voxels, peak = 22), gca=22.3 gca peak = 0.26829 (96) mri peak = 0.12269 (94) Right_Pallidum (52): linear fit = 0.98 x + 0.0 (1030 voxels, overlap=0.930) Right_Pallidum (52): linear fit = 0.98 x + 0.0 (1030 voxels, peak = 94), gca=93.6 gca peak = 0.20183 (93) mri peak = 0.08962 (96) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (916 voxels, overlap=1.009) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (916 voxels, peak = 93), gca=92.5 gca peak = 0.21683 (55) mri peak = 0.10297 (68) Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (1218 voxels, overlap=0.045) Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (1218 voxels, peak = 64), gca=63.5 gca peak = 0.30730 (58) mri peak = 0.11276 (67) Left_Hippocampus (17): linear fit = 1.16 x + 0.0 (1134 voxels, overlap=0.042) Left_Hippocampus (17): linear fit = 1.16 x + 0.0 (1134 voxels, peak = 68), gca=67.6 gca peak = 0.11430 (101) mri peak = 0.16454 (104) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (70307 voxels, overlap=0.619) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (70307 voxels, peak = 104), gca=103.5 gca peak = 0.12076 (102) mri peak = 0.13563 (105) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (75083 voxels, overlap=0.587) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (75083 voxels, peak = 105), gca=104.5 gca peak = 0.14995 (59) mri peak = 0.03737 (65) Left_Cerebral_Cortex (3): linear fit = 1.14 x + 0.0 (40458 voxels, overlap=0.285) Left_Cerebral_Cortex (3): linear fit = 1.14 x + 0.0 (40458 voxels, peak = 68), gca=67.6 gca peak = 0.15082 (58) mri peak = 0.03867 (67) Right_Cerebral_Cortex (42): linear fit = 1.14 x + 0.0 (39502 voxels, overlap=0.385) Right_Cerebral_Cortex (42): linear fit = 1.14 x + 0.0 (39502 voxels, peak = 66), gca=66.4 gca peak = 0.14161 (67) mri peak = 0.10027 (76) Right_Caudate (50): linear fit = 1.13 x + 0.0 (782 voxels, overlap=0.202) Right_Caudate (50): linear fit = 1.13 x + 0.0 (782 voxels, peak = 76), gca=76.0 gca peak = 0.15243 (71) mri peak = 0.09204 (81) Left_Caudate (11): linear fit = 1.09 x + 0.0 (1137 voxels, overlap=0.540) Left_Caudate (11): linear fit = 1.09 x + 0.0 (1137 voxels, peak = 77), gca=77.0 gca peak = 0.13336 (57) mri peak = 0.05431 (66) Left_Cerebellum_Cortex (8): linear fit = 1.16 x + 0.0 (28860 voxels, overlap=0.549) Left_Cerebellum_Cortex (8): linear fit = 1.16 x + 0.0 (28860 voxels, peak = 66), gca=66.4 gca peak = 0.13252 (56) mri peak = 0.05542 (66) Right_Cerebellum_Cortex (47): linear fit = 1.16 x + 0.0 (34878 voxels, overlap=0.555) Right_Cerebellum_Cortex (47): linear fit = 1.16 x + 0.0 (34878 voxels, peak = 65), gca=65.2 gca peak = 0.18181 (84) mri peak = 0.07365 (87) Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (10702 voxels, overlap=0.805) Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (10702 voxels, peak = 88), gca=87.8 gca peak = 0.20573 (83) mri peak = 0.10543 (86) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (9263 voxels, overlap=0.872) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (9263 voxels, peak = 86), gca=85.9 gca peak = 0.21969 (57) mri peak = 0.13371 (70) Left_Amygdala (18): linear fit = 1.23 x + 0.0 (529 voxels, overlap=0.040) Left_Amygdala (18): linear fit = 1.23 x + 0.0 (529 voxels, peak = 70), gca=69.8 gca peak = 0.39313 (56) mri peak = 0.10647 (70) Right_Amygdala (54): linear fit = 1.21 x + 0.0 (607 voxels, overlap=0.014) Right_Amygdala (54): linear fit = 1.21 x + 0.0 (607 voxels, peak = 67), gca=67.5 gca peak = 0.14181 (85) mri peak = 0.07128 (94) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (5860 voxels, overlap=0.735) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (5860 voxels, peak = 91), gca=90.5 gca peak = 0.11978 (83) mri peak = 0.07031 (89) Right_Thalamus_Proper (49): linear fit = 1.07 x + 0.0 (4854 voxels, overlap=0.885) Right_Thalamus_Proper (49): linear fit = 1.07 x + 0.0 (4854 voxels, peak = 88), gca=88.4 gca peak = 0.13399 (79) mri peak = 0.08543 (87) Left_Putamen (12): linear fit = 1.10 x + 0.0 (2815 voxels, overlap=0.602) Left_Putamen (12): linear fit = 1.10 x + 0.0 (2815 voxels, peak = 87), gca=86.5 gca peak = 0.14159 (79) mri peak = 0.07697 (82) Right_Putamen (51): linear fit = 1.04 x + 0.0 (2620 voxels, overlap=0.913) Right_Putamen (51): linear fit = 1.04 x + 0.0 (2620 voxels, peak = 83), gca=82.6 gca peak = 0.10025 (80) mri peak = 0.11506 (85) Brain_Stem (16): linear fit = 1.10 x + 0.0 (12931 voxels, overlap=0.401) Brain_Stem (16): linear fit = 1.10 x + 0.0 (12931 voxels, peak = 88), gca=87.6 gca peak = 0.13281 (86) mri peak = 0.09801 (93) Right_VentralDC (60): linear fit = 1.04 x + 0.0 (1384 voxels, overlap=0.647) Right_VentralDC (60): linear fit = 1.04 x + 0.0 (1384 voxels, peak = 90), gca=89.9 gca peak = 0.12801 (89) mri peak = 0.09139 (91) Left_VentralDC (28): linear fit = 1.05 x + 0.0 (1785 voxels, overlap=0.618) Left_VentralDC (28): linear fit = 1.05 x + 0.0 (1785 voxels, peak = 94), gca=93.9 gca peak = 0.20494 (23) mri peak = 1.00000 (33) gca peak = 0.15061 (21) mri peak = 0.14840 (23) Fourth_Ventricle (15): linear fit = 1.30 x + 0.0 (468 voxels, overlap=0.515) Fourth_Ventricle (15): linear fit = 1.30 x + 0.0 (468 voxels, peak = 27), gca=27.4 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 1.17 x + 0.0 estimating mean wm scale to be 1.02 x + 0.0 estimating mean csf scale to be 1.32 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=0.642, neg=0, invalid=762 0118: dt=144.937618, rms=0.630 (1.853%), neg=0, invalid=762 0119: dt=295.936000, rms=0.625 (0.846%), neg=0, invalid=762 0120: dt=129.472000, rms=0.623 (0.265%), neg=0, invalid=762 0121: dt=369.920000, rms=0.621 (0.320%), neg=0, invalid=762 0122: dt=110.976000, rms=0.620 (0.251%), neg=0, invalid=762 0123: dt=129.472000, rms=0.619 (0.071%), neg=0, invalid=762 0124: dt=443.904000, rms=0.618 (0.232%), neg=0, invalid=762 0125: dt=73.984000, rms=0.617 (0.104%), neg=0, invalid=762 0126: dt=887.808000, rms=0.616 (0.206%), neg=0, invalid=762 0127: dt=129.472000, rms=0.615 (0.218%), neg=0, invalid=762 0128: dt=55.488000, rms=0.615 (0.010%), neg=0, invalid=762 0129: dt=55.488000, rms=0.615 (0.012%), neg=0, invalid=762 0130: dt=55.488000, rms=0.614 (0.019%), neg=0, invalid=762 0131: dt=55.488000, rms=0.614 (0.036%), neg=0, invalid=762 0132: dt=55.488000, rms=0.614 (0.060%), neg=0, invalid=762 0133: dt=55.488000, rms=0.613 (0.071%), neg=0, invalid=762 0134: dt=55.488000, rms=0.613 (0.069%), neg=0, invalid=762 0135: dt=55.488000, rms=0.613 (0.068%), neg=0, invalid=762 0136: dt=55.488000, rms=0.612 (0.062%), neg=0, invalid=762 0137: dt=55.488000, rms=0.612 (0.059%), neg=0, invalid=762 0138: dt=55.488000, rms=0.612 (0.061%), neg=0, invalid=762 0139: dt=55.488000, rms=0.611 (0.067%), neg=0, invalid=762 0140: dt=55.488000, rms=0.611 (0.069%), neg=0, invalid=762 0141: dt=55.488000, rms=0.610 (0.064%), neg=0, invalid=762 0142: dt=55.488000, rms=0.610 (0.057%), neg=0, invalid=762 0143: dt=55.488000, rms=0.610 (0.054%), neg=0, invalid=762 0144: dt=55.488000, rms=0.609 (0.051%), neg=0, invalid=762 0145: dt=55.488000, rms=0.609 (0.050%), neg=0, invalid=762 0146: dt=55.488000, rms=0.609 (0.051%), neg=0, invalid=762 0147: dt=55.488000, rms=0.608 (0.048%), neg=0, invalid=762 0148: dt=55.488000, rms=0.608 (0.044%), neg=0, invalid=762 0149: dt=55.488000, rms=0.608 (0.042%), neg=0, invalid=762 0150: dt=55.488000, rms=0.608 (0.038%), neg=0, invalid=762 0151: dt=55.488000, rms=0.607 (0.038%), neg=0, invalid=762 0152: dt=55.488000, rms=0.607 (0.036%), neg=0, invalid=762 0153: dt=55.488000, rms=0.607 (0.035%), neg=0, invalid=762 0154: dt=55.488000, rms=0.607 (0.039%), neg=0, invalid=762 0155: dt=55.488000, rms=0.606 (0.040%), neg=0, invalid=762 0156: dt=55.488000, rms=0.606 (0.042%), neg=0, invalid=762 0157: dt=55.488000, rms=0.606 (0.038%), neg=0, invalid=762 0158: dt=55.488000, rms=0.606 (0.035%), neg=0, invalid=762 0159: dt=55.488000, rms=0.606 (0.036%), neg=0, invalid=762 0160: dt=55.488000, rms=0.605 (0.038%), neg=0, invalid=762 0161: dt=55.488000, rms=0.605 (0.037%), neg=0, invalid=762 0162: dt=55.488000, rms=0.605 (0.036%), neg=0, invalid=762 0163: dt=55.488000, rms=0.605 (0.033%), neg=0, invalid=762 0164: dt=55.488000, rms=0.605 (0.031%), neg=0, invalid=762 0165: dt=55.488000, rms=0.604 (0.028%), neg=0, invalid=762 0166: dt=55.488000, rms=0.604 (0.030%), neg=0, invalid=762 0167: dt=55.488000, rms=0.604 (0.030%), neg=0, invalid=762 0168: dt=55.488000, rms=0.604 (0.033%), neg=0, invalid=762 0169: dt=55.488000, rms=0.604 (0.035%), neg=0, invalid=762 0170: dt=55.488000, rms=0.603 (0.032%), neg=0, invalid=762 0171: dt=55.488000, rms=0.603 (0.031%), neg=0, invalid=762 0172: dt=55.488000, rms=0.603 (0.028%), neg=0, invalid=762 0173: dt=55.488000, rms=0.603 (0.026%), neg=0, invalid=762 0174: dt=55.488000, rms=0.603 (0.029%), neg=0, invalid=762 0175: dt=55.488000, rms=0.603 (0.029%), neg=0, invalid=762 0176: dt=55.488000, rms=0.602 (0.028%), neg=0, invalid=762 0177: dt=55.488000, rms=0.602 (0.026%), neg=0, invalid=762 0178: dt=55.488000, rms=0.602 (0.025%), neg=0, invalid=762 0179: dt=55.488000, rms=0.602 (0.023%), neg=0, invalid=762 0180: dt=369.920000, rms=0.602 (0.001%), neg=0, invalid=762 0181: dt=369.920000, rms=0.602 (0.048%), neg=0, invalid=762 0182: dt=369.920000, rms=0.602 (-0.108%), neg=0, invalid=762 0183: dt=0.000000, rms=0.602 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.602, neg=0, invalid=762 0184: dt=129.472000, rms=0.601 (0.143%), neg=0, invalid=762 0185: dt=517.888000, rms=0.600 (0.184%), neg=0, invalid=762 0186: dt=27.744000, rms=0.600 (-0.002%), neg=0, invalid=762 0187: dt=27.744000, rms=0.600 (0.003%), neg=0, invalid=762 0188: dt=27.744000, rms=0.600 (-0.005%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.601, neg=0, invalid=762 0189: dt=102.773723, rms=0.598 (0.530%), neg=0, invalid=762 0190: dt=248.832000, rms=0.588 (1.618%), neg=0, invalid=762 0191: dt=48.564706, rms=0.585 (0.457%), neg=0, invalid=762 0192: dt=145.152000, rms=0.583 (0.390%), neg=0, invalid=762 0193: dt=145.152000, rms=0.579 (0.644%), neg=0, invalid=762 0194: dt=36.288000, rms=0.578 (0.177%), neg=0, invalid=762 0195: dt=124.416000, rms=0.577 (0.196%), neg=0, invalid=762 0196: dt=119.523179, rms=0.575 (0.395%), neg=0, invalid=762 0197: dt=36.288000, rms=0.574 (0.164%), neg=0, invalid=762 0198: dt=124.416000, rms=0.573 (0.183%), neg=0, invalid=762 0199: dt=103.680000, rms=0.571 (0.291%), neg=0, invalid=762 0200: dt=63.106977, rms=0.570 (0.144%), neg=0, invalid=762 0201: dt=331.776000, rms=0.568 (0.440%), neg=0, invalid=762 0202: dt=36.288000, rms=0.567 (0.214%), neg=0, invalid=762 0203: dt=103.680000, rms=0.566 (0.131%), neg=0, invalid=762 0204: dt=82.944000, rms=0.565 (0.160%), neg=0, invalid=762 0205: dt=82.944000, rms=0.564 (0.091%), neg=0, invalid=762 0206: dt=124.416000, rms=0.564 (0.154%), neg=0, invalid=762 0207: dt=36.288000, rms=0.563 (0.085%), neg=0, invalid=762 0208: dt=331.776000, rms=0.562 (0.234%), neg=0, invalid=762 0209: dt=36.288000, rms=0.561 (0.193%), neg=0, invalid=762 0210: dt=145.152000, rms=0.560 (0.145%), neg=0, invalid=762 0211: dt=62.208000, rms=0.559 (0.079%), neg=0, invalid=762 0212: dt=145.152000, rms=0.559 (0.125%), neg=0, invalid=762 0213: dt=82.944000, rms=0.558 (0.092%), neg=0, invalid=762 0214: dt=82.944000, rms=0.558 (0.072%), neg=0, invalid=762 0215: dt=103.680000, rms=0.557 (0.093%), neg=0, invalid=762 0216: dt=36.288000, rms=0.557 (0.051%), neg=0, invalid=762 0217: dt=580.608000, rms=0.555 (0.363%), neg=0, invalid=762 0218: dt=36.288000, rms=0.554 (0.118%), neg=0, invalid=762 0219: dt=145.152000, rms=0.554 (0.092%), neg=0, invalid=762 0220: dt=82.944000, rms=0.553 (0.064%), neg=0, invalid=762 0221: dt=82.944000, rms=0.553 (0.048%), neg=0, invalid=762 0222: dt=82.944000, rms=0.553 (0.066%), neg=0, invalid=762 0223: dt=82.944000, rms=0.552 (0.095%), neg=0, invalid=762 0224: dt=82.944000, rms=0.552 (0.130%), neg=0, invalid=762 0225: dt=82.944000, rms=0.551 (0.174%), neg=0, invalid=762 0226: dt=82.944000, rms=0.550 (0.191%), neg=0, invalid=762 0227: dt=82.944000, rms=0.548 (0.197%), neg=0, invalid=762 0228: dt=82.944000, rms=0.547 (0.189%), neg=0, invalid=762 0229: dt=82.944000, rms=0.546 (0.225%), neg=0, invalid=762 0230: dt=82.944000, rms=0.545 (0.199%), neg=0, invalid=762 0231: dt=82.944000, rms=0.544 (0.188%), neg=0, invalid=762 0232: dt=82.944000, rms=0.543 (0.175%), neg=0, invalid=762 0233: dt=82.944000, rms=0.542 (0.185%), neg=0, invalid=762 0234: dt=82.944000, rms=0.541 (0.157%), neg=0, invalid=762 0235: dt=82.944000, rms=0.540 (0.151%), neg=0, invalid=762 0236: dt=82.944000, rms=0.540 (0.027%), neg=0, invalid=762 0237: dt=82.944000, rms=0.540 (0.037%), neg=0, invalid=762 0238: dt=82.944000, rms=0.540 (0.042%), neg=0, invalid=762 0239: dt=82.944000, rms=0.540 (0.066%), neg=0, invalid=762 0240: dt=82.944000, rms=0.539 (0.067%), neg=0, invalid=762 0241: dt=82.944000, rms=0.539 (0.069%), neg=0, invalid=762 0242: dt=82.944000, rms=0.538 (0.072%), neg=0, invalid=762 0243: dt=82.944000, rms=0.538 (0.091%), neg=0, invalid=762 0244: dt=82.944000, rms=0.537 (0.085%), neg=0, invalid=762 0245: dt=82.944000, rms=0.537 (0.088%), neg=0, invalid=762 0246: dt=82.944000, rms=0.537 (0.086%), neg=0, invalid=762 0247: dt=82.944000, rms=0.536 (0.099%), neg=0, invalid=762 0248: dt=82.944000, rms=0.536 (0.094%), neg=0, invalid=762 0249: dt=82.944000, rms=0.535 (0.079%), neg=0, invalid=762 0250: dt=82.944000, rms=0.535 (0.022%), neg=0, invalid=762 0251: dt=82.944000, rms=0.535 (0.019%), neg=0, invalid=762 0252: dt=36.288000, rms=0.535 (0.005%), neg=0, invalid=762 0253: dt=4.536000, rms=0.535 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.535, neg=0, invalid=762 0254: dt=145.152000, rms=0.532 (0.547%), neg=0, invalid=762 0255: dt=36.288000, rms=0.532 (0.080%), neg=0, invalid=762 0256: dt=82.944000, rms=0.532 (0.037%), neg=0, invalid=762 0257: dt=82.944000, rms=0.531 (0.078%), neg=0, invalid=762 0258: dt=82.944000, rms=0.531 (0.107%), neg=0, invalid=762 0259: dt=82.944000, rms=0.530 (0.110%), neg=0, invalid=762 0260: dt=82.944000, rms=0.530 (0.097%), neg=0, invalid=762 0261: dt=82.944000, rms=0.529 (0.106%), neg=0, invalid=762 0262: dt=82.944000, rms=0.529 (0.104%), neg=0, invalid=762 0263: dt=82.944000, rms=0.528 (0.084%), neg=0, invalid=762 0264: dt=82.944000, rms=0.528 (0.074%), neg=0, invalid=762 0265: dt=82.944000, rms=0.527 (0.085%), neg=0, invalid=762 0266: dt=82.944000, rms=0.527 (0.099%), neg=0, invalid=762 0267: dt=82.944000, rms=0.526 (0.085%), neg=0, invalid=762 0268: dt=82.944000, rms=0.526 (0.080%), neg=0, invalid=762 0269: dt=82.944000, rms=0.525 (0.091%), neg=0, invalid=762 0270: dt=82.944000, rms=0.525 (0.099%), neg=0, invalid=762 0271: dt=82.944000, rms=0.524 (0.088%), neg=0, invalid=762 0272: dt=82.944000, rms=0.524 (0.074%), neg=0, invalid=762 0273: dt=82.944000, rms=0.524 (0.076%), neg=0, invalid=762 0274: dt=82.944000, rms=0.523 (0.072%), neg=0, invalid=762 0275: dt=82.944000, rms=0.523 (0.065%), neg=0, invalid=762 0276: dt=82.944000, rms=0.523 (0.071%), neg=0, invalid=762 0277: dt=82.944000, rms=0.522 (0.064%), neg=0, invalid=762 0278: dt=82.944000, rms=0.522 (0.045%), neg=0, invalid=762 0279: dt=82.944000, rms=0.522 (0.016%), neg=0, invalid=762 0280: dt=82.944000, rms=0.522 (0.016%), neg=0, invalid=762 0281: dt=82.944000, rms=0.522 (0.021%), neg=0, invalid=762 0282: dt=82.944000, rms=0.522 (0.010%), neg=0, invalid=762 0283: dt=2.268000, rms=0.522 (-0.003%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.530, neg=0, invalid=762 0284: dt=0.043750, rms=0.530 (0.092%), neg=0, invalid=762 0285: dt=0.010937, rms=0.530 (0.000%), neg=0, invalid=762 0286: dt=0.010937, rms=0.530 (0.000%), neg=0, invalid=762 0287: dt=0.001367, rms=0.530 (0.000%), neg=0, invalid=762 0288: dt=0.000021, rms=0.530 (0.000%), neg=0, invalid=762 0289: dt=0.000000, rms=0.530 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.530, neg=0, invalid=762 0290: dt=82.758621, rms=0.526 (0.772%), neg=0, invalid=762 0291: dt=44.800000, rms=0.521 (1.006%), neg=0, invalid=762 0292: dt=29.589041, rms=0.519 (0.326%), neg=0, invalid=762 0293: dt=66.434783, rms=0.517 (0.484%), neg=0, invalid=762 0294: dt=23.250000, rms=0.515 (0.425%), neg=0, invalid=762 0295: dt=44.800000, rms=0.513 (0.347%), neg=0, invalid=762 0296: dt=32.000000, rms=0.512 (0.231%), neg=0, invalid=762 0297: dt=38.400000, rms=0.511 (0.222%), neg=0, invalid=762 0298: dt=11.200000, rms=0.510 (0.135%), neg=0, invalid=762 0299: dt=2.800000, rms=0.510 (0.027%), neg=0, invalid=762 0300: dt=1.400000, rms=0.510 (0.012%), neg=0, invalid=762 0301: dt=0.350000, rms=0.510 (0.002%), neg=0, invalid=762 0302: dt=0.087500, rms=0.510 (0.001%), neg=0, invalid=762 0303: dt=0.010937, rms=0.510 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.527, neg=0, invalid=762 0304: dt=4.585366, rms=0.526 (0.229%), neg=0, invalid=762 0305: dt=4.032000, rms=0.526 (0.049%), neg=0, invalid=762 0306: dt=4.032000, rms=0.525 (0.036%), neg=0, invalid=762 0307: dt=4.032000, rms=0.525 (-0.011%), neg=0, invalid=762 0308: dt=6.666667, rms=0.525 (0.043%), neg=0, invalid=762 0309: dt=12.869565, rms=0.525 (0.082%), neg=0, invalid=762 0310: dt=39.304348, rms=0.523 (0.309%), neg=0, invalid=762 0311: dt=11.520000, rms=0.523 (0.032%), neg=0, invalid=762 0312: dt=11.520000, rms=0.522 (0.100%), neg=0, invalid=762 0313: dt=11.520000, rms=0.522 (0.117%), neg=0, invalid=762 0314: dt=11.520000, rms=0.521 (0.135%), neg=0, invalid=762 0315: dt=11.520000, rms=0.520 (0.151%), neg=0, invalid=762 0316: dt=11.520000, rms=0.520 (0.152%), neg=0, invalid=762 0317: dt=11.520000, rms=0.520 (-0.005%), neg=0, invalid=762 0318: dt=4.032000, rms=0.520 (0.002%), neg=0, invalid=762 0319: dt=4.032000, rms=0.520 (0.002%), neg=0, invalid=762 0320: dt=13.824000, rms=0.520 (0.008%), neg=0, invalid=762 0321: dt=0.252000, rms=0.520 (0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.520, neg=0, invalid=762 0322: dt=5.333333, rms=0.519 (0.111%), neg=0, invalid=762 0323: dt=4.032000, rms=0.519 (0.004%), neg=0, invalid=762 0324: dt=4.032000, rms=0.519 (0.007%), neg=0, invalid=762 0325: dt=4.032000, rms=0.519 (-0.003%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.538, neg=0, invalid=762 0326: dt=0.000000, rms=0.537 (0.076%), neg=0, invalid=762 0327: dt=0.000000, rms=0.537 (0.000%), neg=0, invalid=762 0328: dt=0.100000, rms=0.537 (-0.097%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.538, neg=0, invalid=762 0329: dt=0.000000, rms=0.537 (0.076%), neg=0, invalid=762 0330: dt=0.000000, rms=0.537 (0.000%), neg=0, invalid=762 0331: dt=0.100000, rms=0.537 (-0.076%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.507, neg=0, invalid=762 0332: dt=0.448000, rms=0.494 (2.717%), neg=0, invalid=762 0333: dt=0.448000, rms=0.491 (0.519%), neg=0, invalid=762 0334: dt=0.448000, rms=0.489 (0.380%), neg=0, invalid=762 0335: dt=0.448000, rms=0.488 (0.195%), neg=0, invalid=762 0336: dt=0.448000, rms=0.487 (0.200%), neg=0, invalid=762 0337: dt=0.448000, rms=0.487 (0.093%), neg=0, invalid=762 0338: dt=0.448000, rms=0.486 (0.133%), neg=0, invalid=762 0339: dt=0.448000, rms=0.486 (0.046%), neg=0, invalid=762 0340: dt=0.448000, rms=0.485 (0.100%), neg=0, invalid=762 0341: dt=0.448000, rms=0.485 (0.113%), neg=0, invalid=762 0342: dt=0.448000, rms=0.484 (0.114%), neg=0, invalid=762 0343: dt=0.448000, rms=0.484 (0.152%), neg=0, invalid=762 0344: dt=0.224000, rms=0.484 (0.018%), neg=0, invalid=762 0345: dt=0.224000, rms=0.483 (0.016%), neg=0, invalid=762 0346: dt=0.000020, rms=0.483 (0.001%), neg=0, invalid=762 0347: dt=0.000020, rms=0.483 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.484, neg=0, invalid=762 0348: dt=0.448000, rms=0.481 (0.691%), neg=0, invalid=762 0349: dt=0.448000, rms=0.480 (0.079%), neg=0, invalid=762 0350: dt=0.112000, rms=0.480 (0.001%), neg=0, invalid=762 0351: dt=0.112000, rms=0.480 (0.004%), neg=0, invalid=762 0352: dt=0.112000, rms=0.480 (0.007%), neg=0, invalid=762 0353: dt=0.112000, rms=0.480 (0.010%), neg=0, invalid=762 0354: dt=0.112000, rms=0.480 (0.012%), neg=0, invalid=762 0355: dt=0.112000, rms=0.480 (0.008%), neg=0, invalid=762 0356: dt=0.112000, rms=0.480 (0.001%), neg=0, invalid=762 0357: dt=0.000000, rms=0.480 (-0.001%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) ********************* ALLOWING NEGATIVE NODES IN DEFORMATION******************************** **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.478, neg=0, invalid=762 0358: dt=0.000000, rms=0.478 (0.100%), neg=0, invalid=762 0359: dt=0.000000, rms=0.478 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.478, neg=0, invalid=762 0360: dt=92.480000, rms=0.478 (0.120%), neg=0, invalid=762 0361: dt=443.904000, rms=0.477 (0.074%), neg=0, invalid=762 0362: dt=443.904000, rms=0.477 (-0.502%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.478, neg=0, invalid=762 0363: dt=31.104000, rms=0.477 (0.153%), neg=0, invalid=762 0364: dt=62.208000, rms=0.477 (0.085%), neg=0, invalid=762 0365: dt=62.208000, rms=0.476 (0.134%), neg=0, invalid=762 0366: dt=62.208000, rms=0.476 (0.126%), neg=0, invalid=762 0367: dt=62.208000, rms=0.475 (0.037%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 0368: dt=62.208000, rms=0.475 (-0.032%), neg=0, invalid=762 0369: dt=414.720000, rms=0.474 (0.366%), neg=0, invalid=762 0370: dt=31.104000, rms=0.473 (0.035%), neg=0, invalid=762 0371: dt=31.104000, rms=0.473 (0.006%), neg=0, invalid=762 0372: dt=31.104000, rms=0.473 (-0.013%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.474, neg=0, invalid=762 0373: dt=103.680000, rms=0.472 (0.479%), neg=0, invalid=762 0374: dt=36.288000, rms=0.471 (0.139%), neg=0, invalid=762 0375: dt=36.288000, rms=0.471 (0.049%), neg=0, invalid=762 0376: dt=36.288000, rms=0.470 (0.068%), neg=0, invalid=762 0377: dt=36.288000, rms=0.470 (0.090%), neg=0, invalid=762 0378: dt=36.288000, rms=0.470 (0.111%), neg=0, invalid=762 0379: dt=36.288000, rms=0.469 (0.110%), neg=0, invalid=762 0380: dt=36.288000, rms=0.469 (0.096%), neg=0, invalid=762 0381: dt=124.416000, rms=0.468 (0.021%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.469, neg=0, invalid=762 0382: dt=38.400000, rms=0.467 (0.558%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 8 iterations, nbhd size=1, neg = 0 0383: dt=84.980716, rms=0.462 (1.045%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0384: dt=11.200000, rms=0.461 (0.239%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0385: dt=11.200000, rms=0.461 (0.074%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 0386: dt=11.200000, rms=0.460 (0.030%), neg=0, invalid=762 0387: dt=11.200000, rms=0.460 (0.056%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 2 iterations, nbhd size=0, neg = 0 0388: dt=11.200000, rms=0.459 (0.176%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 13 iterations, nbhd size=1, neg = 0 0389: dt=11.200000, rms=0.458 (0.285%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 7 iterations, nbhd size=1, neg = 0 0390: dt=11.200000, rms=0.457 (0.281%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 2 iterations, nbhd size=0, neg = 0 0391: dt=11.200000, rms=0.456 (0.223%), neg=0, invalid=762 iter 0, gcam->neg = 12 after 9 iterations, nbhd size=1, neg = 0 0392: dt=11.200000, rms=0.455 (0.160%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 2 iterations, nbhd size=0, neg = 0 0393: dt=11.200000, rms=0.455 (0.095%), neg=0, invalid=762 iter 0, gcam->neg = 18 after 12 iterations, nbhd size=1, neg = 0 0394: dt=11.200000, rms=0.454 (0.039%), neg=0, invalid=762 0395: dt=32.000000, rms=0.454 (0.062%), neg=0, invalid=762 0396: dt=11.200000, rms=0.454 (0.010%), neg=0, invalid=762 0397: dt=11.200000, rms=0.454 (0.010%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0398: dt=11.200000, rms=0.454 (0.022%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0399: dt=11.200000, rms=0.454 (0.025%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 0400: dt=11.200000, rms=0.454 (0.037%), neg=0, invalid=762 0401: dt=11.200000, rms=0.453 (0.042%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0402: dt=11.200000, rms=0.453 (0.046%), neg=0, invalid=762 0403: dt=11.200000, rms=0.453 (0.049%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 9 iterations, nbhd size=1, neg = 0 0404: dt=11.200000, rms=0.453 (0.044%), neg=0, invalid=762 0405: dt=11.200000, rms=0.453 (0.048%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0406: dt=11.200000, rms=0.452 (0.051%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0407: dt=11.200000, rms=0.452 (0.052%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 1 iterations, nbhd size=0, neg = 0 0408: dt=11.200000, rms=0.452 (0.062%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 10 iterations, nbhd size=1, neg = 0 0409: dt=11.200000, rms=0.452 (0.054%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.452, neg=0, invalid=762 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 0410: dt=67.781818, rms=0.448 (0.825%), neg=0, invalid=762 0411: dt=11.200000, rms=0.448 (0.168%), neg=0, invalid=762 0412: dt=11.200000, rms=0.447 (0.066%), neg=0, invalid=762 0413: dt=11.200000, rms=0.447 (0.057%), neg=0, invalid=762 0414: dt=11.200000, rms=0.447 (0.035%), neg=0, invalid=762 0415: dt=44.800000, rms=0.446 (0.198%), neg=0, invalid=762 0416: dt=11.200000, rms=0.446 (0.019%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.453, neg=0, invalid=762 0417: dt=1.008000, rms=0.453 (0.122%), neg=0, invalid=762 0418: dt=1.008000, rms=0.453 (0.009%), neg=0, invalid=762 0419: dt=1.008000, rms=0.453 (-0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.453, neg=0, invalid=762 0420: dt=4.941176, rms=0.452 (0.191%), neg=0, invalid=762 0421: dt=4.400000, rms=0.452 (0.033%), neg=0, invalid=762 0422: dt=4.400000, rms=0.452 (0.023%), neg=0, invalid=762 0423: dt=4.400000, rms=0.452 (-0.031%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.461, neg=0, invalid=762 0424: dt=0.000000, rms=0.461 (0.104%), neg=0, invalid=762 0425: dt=0.000000, rms=0.461 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.461, neg=0, invalid=762 0426: dt=0.768000, rms=0.460 (0.162%), neg=0, invalid=762 0427: dt=0.448000, rms=0.460 (0.023%), neg=0, invalid=762 0428: dt=0.448000, rms=0.460 (0.009%), neg=0, invalid=762 0429: dt=0.448000, rms=0.460 (-0.013%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.450, neg=0, invalid=762 iter 0, gcam->neg = 753 after 16 iterations, nbhd size=1, neg = 0 0430: dt=1.960417, rms=0.426 (5.215%), neg=0, invalid=762 0431: dt=0.064000, rms=0.426 (0.025%), neg=0, invalid=762 0432: dt=0.064000, rms=0.426 (-0.036%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.427, neg=0, invalid=762 0433: dt=0.028000, rms=0.426 (0.143%), neg=0, invalid=762 0434: dt=0.024000, rms=0.426 (0.003%), neg=0, invalid=762 0435: dt=0.024000, rms=0.426 (-0.004%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.415, neg=0, invalid=762 0436: dt=0.000000, rms=0.415 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.415, neg=0, invalid=762 0437: dt=0.000000, rms=0.415 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.415, neg=0, invalid=762 0438: dt=0.000000, rms=0.415 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.415, neg=0, invalid=762 0439: dt=36.288000, rms=0.415 (0.041%), neg=0, invalid=762 0440: dt=103.680000, rms=0.415 (0.044%), neg=0, invalid=762 0441: dt=145.152000, rms=0.414 (0.089%), neg=0, invalid=762 0442: dt=25.920000, rms=0.414 (0.003%), neg=0, invalid=762 0443: dt=25.920000, rms=0.414 (0.003%), neg=0, invalid=762 0444: dt=25.920000, rms=0.414 (0.005%), neg=0, invalid=762 0445: dt=25.920000, rms=0.414 (0.009%), neg=0, invalid=762 0446: dt=25.920000, rms=0.414 (0.014%), neg=0, invalid=762 0447: dt=25.920000, rms=0.414 (0.019%), neg=0, invalid=762 0448: dt=25.920000, rms=0.414 (0.019%), neg=0, invalid=762 0449: dt=25.920000, rms=0.414 (0.015%), neg=0, invalid=762 0450: dt=25.920000, rms=0.414 (0.010%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.414, neg=0, invalid=762 0451: dt=11.200000, rms=0.414 (0.069%), neg=0, invalid=762 0452: dt=11.200000, rms=0.414 (0.042%), neg=0, invalid=762 0453: dt=11.200000, rms=0.414 (0.034%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 9 iterations, nbhd size=1, neg = 0 0454: dt=11.200000, rms=0.414 (0.008%), neg=0, invalid=762 iter 0, gcam->neg = 17 after 9 iterations, nbhd size=1, neg = 0 0455: dt=11.200000, rms=0.414 (-0.074%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.414, neg=0, invalid=762 iter 0, gcam->neg = 6 after 8 iterations, nbhd size=1, neg = 0 0456: dt=44.800000, rms=0.411 (0.633%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0457: dt=23.272727, rms=0.411 (0.126%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0458: dt=23.272727, rms=0.410 (0.125%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 11 iterations, nbhd size=1, neg = 0 0459: dt=23.272727, rms=0.410 (0.126%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 1 iterations, nbhd size=0, neg = 0 0460: dt=23.272727, rms=0.409 (0.170%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 1 iterations, nbhd size=0, neg = 0 0461: dt=23.272727, rms=0.408 (0.162%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 5 iterations, nbhd size=0, neg = 0 0462: dt=23.272727, rms=0.407 (0.179%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 9 iterations, nbhd size=1, neg = 0 0463: dt=23.272727, rms=0.407 (0.126%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 4 iterations, nbhd size=0, neg = 0 0464: dt=23.272727, rms=0.406 (0.106%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 0 iterations, nbhd size=0, neg = 0 0465: dt=23.272727, rms=0.406 (0.083%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0466: dt=44.800000, rms=0.406 (0.049%), neg=0, invalid=762 0467: dt=44.800000, rms=0.406 (-0.121%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.410, neg=0, invalid=762 0468: dt=3.456000, rms=0.409 (0.053%), neg=0, invalid=762 0469: dt=1.008000, rms=0.409 (0.004%), neg=0, invalid=762 0470: dt=1.008000, rms=0.409 (0.000%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 0471: dt=1.008000, rms=0.409 (-0.010%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.409, neg=0, invalid=762 0472: dt=8.989691, rms=0.409 (0.113%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 8 iterations, nbhd size=1, neg = 0 0473: dt=17.250000, rms=0.408 (0.132%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 2 iterations, nbhd size=0, neg = 0 0474: dt=25.142857, rms=0.408 (0.120%), neg=0, invalid=762 iter 0, gcam->neg = 69 after 12 iterations, nbhd size=1, neg = 0 0475: dt=25.142857, rms=0.408 (-0.161%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.413, neg=0, invalid=762 0476: dt=0.000060, rms=0.413 (0.000%), neg=0, invalid=762 0477: dt=0.000000, rms=0.413 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.413, neg=0, invalid=762 0478: dt=0.000000, rms=0.413 (0.000%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.404, neg=0, invalid=762 iter 0, gcam->neg = 186 after 11 iterations, nbhd size=1, neg = 0 0479: dt=0.933839, rms=0.399 (1.385%), neg=0, invalid=762 0480: dt=0.112000, rms=0.399 (0.042%), neg=0, invalid=762 0481: dt=0.112000, rms=0.398 (0.029%), neg=0, invalid=762 0482: dt=0.112000, rms=0.398 (-0.010%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.398, neg=0, invalid=762 0483: dt=0.448000, rms=0.397 (0.480%), neg=0, invalid=762 0484: dt=0.384000, rms=0.396 (0.107%), neg=0, invalid=762 0485: dt=0.384000, rms=0.396 (0.093%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0486: dt=0.384000, rms=0.395 (0.074%), neg=0, invalid=762 iter 0, gcam->neg = 11 after 2 iterations, nbhd size=0, neg = 0 0487: dt=0.384000, rms=0.395 (0.039%), neg=0, invalid=762 0488: dt=0.192000, rms=0.395 (0.046%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 3 iterations, nbhd size=0, neg = 0 0489: dt=0.448000, rms=0.395 (0.063%), neg=0, invalid=762 0490: dt=0.000013, rms=0.395 (0.000%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 1 hours, 20 minutes and 10 seconds. mri_ca_register utimesec 5885.113456 mri_ca_register stimesec 6.071282 mri_ca_register ru_maxrss 1338588 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 4838579 mri_ca_register ru_majflt 10 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 1952 mri_ca_register ru_oublock 0 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 10600 mri_ca_register ru_nivcsw 11177 FSRUNTIME@ mri_ca_register 1.3362 hours 3 threads #-------------------------------------- #@# SubCort Seg Thu Sep 2 09:38:31 UTC 2021 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz sysname Linux hostname 9e1e1df09144 machine x86_64 setenv SUBJECTS_DIR /out/freesurfer cd /out/freesurfer/sub-M1215054/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz == Number of threads available to mri_ca_label for OpenMP = 3 == relabeling unlikely voxels with window_size = 9 and prior threshold 0.30 using Gibbs prior factor = 0.500 renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes reading classifier array from /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca reading input volume from norm.mgz average std[0] = 7.3 reading transform from transforms/talairach.m3z setting orig areas to linear transform determinant scaled 6.81 Atlas used for the 3D morph was /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca average std = 7.3 using min determinant for regularization = 5.3 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.16259 (20) mri peak = 0.14417 (25) Left_Lateral_Ventricle (4): linear fit = 1.20 x + 0.0 (1538 voxels, overlap=0.718) Left_Lateral_Ventricle (4): linear fit = 1.20 x + 0.0 (1538 voxels, peak = 24), gca=23.9 gca peak = 0.17677 (13) mri peak = 0.16150 (25) Right_Lateral_Ventricle (43): linear fit = 1.73 x + 0.0 (1240 voxels, overlap=0.322) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (1240 voxels, peak = 22), gca=19.5 gca peak = 0.28129 (95) mri peak = 0.16118 (95) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (850 voxels, overlap=1.006) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (850 voxels, peak = 94), gca=93.6 gca peak = 0.16930 (96) mri peak = 0.14500 (96) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (763 voxels, overlap=0.978) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (763 voxels, peak = 97), gca=97.4 gca peak = 0.24553 (55) mri peak = 0.09758 (68) Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (1359 voxels, overlap=0.062) Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (1359 voxels, peak = 64), gca=63.5 gca peak = 0.30264 (59) mri peak = 0.11364 (69) Left_Hippocampus (17): linear fit = 1.14 x + 0.0 (1319 voxels, overlap=0.018) Left_Hippocampus (17): linear fit = 1.14 x + 0.0 (1319 voxels, peak = 68), gca=67.6 gca peak = 0.07580 (103) mri peak = 0.18362 (104) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (50441 voxels, overlap=0.595) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (50441 voxels, peak = 104), gca=103.5 gca peak = 0.07714 (104) mri peak = 0.15187 (105) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (51523 voxels, overlap=0.566) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (51523 voxels, peak = 105), gca=104.5 gca peak = 0.09712 (58) mri peak = 0.04131 (66) Left_Cerebral_Cortex (3): linear fit = 1.15 x + 0.0 (44830 voxels, overlap=0.447) Left_Cerebral_Cortex (3): linear fit = 1.15 x + 0.0 (44830 voxels, peak = 67), gca=67.0 gca peak = 0.11620 (58) mri peak = 0.04108 (68) Right_Cerebral_Cortex (42): linear fit = 1.14 x + 0.0 (41328 voxels, overlap=0.548) Right_Cerebral_Cortex (42): linear fit = 1.14 x + 0.0 (41328 voxels, peak = 66), gca=66.4 gca peak = 0.30970 (66) mri peak = 0.11948 (80) Right_Caudate (50): linear fit = 1.17 x + 0.0 (1155 voxels, overlap=0.016) Right_Caudate (50): linear fit = 1.17 x + 0.0 (1155 voxels, peak = 78), gca=77.5 gca peak = 0.15280 (69) mri peak = 0.13063 (79) Left_Caudate (11): linear fit = 1.05 x + 0.0 (1332 voxels, overlap=0.503) Left_Caudate (11): linear fit = 1.05 x + 0.0 (1332 voxels, peak = 73), gca=72.8 gca peak = 0.13902 (56) mri peak = 0.06285 (68) Left_Cerebellum_Cortex (8): linear fit = 1.21 x + 0.0 (28176 voxels, overlap=0.220) Left_Cerebellum_Cortex (8): linear fit = 1.21 x + 0.0 (28176 voxels, peak = 67), gca=67.5 gca peak = 0.14777 (55) mri peak = 0.06280 (66) Right_Cerebellum_Cortex (47): linear fit = 1.17 x + 0.0 (28995 voxels, overlap=0.439) Right_Cerebellum_Cortex (47): linear fit = 1.17 x + 0.0 (28995 voxels, peak = 65), gca=64.6 gca peak = 0.16765 (84) mri peak = 0.12040 (87) Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (7064 voxels, overlap=0.810) Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (7064 voxels, peak = 87), gca=86.9 gca peak = 0.18739 (84) mri peak = 0.13367 (86) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (6316 voxels, overlap=0.742) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (6316 voxels, peak = 87), gca=86.9 gca peak = 0.29869 (57) mri peak = 0.12542 (70) Left_Amygdala (18): linear fit = 1.22 x + 0.0 (589 voxels, overlap=0.057) Left_Amygdala (18): linear fit = 1.22 x + 0.0 (589 voxels, peak = 69), gca=69.3 gca peak = 0.33601 (57) mri peak = 0.11614 (70) Right_Amygdala (54): linear fit = 1.18 x + 0.0 (661 voxels, overlap=0.046) Right_Amygdala (54): linear fit = 1.18 x + 0.0 (661 voxels, peak = 68), gca=67.5 gca peak = 0.11131 (90) mri peak = 0.07549 (92) Left_Thalamus_Proper (10): linear fit = 1.04 x + 0.0 (4671 voxels, overlap=0.834) Left_Thalamus_Proper (10): linear fit = 1.04 x + 0.0 (4671 voxels, peak = 94), gca=94.0 gca peak = 0.11793 (83) mri peak = 0.08499 (89) Right_Thalamus_Proper (49): linear fit = 1.09 x + 0.0 (4528 voxels, overlap=0.820) Right_Thalamus_Proper (49): linear fit = 1.09 x + 0.0 (4528 voxels, peak = 90), gca=90.1 gca peak = 0.08324 (81) mri peak = 0.10974 (87) Left_Putamen (12): linear fit = 1.08 x + 0.0 (2183 voxels, overlap=0.632) Left_Putamen (12): linear fit = 1.08 x + 0.0 (2183 voxels, peak = 87), gca=87.1 gca peak = 0.10360 (77) mri peak = 0.08145 (82) Right_Putamen (51): linear fit = 1.07 x + 0.0 (2170 voxels, overlap=0.750) Right_Putamen (51): linear fit = 1.07 x + 0.0 (2170 voxels, peak = 82), gca=82.0 gca peak = 0.08424 (78) mri peak = 0.11250 (85) Brain_Stem (16): linear fit = 1.04 x + 0.0 (12606 voxels, overlap=0.476) Brain_Stem (16): linear fit = 1.04 x + 0.0 (12606 voxels, peak = 82), gca=81.5 gca peak = 0.12631 (89) mri peak = 0.09733 (93) Right_VentralDC (60): linear fit = 1.05 x + 0.0 (1644 voxels, overlap=0.737) Right_VentralDC (60): linear fit = 1.05 x + 0.0 (1644 voxels, peak = 94), gca=93.9 gca peak = 0.14500 (87) mri peak = 0.09033 (92) Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1703 voxels, overlap=0.723) Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1703 voxels, peak = 93), gca=92.7 gca peak = 0.14975 (24) mri peak = 0.11655 (22) gca peak = 0.19357 (14) mri peak = 0.17462 (23) Fourth_Ventricle (15): linear fit = 1.47 x + 0.0 (364 voxels, overlap=0.316) Fourth_Ventricle (15): linear fit = 1.47 x + 0.0 (364 voxels, peak = 21), gca=20.5 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 1.00000 (94) gca peak Third_Ventricle = 0.14975 (24) gca peak CSF = 0.23379 (36) gca peak Left_Accumbens_area = 0.70037 (62) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.24655 (23) gca peak Right_Accumbens_area = 0.45042 (65) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.65475 (32) gca peak WM_hypointensities = 0.07854 (76) gca peak non_WM_hypointensities = 0.08491 (43) gca peak Optic_Chiasm = 0.71127 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.17 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.39 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15914 (22) mri peak = 0.14417 (25) Left_Lateral_Ventricle (4): linear fit = 1.01 x + 0.0 (1538 voxels, overlap=0.822) Left_Lateral_Ventricle (4): linear fit = 1.01 x + 0.0 (1538 voxels, peak = 22), gca=22.3 gca peak = 0.13759 (19) mri peak = 0.16150 (25) Right_Lateral_Ventricle (43): linear fit = 1.13 x + 0.0 (1240 voxels, overlap=0.624) Right_Lateral_Ventricle (43): linear fit = 1.13 x + 0.0 (1240 voxels, peak = 22), gca=21.6 gca peak = 0.23216 (93) mri peak = 0.16118 (95) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (850 voxels, overlap=1.002) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (850 voxels, peak = 94), gca=94.4 gca peak = 0.16287 (96) mri peak = 0.14500 (96) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (763 voxels, overlap=0.999) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (763 voxels, peak = 96), gca=95.5 gca peak = 0.24791 (64) mri peak = 0.09758 (68) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1359 voxels, overlap=1.003) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1359 voxels, peak = 64), gca=64.0 gca peak = 0.22429 (64) mri peak = 0.11364 (69) Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (1319 voxels, overlap=1.004) Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (1319 voxels, peak = 66), gca=65.6 gca peak = 0.07875 (103) mri peak = 0.18362 (104) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (50441 voxels, overlap=0.616) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (50441 voxels, peak = 103), gca=103.0 gca peak = 0.07908 (105) mri peak = 0.15187 (105) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (51523 voxels, overlap=0.589) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (51523 voxels, peak = 105), gca=105.0 gca peak = 0.08515 (67) mri peak = 0.04131 (66) Left_Cerebral_Cortex (3): linear fit = 1.03 x + 0.0 (44830 voxels, overlap=0.960) Left_Cerebral_Cortex (3): linear fit = 1.03 x + 0.0 (44830 voxels, peak = 69), gca=69.3 gca peak = 0.10296 (66) mri peak = 0.04108 (68) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (41328 voxels, overlap=0.962) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (41328 voxels, peak = 66), gca=66.0 gca peak = 0.23088 (78) mri peak = 0.11948 (80) Right_Caudate (50): linear fit = 0.99 x + 0.0 (1155 voxels, overlap=1.000) Right_Caudate (50): linear fit = 0.99 x + 0.0 (1155 voxels, peak = 77), gca=76.8 gca peak = 0.15187 (72) mri peak = 0.13063 (79) Left_Caudate (11): linear fit = 0.99 x + 0.0 (1332 voxels, overlap=0.745) Left_Caudate (11): linear fit = 0.99 x + 0.0 (1332 voxels, peak = 71), gca=70.9 gca peak = 0.11916 (67) mri peak = 0.06285 (68) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (28176 voxels, overlap=0.986) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (28176 voxels, peak = 66), gca=66.0 gca peak = 0.12940 (64) mri peak = 0.06280 (66) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (28995 voxels, overlap=0.986) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (28995 voxels, peak = 64), gca=64.0 gca peak = 0.15906 (87) mri peak = 0.12040 (87) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (7064 voxels, overlap=0.926) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (7064 voxels, peak = 87), gca=86.6 gca peak = 0.18394 (87) mri peak = 0.13367 (86) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6316 voxels, overlap=0.889) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6316 voxels, peak = 87), gca=87.0 gca peak = 0.28068 (69) mri peak = 0.12542 (70) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (589 voxels, overlap=1.012) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (589 voxels, peak = 69), gca=69.0 gca peak = 0.29910 (68) mri peak = 0.11614 (70) Right_Amygdala (54): linear fit = 1.01 x + 0.0 (661 voxels, overlap=1.003) Right_Amygdala (54): linear fit = 1.01 x + 0.0 (661 voxels, peak = 69), gca=69.0 gca peak = 0.11190 (94) mri peak = 0.07549 (92) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4671 voxels, overlap=0.957) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4671 voxels, peak = 94), gca=93.5 gca peak = 0.10362 (90) mri peak = 0.08499 (89) Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (4528 voxels, overlap=0.932) Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (4528 voxels, peak = 89), gca=88.7 gca peak = 0.07860 (81) mri peak = 0.10974 (87) Left_Putamen (12): linear fit = 1.01 x + 0.0 (2183 voxels, overlap=0.861) Left_Putamen (12): linear fit = 1.01 x + 0.0 (2183 voxels, peak = 82), gca=82.2 gca peak = 0.09474 (82) mri peak = 0.08145 (82) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2170 voxels, overlap=0.941) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2170 voxels, peak = 82), gca=82.0 gca peak = 0.08474 (82) mri peak = 0.11250 (85) Brain_Stem (16): linear fit = 1.01 x + 0.0 (12606 voxels, overlap=0.677) Brain_Stem (16): linear fit = 1.01 x + 0.0 (12606 voxels, peak = 83), gca=83.2 gca peak = 0.13382 (94) mri peak = 0.09733 (93) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1644 voxels, overlap=0.827) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1644 voxels, peak = 94), gca=93.5 gca peak = 0.14383 (91) mri peak = 0.09033 (92) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1703 voxels, overlap=0.890) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1703 voxels, peak = 90), gca=89.6 gca peak = 0.12947 (35) mri peak = 0.11655 (22) gca peak = 0.14735 (22) mri peak = 0.17462 (23) Fourth_Ventricle (15): linear fit = 1.01 x + 0.0 (364 voxels, overlap=0.733) Fourth_Ventricle (15): linear fit = 1.01 x + 0.0 (364 voxels, peak = 22), gca=22.3 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16611 (31) gca peak Left_Thalamus = 0.36646 (102) gca peak Third_Ventricle = 0.12947 (35) gca peak CSF = 0.15453 (51) gca peak Left_Accumbens_area = 0.58310 (66) gca peak Left_undetermined = 0.98573 (27) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.11914 (35) gca peak Right_Inf_Lat_Vent = 0.18678 (27) gca peak Right_Accumbens_area = 0.29771 (76) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14506 (37) gca peak Fifth_Ventricle = 0.75707 (43) gca peak WM_hypointensities = 0.08019 (76) gca peak non_WM_hypointensities = 0.07977 (77) gca peak Optic_Chiasm = 0.70889 (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 49986 voxels changed in iteration 0 of unlikely voxel relabeling 367 voxels changed in iteration 1 of unlikely voxel relabeling 27 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 55175 gm and wm labels changed (%31 to gray, %69 to white out of all changed labels) 441 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 59116 changed. image ll: -2.089, PF=0.500 pass 2: 15356 changed. image ll: -2.088, PF=0.500 pass 3: 5052 changed. pass 4: 1880 changed. 42230 voxels changed in iteration 0 of unlikely voxel relabeling 303 voxels changed in iteration 1 of unlikely voxel relabeling 8 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 7774 voxels changed in iteration 0 of unlikely voxel relabeling 176 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 6692 voxels changed in iteration 0 of unlikely voxel relabeling 85 voxels changed in iteration 1 of unlikely voxel relabeling 2 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 6339 voxels changed in iteration 0 of unlikely voxel relabeling 47 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 MRItoUCHAR: min=0, max=85 MRItoUCHAR: converting to UCHAR writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 1899.982794 mri_ca_label stimesec 3.630750 mri_ca_label ru_maxrss 2114856 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 755177 mri_ca_label ru_majflt 8 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 1616 mri_ca_label ru_oublock 0 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 4641 mri_ca_label ru_nivcsw 3301 auto-labeling took 31 minutes and 7 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /out/freesurfer/sub-M1215054/mri/transforms/cc_up.lta sub-M1215054 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /out/freesurfer/sub-M1215054/mri/transforms/cc_up.lta reading aseg from /out/freesurfer/sub-M1215054/mri/aseg.auto_noCCseg.mgz reading norm from /out/freesurfer/sub-M1215054/mri/norm.mgz 72734 voxels in left wm, 50222 in right wm, xrange [127, 139] searching rotation angles z=[-6 8], y=[-4 10] searching scale 1 Z rot -6.0 searching scale 1 Z rot -5.8 searching scale 1 Z rot -5.5 searching scale 1 Z rot -5.3 searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.8 searching scale 1 Z rot -4.5 searching scale 1 Z rot -4.3 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.8 searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.3 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.8 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.3 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.8 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.3 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.8 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.3 searching scale 1 Z rot -0.0 searching scale 1 Z rot 0.2 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.7 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.2 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.7 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.2 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.7 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.2 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.7 searching scale 1 Z rot 4.0 searching scale 1 Z rot 4.2 searching scale 1 Z rot 4.5 searching scale 1 Z rot 4.7 searching scale 1 Z rot 5.0 searching scale 1 Z rot 5.2 searching scale 1 Z rot 5.5 searching scale 1 Z rot 5.7 searching scale 1 Z rot 6.0 searching scale 1 Z rot 6.2 searching scale 1 Z rot 6.5 searching scale 1 Z rot 6.7 searching scale 1 Z rot 7.0 searching scale 1 Z rot 7.2 searching scale 1 Z rot 7.5 searching scale 1 Z rot 7.7 global minimum found at slice 131.7, rotations (2.63, 1.00) final transformation (x=131.7, yr=2.630, zr=1.000): 0.99879 -0.01745 0.04588 -6.74221; 0.01743 0.99985 0.00080 8.63114; -0.04589 -0.00000 0.99895 19.16309; 0.00000 0.00000 0.00000 1.00000; updating x range to be [125, 129] in xformed coordinates best xformed slice 126 cc center is found at 126 117 115 eigenvectors: 0.00142 -0.00068 1.00000; 0.03694 -0.99932 -0.00074; 0.99932 0.03694 -0.00140; writing aseg with callosum to /out/freesurfer/sub-M1215054/mri/aseg.auto.mgz... corpus callosum segmentation took 0.7 minutes #-------------------------------------- #@# Merge ASeg Thu Sep 2 10:10:22 UTC 2021 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Thu Sep 2 10:10:22 UTC 2021 /out/freesurfer/sub-M1215054/mri mri_normalize -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz assuming input volume is MGH (Van der Kouwe) MP-RAGE using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... INFO: MRImask() using MRImaskDifferentGeometry() Reading aseg aseg.presurf.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 737 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 76 (76), valley at 0 (-1) csf peak at 38, setting threshold to 63 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 74 (74), valley at 0 (-1) csf peak at 37, setting threshold to 61 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 1 minutes and 51 seconds. #-------------------------------------------- #@# Mask BFS Thu Sep 2 10:12:17 UTC 2021 /out/freesurfer/sub-M1215054/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1453777 voxels in mask (pct= 8.67) INFO: MRImask() using MRImaskDifferentGeometry() Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Thu Sep 2 10:12:21 UTC 2021 mri_segment -mprage brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (102.0): 101.1 +- 7.0 [79.0 --> 125.0] GM (74.0) : 73.2 +- 8.4 [30.0 --> 95.0] setting bottom of white matter range to 81.5 setting top of gray matter range to 89.9 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... 2755 sparsely connected voxels removed... thickening thin strands.... 20 segments, 2764 filled 689 bright non-wm voxels segmented. 1832 diagonally connected voxels added... white matter segmentation took 1.0 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 0.28 minutes reading wm segmentation from wm.seg.mgz... 130 voxels added to wm to prevent paths from MTL structures to cortex 2582 additional wm voxels added 0 additional wm voxels added SEG EDIT: 38170 voxels turned on, 51862 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 110 new 110 115,126,128 old 110 new 110 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 12 found - 12 modified | TOTAL: 12 pass 2 (xy+): 0 found - 12 modified | TOTAL: 12 pass 1 (xy-): 8 found - 8 modified | TOTAL: 20 pass 2 (xy-): 0 found - 8 modified | TOTAL: 20 pass 1 (yz+): 19 found - 19 modified | TOTAL: 39 pass 2 (yz+): 0 found - 19 modified | TOTAL: 39 pass 1 (yz-): 12 found - 12 modified | TOTAL: 51 pass 2 (yz-): 0 found - 12 modified | TOTAL: 51 pass 1 (xz+): 6 found - 6 modified | TOTAL: 57 pass 2 (xz+): 0 found - 6 modified | TOTAL: 57 pass 1 (xz-): 13 found - 13 modified | TOTAL: 70 pass 2 (xz-): 0 found - 13 modified | TOTAL: 70 Iteration Number : 1 pass 1 (+++): 21 found - 21 modified | TOTAL: 21 pass 2 (+++): 0 found - 21 modified | TOTAL: 21 pass 1 (+++): 18 found - 18 modified | TOTAL: 39 pass 2 (+++): 0 found - 18 modified | TOTAL: 39 pass 1 (+++): 16 found - 16 modified | TOTAL: 55 pass 2 (+++): 0 found - 16 modified | TOTAL: 55 pass 1 (+++): 21 found - 21 modified | TOTAL: 76 pass 2 (+++): 0 found - 21 modified | TOTAL: 76 Iteration Number : 1 pass 1 (++): 51 found - 51 modified | TOTAL: 51 pass 2 (++): 0 found - 51 modified | TOTAL: 51 pass 1 (+-): 20 found - 20 modified | TOTAL: 71 pass 2 (+-): 0 found - 20 modified | TOTAL: 71 pass 1 (--): 37 found - 37 modified | TOTAL: 108 pass 2 (--): 0 found - 37 modified | TOTAL: 108 pass 1 (-+): 48 found - 48 modified | TOTAL: 156 pass 2 (-+): 0 found - 48 modified | TOTAL: 156 Iteration Number : 2 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 2 found - 2 modified | TOTAL: 4 pass 2 (xy-): 0 found - 2 modified | TOTAL: 4 pass 1 (yz+): 4 found - 4 modified | TOTAL: 8 pass 2 (yz+): 0 found - 4 modified | TOTAL: 8 pass 1 (yz-): 3 found - 3 modified | TOTAL: 11 pass 2 (yz-): 0 found - 3 modified | TOTAL: 11 pass 1 (xz+): 4 found - 4 modified | TOTAL: 15 pass 2 (xz+): 0 found - 4 modified | TOTAL: 15 pass 1 (xz-): 3 found - 3 modified | TOTAL: 18 pass 2 (xz-): 0 found - 3 modified | TOTAL: 18 Iteration Number : 2 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 : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 3 found - 3 modified | TOTAL: 3 pass 2 (+-): 0 found - 3 modified | TOTAL: 3 pass 1 (--): 0 found - 0 modified | TOTAL: 3 pass 1 (-+): 3 found - 3 modified | TOTAL: 6 pass 2 (-+): 0 found - 3 modified | TOTAL: 6 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-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 3 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 (+++): 1 found - 1 modified | TOTAL: 3 pass 2 (+++): 0 found - 1 modified | TOTAL: 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 3 Iteration Number : 3 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 333 (out of 637950: 0.052198) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Thu Sep 2 10:13:41 UTC 2021 /out/freesurfer/sub-M1215054/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 1.08084 -0.03070 0.01239 -12.82388; 0.02586 1.12078 0.12127 -44.66101; -0.01729 -0.13573 0.95397 18.48688; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.08084 -0.03070 0.01239 -12.82388; 0.02586 1.12078 0.12127 -44.66101; -0.01729 -0.13573 0.95397 18.48688; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1330 (min = 350, max = 1400), aspect = 0.49 (min = 0.10, max = 0.75) no need to search using seed (124, 118, 148), TAL = (4.0, 20.0, 10.0) talairach voxel to voxel transform 0.92441 0.02351 -0.01499 13.18156; -0.02279 0.87813 -0.11133 40.98401; 0.01352 0.12537 1.03214 -13.30859; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (124, 118, 148) --> (4.0, 20.0, 10.0) done. writing output to filled.mgz... filling took 0.4 minutes talairach cc position changed to (4.00, 20.00, 10.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(22.00, 20.00, 10.00) SRC: (111.72, 125.71, 155.67) search lh wm seed point around talairach space (-14.00, 20.00, 10.00), SRC: (145.00, 124.89, 156.16) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... Started at Thu Sep 2 08:11:49 UTC 2021 Ended at Thu Sep 2 10:14:05 UTC 2021 #@#%# recon-all-run-time-hours 2.038 recon-all -s sub-M1215054 finished without error at Thu Sep 2 10:14:06 UTC 2021 New invocation of recon-all Thu Sep 2 13:09:20 UTC 2021 /out/freesurfer/sub-M1215054 /opt/freesurfer/bin/recon-all -parallel -subjid sub-M1215054 -sd /out/freesurfer -cortribbon subjid sub-M1215054 setenv SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /opt/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a Linux 9e1e1df09144 5.4.72-microsoft-standard-WSL2 #1 SMP Wed Oct 28 23:40:43 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1048576 memorylocked 82000 kbytes maxproc unlimited maxlocks unlimited maxsignal 23036 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 5902064 1682424 2042884 189624 2176756 3713032 Swap: 2097152 332800 1764352 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:09:20-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:09:21-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:09:21-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-13:09:21-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:09:21-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:09:21-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-13:09:21-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-13:09:21-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-13:09:21-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-13:09:21-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-13:09:21-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-13:09:21-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:09:21-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:09:21-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-13:09:21-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:09:21-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:09:21-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:09:21-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:09:21-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:09:21-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:09:21-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-13:09:21-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:09:21-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:09:21-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:09:21-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-13:09:21-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:09:21-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-13:09:21-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:09:21-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:09:22-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:09:22-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:09:22-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:09:22-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:09:22-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:09:22-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:09:22-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:09:22-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:09:22-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:09:22-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /opt/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /opt/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #-------------------------------------------- #@# Cortical ribbon mask Thu Sep 2 13:09:22 UTC 2021 /out/freesurfer/sub-M1215054/mri mris_volmask --aseg_name aseg.presurf --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon sub-M1215054 SUBJECTS_DIR is /out/freesurfer loading input data... computing distance to left white surface computing distance to left pial surface computing distance to right white surface computing distance to right pial surface hemi masks overlap voxels = 90 writing volume /out/freesurfer/sub-M1215054/mri/ribbon.mgz mris_volmask took 10.92 minutes writing ribbon files Started at Thu Sep 2 13:09:20 UTC 2021 Ended at Thu Sep 2 13:20:17 UTC 2021 #@#%# recon-all-run-time-hours 0.183 recon-all -s sub-M1215054 finished without error at Thu Sep 2 13:20:17 UTC 2021 New invocation of recon-all Thu Sep 2 13:40:22 UTC 2021 /out/freesurfer/sub-M1215054 /opt/freesurfer/bin/recon-all -autorecon3 -openmp 3 -subjid sub-M1215054 -sd /out/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nocortribbon -nobalabels subjid sub-M1215054 setenv SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /opt/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a Linux 9e1e1df09144 5.4.72-microsoft-standard-WSL2 #1 SMP Wed Oct 28 23:40:43 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1048576 memorylocked 82000 kbytes maxproc unlimited maxlocks unlimited maxsignal 23036 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 5902064 1683672 2036168 189624 2182224 3711384 Swap: 2097152 332800 1764352 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:40:22-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:40:22-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:40:22-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-13:40:22-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:40:22-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:40:22-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-13:40:22-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-13:40:22-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-13:40:22-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-13:40:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-13:40:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-13:40:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:40:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:40:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-13:40:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:40:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:40:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:40:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:40:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:40:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:40:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-13:40:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:40:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:40:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:40:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-13:40:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:40:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/02-13:40:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:40:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:40:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:40:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:40:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:40:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:40:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:40:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:40:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:40:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:40:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/02-13:40:23-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: root Machine: 9e1e1df09144 Platform: Linux PlatformVersion: 5.4.72-microsoft-standard-WSL2 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /opt/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /opt/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #----------------------------------------- #@# Relabel Hypointensities Thu Sep 2 13:40:23 UTC 2021 /out/freesurfer/sub-M1215054/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 4504 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 3209 voxels changed to hypointensity... 7722 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg aparc Thu Sep 2 13:40:41 UTC 2021 /out/freesurfer/sub-M1215054 mri_aparc2aseg --s sub-M1215054 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /out/freesurfer subject sub-M1215054 outvol /out/freesurfer/sub-M1215054/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /out/freesurfer/sub-M1215054/surf/lh.white Reading lh pial surface /out/freesurfer/sub-M1215054/surf/lh.pial Loading lh annotations from /out/freesurfer/sub-M1215054/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading rh white surface /out/freesurfer/sub-M1215054/surf/rh.white Reading rh pial surface /out/freesurfer/sub-M1215054/surf/rh.pial Loading rh annotations from /out/freesurfer/sub-M1215054/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /out/freesurfer/sub-M1215054/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /out/freesurfer/sub-M1215054/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -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; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 6.81 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 105 rescaling Left_Cerebral_Cortex from 61 --> 69 rescaling Left_Lateral_Ventricle from 13 --> 22 rescaling Left_Inf_Lat_Vent from 34 --> 32 rescaling Left_Cerebellum_White_Matter from 86 --> 87 rescaling Left_Cerebellum_Cortex from 60 --> 66 rescaling Left_Thalamus from 94 --> 103 rescaling Left_Thalamus_Proper from 84 --> 94 rescaling Left_Caudate from 75 --> 71 rescaling Left_Putamen from 80 --> 82 rescaling Left_Pallidum from 98 --> 96 rescaling Third_Ventricle from 25 --> 37 rescaling Fourth_Ventricle from 22 --> 22 rescaling Brain_Stem from 81 --> 83 rescaling Left_Hippocampus from 57 --> 66 rescaling Left_Amygdala from 56 --> 69 rescaling CSF from 32 --> 54 rescaling Left_Accumbens_area from 62 --> 65 rescaling Left_VentralDC from 87 --> 90 rescaling Right_Cerebral_White_Matter from 105 --> 103 rescaling Right_Cerebral_Cortex from 58 --> 66 rescaling Right_Lateral_Ventricle from 13 --> 22 rescaling Right_Inf_Lat_Vent from 25 --> 27 rescaling Right_Cerebellum_White_Matter from 87 --> 87 rescaling Right_Cerebellum_Cortex from 59 --> 64 rescaling Right_Thalamus_Proper from 85 --> 89 rescaling Right_Caudate from 62 --> 77 rescaling Right_Putamen from 80 --> 82 rescaling Right_Pallidum from 97 --> 94 rescaling Right_Hippocampus from 53 --> 64 rescaling Right_Amygdala from 55 --> 69 rescaling Right_Accumbens_area from 65 --> 75 rescaling Right_VentralDC from 86 --> 94 rescaling Fifth_Ventricle from 40 --> 45 rescaling WM_hypointensities from 78 --> 76 rescaling non_WM_hypointensities from 40 --> 77 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 509971 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 95 changed. pass 2: 10 changed. pass 3: 3 changed. pass 4: 1 changed. pass 5: 0 changed. nchanged = 0 Writing output aseg to /out/freesurfer/sub-M1215054/mri/aparc+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg a2009s Thu Sep 2 13:44:49 UTC 2021 /out/freesurfer/sub-M1215054 mri_aparc2aseg --s sub-M1215054 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --a2009s relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /out/freesurfer subject sub-M1215054 outvol /out/freesurfer/sub-M1215054/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /out/freesurfer/sub-M1215054/surf/lh.white Reading lh pial surface /out/freesurfer/sub-M1215054/surf/lh.pial Loading lh annotations from /out/freesurfer/sub-M1215054/label/lh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Reading rh white surface /out/freesurfer/sub-M1215054/surf/rh.white Reading rh pial surface /out/freesurfer/sub-M1215054/surf/rh.pial Loading rh annotations from /out/freesurfer/sub-M1215054/label/rh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /out/freesurfer/sub-M1215054/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /out/freesurfer/sub-M1215054/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -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; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 6.81 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 105 rescaling Left_Cerebral_Cortex from 61 --> 69 rescaling Left_Lateral_Ventricle from 13 --> 22 rescaling Left_Inf_Lat_Vent from 34 --> 32 rescaling Left_Cerebellum_White_Matter from 86 --> 87 rescaling Left_Cerebellum_Cortex from 60 --> 66 rescaling Left_Thalamus from 94 --> 103 rescaling Left_Thalamus_Proper from 84 --> 94 rescaling Left_Caudate from 75 --> 71 rescaling Left_Putamen from 80 --> 82 rescaling Left_Pallidum from 98 --> 96 rescaling Third_Ventricle from 25 --> 37 rescaling Fourth_Ventricle from 22 --> 22 rescaling Brain_Stem from 81 --> 83 rescaling Left_Hippocampus from 57 --> 66 rescaling Left_Amygdala from 56 --> 69 rescaling CSF from 32 --> 54 rescaling Left_Accumbens_area from 62 --> 65 rescaling Left_VentralDC from 87 --> 90 rescaling Right_Cerebral_White_Matter from 105 --> 103 rescaling Right_Cerebral_Cortex from 58 --> 66 rescaling Right_Lateral_Ventricle from 13 --> 22 rescaling Right_Inf_Lat_Vent from 25 --> 27 rescaling Right_Cerebellum_White_Matter from 87 --> 87 rescaling Right_Cerebellum_Cortex from 59 --> 64 rescaling Right_Thalamus_Proper from 85 --> 89 rescaling Right_Caudate from 62 --> 77 rescaling Right_Putamen from 80 --> 82 rescaling Right_Pallidum from 97 --> 94 rescaling Right_Hippocampus from 53 --> 64 rescaling Right_Amygdala from 55 --> 69 rescaling Right_Accumbens_area from 65 --> 75 rescaling Right_VentralDC from 86 --> 94 rescaling Fifth_Ventricle from 40 --> 45 rescaling WM_hypointensities from 78 --> 76 rescaling non_WM_hypointensities from 40 --> 77 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 510025 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 95 changed. pass 2: 10 changed. pass 3: 3 changed. pass 4: 1 changed. pass 5: 0 changed. nchanged = 0 Writing output aseg to /out/freesurfer/sub-M1215054/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg DKTatlas Thu Sep 2 15:34:31 UTC 2021 /out/freesurfer/sub-M1215054 mri_aparc2aseg --s sub-M1215054 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --annot aparc.DKTatlas --o mri/aparc.DKTatlas+aseg.mgz relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /out/freesurfer subject sub-M1215054 outvol mri/aparc.DKTatlas+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /out/freesurfer/sub-M1215054/surf/lh.white Reading lh pial surface /out/freesurfer/sub-M1215054/surf/lh.pial Loading lh annotations from /out/freesurfer/sub-M1215054/label/lh.aparc.DKTatlas.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading rh white surface /out/freesurfer/sub-M1215054/surf/rh.white Reading rh pial surface /out/freesurfer/sub-M1215054/surf/rh.pial Loading rh annotations from /out/freesurfer/sub-M1215054/label/rh.aparc.DKTatlas.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /out/freesurfer/sub-M1215054/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /out/freesurfer/sub-M1215054/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -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; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 6.81 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 105 rescaling Left_Cerebral_Cortex from 61 --> 69 rescaling Left_Lateral_Ventricle from 13 --> 22 rescaling Left_Inf_Lat_Vent from 34 --> 32 rescaling Left_Cerebellum_White_Matter from 86 --> 87 rescaling Left_Cerebellum_Cortex from 60 --> 66 rescaling Left_Thalamus from 94 --> 103 rescaling Left_Thalamus_Proper from 84 --> 94 rescaling Left_Caudate from 75 --> 71 rescaling Left_Putamen from 80 --> 82 rescaling Left_Pallidum from 98 --> 96 rescaling Third_Ventricle from 25 --> 37 rescaling Fourth_Ventricle from 22 --> 22 rescaling Brain_Stem from 81 --> 83 rescaling Left_Hippocampus from 57 --> 66 rescaling Left_Amygdala from 56 --> 69 rescaling CSF from 32 --> 54 rescaling Left_Accumbens_area from 62 --> 65 rescaling Left_VentralDC from 87 --> 90 rescaling Right_Cerebral_White_Matter from 105 --> 103 rescaling Right_Cerebral_Cortex from 58 --> 66 rescaling Right_Lateral_Ventricle from 13 --> 22 rescaling Right_Inf_Lat_Vent from 25 --> 27 rescaling Right_Cerebellum_White_Matter from 87 --> 87 rescaling Right_Cerebellum_Cortex from 59 --> 64 rescaling Right_Thalamus_Proper from 85 --> 89 rescaling Right_Caudate from 62 --> 77 rescaling Right_Putamen from 80 --> 82 rescaling Right_Pallidum from 97 --> 94 rescaling Right_Hippocampus from 53 --> 64 rescaling Right_Amygdala from 55 --> 69 rescaling Right_Accumbens_area from 65 --> 75 rescaling Right_VentralDC from 86 --> 94 rescaling Fifth_Ventricle from 40 --> 45 rescaling WM_hypointensities from 78 --> 76 rescaling non_WM_hypointensities from 40 --> 77 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 510025 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 95 changed. pass 2: 10 changed. pass 3: 3 changed. pass 4: 1 changed. pass 5: 0 changed. nchanged = 0 Writing output aseg to mri/aparc.DKTatlas+aseg.mgz #----------------------------------------- #@# APas-to-ASeg Thu Sep 2 15:38:05 UTC 2021 /out/freesurfer/sub-M1215054/mri apas2aseg --i aparc+aseg.mgz --o aseg.mgz Thu Sep 2 15:38:05 UTC 2021 setenv SUBJECTS_DIR /out/freesurfer cd /out/freesurfer/sub-M1215054/mri /opt/freesurfer/bin/apas2aseg --i aparc+aseg.mgz --o aseg.mgz freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a $Id: apas2aseg,v 1.2 2016/02/12 21:43:14 zkaufman Exp $ Linux 9e1e1df09144 5.4.72-microsoft-standard-WSL2 #1 SMP Wed Oct 28 23:40:43 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux mri_binarize --i aparc+aseg.mgz --o aseg.mgz --replace 1000 3 --replace 2000 42 --replace 1001 3 --replace 2001 42 --replace 1002 3 --replace 2002 42 --replace 1003 3 --replace 2003 42 --replace 1004 3 --replace 2004 42 --replace 1005 3 --replace 2005 42 --replace 1006 3 --replace 2006 42 --replace 1007 3 --replace 2007 42 --replace 1008 3 --replace 2008 42 --replace 1009 3 --replace 2009 42 --replace 1010 3 --replace 2010 42 --replace 1011 3 --replace 2011 42 --replace 1012 3 --replace 2012 42 --replace 1013 3 --replace 2013 42 --replace 1014 3 --replace 2014 42 --replace 1015 3 --replace 2015 42 --replace 1016 3 --replace 2016 42 --replace 1017 3 --replace 2017 42 --replace 1018 3 --replace 2018 42 --replace 1019 3 --replace 2019 42 --replace 1020 3 --replace 2020 42 --replace 1021 3 --replace 2021 42 --replace 1022 3 --replace 2022 42 --replace 1023 3 --replace 2023 42 --replace 1024 3 --replace 2024 42 --replace 1025 3 --replace 2025 42 --replace 1026 3 --replace 2026 42 --replace 1027 3 --replace 2027 42 --replace 1028 3 --replace 2028 42 --replace 1029 3 --replace 2029 42 --replace 1030 3 --replace 2030 42 --replace 1031 3 --replace 2031 42 --replace 1032 3 --replace 2032 42 --replace 1033 3 --replace 2033 42 --replace 1034 3 --replace 2034 42 --replace 1035 3 --replace 2035 42 $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /out/freesurfer/sub-M1215054/mri cmdline mri_binarize.bin --i aparc+aseg.mgz --o aseg.mgz --replace 1000 3 --replace 2000 42 --replace 1001 3 --replace 2001 42 --replace 1002 3 --replace 2002 42 --replace 1003 3 --replace 2003 42 --replace 1004 3 --replace 2004 42 --replace 1005 3 --replace 2005 42 --replace 1006 3 --replace 2006 42 --replace 1007 3 --replace 2007 42 --replace 1008 3 --replace 2008 42 --replace 1009 3 --replace 2009 42 --replace 1010 3 --replace 2010 42 --replace 1011 3 --replace 2011 42 --replace 1012 3 --replace 2012 42 --replace 1013 3 --replace 2013 42 --replace 1014 3 --replace 2014 42 --replace 1015 3 --replace 2015 42 --replace 1016 3 --replace 2016 42 --replace 1017 3 --replace 2017 42 --replace 1018 3 --replace 2018 42 --replace 1019 3 --replace 2019 42 --replace 1020 3 --replace 2020 42 --replace 1021 3 --replace 2021 42 --replace 1022 3 --replace 2022 42 --replace 1023 3 --replace 2023 42 --replace 1024 3 --replace 2024 42 --replace 1025 3 --replace 2025 42 --replace 1026 3 --replace 2026 42 --replace 1027 3 --replace 2027 42 --replace 1028 3 --replace 2028 42 --replace 1029 3 --replace 2029 42 --replace 1030 3 --replace 2030 42 --replace 1031 3 --replace 2031 42 --replace 1032 3 --replace 2032 42 --replace 1033 3 --replace 2033 42 --replace 1034 3 --replace 2034 42 --replace 1035 3 --replace 2035 42 sysname Linux hostname 9e1e1df09144 machine x86_64 user root input aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output aseg.mgz Binarizing based on threshold min -infinity max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Replacing 72 1: 1000 3 2: 2000 42 3: 1001 3 4: 2001 42 5: 1002 3 6: 2002 42 7: 1003 3 8: 2003 42 9: 1004 3 10: 2004 42 11: 1005 3 12: 2005 42 13: 1006 3 14: 2006 42 15: 1007 3 16: 2007 42 17: 1008 3 18: 2008 42 19: 1009 3 20: 2009 42 21: 1010 3 22: 2010 42 23: 1011 3 24: 2011 42 25: 1012 3 26: 2012 42 27: 1013 3 28: 2013 42 29: 1014 3 30: 2014 42 31: 1015 3 32: 2015 42 33: 1016 3 34: 2016 42 35: 1017 3 36: 2017 42 37: 1018 3 38: 2018 42 39: 1019 3 40: 2019 42 41: 1020 3 42: 2020 42 43: 1021 3 44: 2021 42 45: 1022 3 46: 2022 42 47: 1023 3 48: 2023 42 49: 1024 3 50: 2024 42 51: 1025 3 52: 2025 42 53: 1026 3 54: 2026 42 55: 1027 3 56: 2027 42 57: 1028 3 58: 2028 42 59: 1029 3 60: 2029 42 61: 1030 3 62: 2030 42 63: 1031 3 64: 2031 42 65: 1032 3 66: 2032 42 67: 1033 3 68: 2033 42 69: 1034 3 70: 2034 42 71: 1035 3 72: 2035 42 Found 0 values in range Counting number of voxels in first frame Found 0 voxels in final mask Count: 0 0.000000 16777216 0.000000 mri_binarize done Started at Thu Sep 2 15:38:05 UTC 2021 Ended at Thu Sep 2 15:38:12 UTC 2021 Apas2aseg-Run-Time-Sec 7 apas2aseg Done #-------------------------------------------- #@# ASeg Stats Thu Sep 2 15:38:12 UTC 2021 /out/freesurfer/sub-M1215054 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /opt/freesurfer/ASegStatsLUT.txt --subject sub-M1215054 $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /opt/freesurfer/ASegStatsLUT.txt --subject sub-M1215054 sysname Linux hostname 9e1e1df09144 machine x86_64 user root UseRobust 0 atlas_icv (eTIV) = 1598339 mm^3 (det: 1.218831 ) Computing euler number orig.nofix lheno = -68, rheno = -74 orig.nofix lhholes = 35, rhholes = 38 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 254265.342 254416.000 diff= -150.7 pctdiff=-0.059 rhCtxGM: 255577.524 255955.000 diff= -377.5 pctdiff=-0.148 lhCtxWM: 258734.988 260106.500 diff=-1371.5 pctdiff=-0.530 rhCtxWM: 256422.570 257102.500 diff= -679.9 pctdiff=-0.265 SubCortGMVol 62100.000 SupraTentVol 1105647.423 (1104812.000) diff=835.423 pctdiff=0.076 SupraTentVolNotVent 1090518.423 (1089683.000) diff=835.423 pctdiff=0.077 BrainSegVol 1247759.000 (1244958.000) diff=2801.000 pctdiff=0.224 BrainSegVolNotVent 1228303.000 (1225676.423) diff=2626.577 pctdiff=0.214 BrainSegVolNotVent 1228303.000 CerebellumVol 138573.000 VentChorVol 15129.000 3rd4th5thCSF 4327.000 CSFVol 1526.000, OptChiasmVol 47.000 MaskVol 1454060.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation Reporting on 45 segmentations Using PrintSegStat mri_segstats done #----------------------------------------- #@# WMParc Thu Sep 2 15:39:35 UTC 2021 /out/freesurfer/sub-M1215054 mri_aparc2aseg --s sub-M1215054 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /out/freesurfer subject sub-M1215054 outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /out/freesurfer/sub-M1215054/mri/aparc+aseg.mgz Reading lh white surface /out/freesurfer/sub-M1215054/surf/lh.white Reading lh pial surface /out/freesurfer/sub-M1215054/surf/lh.pial Loading lh annotations from /out/freesurfer/sub-M1215054/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading rh white surface /out/freesurfer/sub-M1215054/surf/rh.white Reading rh pial surface /out/freesurfer/sub-M1215054/surf/rh.pial Loading rh annotations from /out/freesurfer/sub-M1215054/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /out/freesurfer/sub-M1215054/mri/ribbon.mgz Loading filled from /out/freesurfer/sub-M1215054/mri/ribbon.mgz Ripping vertices labeled as unkown Ripped 7938 vertices from left hemi Ripped 8244 vertices from right hemi Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /out/freesurfer/sub-M1215054/mri/aseg.mgz Loading Ctx Seg File /out/freesurfer/sub-M1215054/mri/aparc+aseg.mgz ASeg Vox2RAS: ----------- -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; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 1023818 Used brute-force search on 169 voxels Fixing Parahip LH WM Found 5 clusters 0 k 1769.000000 1 k 17.000000 2 k 2.000000 3 k 1.000000 4 k 2.000000 Fixing Parahip RH WM Found 11 clusters 0 k 1.000000 1 k 1.000000 2 k 26.000000 3 k 2.000000 4 k 1.000000 5 k 1.000000 6 k 1.000000 7 k 1196.000000 8 k 1.000000 9 k 1.000000 10 k 3.000000 Writing output aseg to mri/wmparc.mgz mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject sub-M1215054 --surf-wm-vol --ctab /opt/freesurfer/WMParcStatsLUT.txt --etiv $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject sub-M1215054 --surf-wm-vol --ctab /opt/freesurfer/WMParcStatsLUT.txt --etiv sysname Linux hostname 9e1e1df09144 machine x86_64 user root UseRobust 0 atlas_icv (eTIV) = 1598339 mm^3 (det: 1.218831 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 254265.342 254416.000 diff= -150.7 pctdiff=-0.059 rhCtxGM: 255577.524 255955.000 diff= -377.5 pctdiff=-0.148 lhCtxWM: 258734.988 260106.500 diff=-1371.5 pctdiff=-0.530 rhCtxWM: 256422.570 257102.500 diff= -679.9 pctdiff=-0.265 SubCortGMVol 62100.000 SupraTentVol 1105647.423 (1104812.000) diff=835.423 pctdiff=0.076 SupraTentVolNotVent 1090518.423 (1089683.000) diff=835.423 pctdiff=0.077 BrainSegVol 1247759.000 (1244958.000) diff=2801.000 pctdiff=0.224 BrainSegVolNotVent 1228303.000 (1225676.423) diff=2626.577 pctdiff=0.214 BrainSegVolNotVent 1228303.000 CerebellumVol 138573.000 VentChorVol 15129.000 3rd4th5thCSF 4327.000 CSFVol 1526.000, OptChiasmVol 47.000 MaskVol 1454060.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 390 segmentations Computing statistics for each segmentation Reporting on 70 segmentations Using PrintSegStat mri_segstats done Started at Thu Sep 2 13:40:22 UTC 2021 Ended at Thu Sep 2 15:45:39 UTC 2021 #@#%# recon-all-run-time-hours 2.088 recon-all -s sub-M1215054 finished without error at Thu Sep 2 15:45:39 UTC 2021