Mon Jun 23 22:31:58 CST 2025 /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer/sub-OAS30001 /opt/freesurfer/bin/recon-all -autorecon1 -i /fs2/home/bnuhe_user04/work/aslprep_0_7_wf/sub_OAS30001_wf/anat_fit_wf/anat_template_wf/anat_merge/sub-OAS30001_ses-d2430_T1w_noise_corrected_ras_template.nii.gz -noskullstrip -noT2pial -noFLAIRpial -openmp 8 -subjid sub-OAS30001 -sd /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer subjid sub-OAS30001 setenv SUBJECTS_DIR /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /opt/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux cn77042 4.18.0-348.cn.x86_64 #1 SMP Wed Sep 14 10:27:16 CST 2022 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 131072 memorylocked unlimited maxproc 1022271 maxlocks unlimited maxsignal 1022271 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 263245652 6265452 251568460 2201688 5411740 244786544 Swap: 0 0 0 ######################################## 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: 2025/06/23-14:32:00-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:32:00-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:32:03-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2025/06/23-14:32:04-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:32:04-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:32:04-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2025/06/23-14:32:05-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2025/06/23-14:32:05-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2025/06/23-14:32:05-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2025/06/23-14:32:05-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2025/06/23-14:32:05-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2025/06/23-14:32:05-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:32:05-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:32:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2025/06/23-14:32:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:32:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:32:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:32:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:32:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:32:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:32:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2025/06/23-14:32:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:32:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:32:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:32:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2025/06/23-14:32:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:32:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2025/06/23-14:32:08-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:32:08-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:32:08-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:32:08-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:32:08-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:32:08-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:32:08-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:32:09-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:32:09-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:32:09-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:32:09-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:32:09-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 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 ####################################### /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer/sub-OAS30001 mri_convert /fs2/home/bnuhe_user04/work/aslprep_0_7_wf/sub_OAS30001_wf/anat_fit_wf/anat_template_wf/anat_merge/sub-OAS30001_ses-d2430_T1w_noise_corrected_ras_template.nii.gz /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer/sub-OAS30001/mri/orig/001.mgz mri_convert.bin /fs2/home/bnuhe_user04/work/aslprep_0_7_wf/sub_OAS30001_wf/anat_fit_wf/anat_template_wf/anat_merge/sub-OAS30001_ses-d2430_T1w_noise_corrected_ras_template.nii.gz /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer/sub-OAS30001/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /fs2/home/bnuhe_user04/work/aslprep_0_7_wf/sub_OAS30001_wf/anat_fit_wf/anat_template_wf/anat_merge/sub-OAS30001_ses-d2430_T1w_noise_corrected_ras_template.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer/sub-OAS30001/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Mon Jun 23 22:32:13 CST 2025 Found 1 runs /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer/sub-OAS30001/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 /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer/sub-OAS30001/mri/orig/001.mgz /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer/sub-OAS30001/mri/rawavg.mgz /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer/sub-OAS30001 mri_convert /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer/sub-OAS30001/mri/rawavg.mgz /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer/sub-OAS30001/mri/orig.mgz --conform mri_convert.bin /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer/sub-OAS30001/mri/rawavg.mgz /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer/sub-OAS30001/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer/sub-OAS30001/mri/rawavg.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer/sub-OAS30001/mri/orig.mgz... mri_add_xform_to_header -c /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer/sub-OAS30001/mri/transforms/talairach.xfm /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer/sub-OAS30001/mri/orig.mgz /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer/sub-OAS30001/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Mon Jun 23 22:32:21 CST 2025 /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer/sub-OAS30001/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer/sub-OAS30001/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 cn77042 4.18.0-348.cn.x86_64 #1 SMP Wed Sep 14 10:27:16 CST 2022 x86_64 x86_64 x86_64 GNU/Linux Mon Jun 23 22:32:21 CST 2025 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /bin/bc tmpdir is ./tmp.mri_nu_correct.mni.155767 /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer/sub-OAS30001/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.155767/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.155767/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.155767/nu0.mnc... -------------------------------------------------------- Iteration 1 Mon Jun 23 22:32:22 CST 2025 nu_correct -clobber ./tmp.mri_nu_correct.mni.155767/nu0.mnc ./tmp.mri_nu_correct.mni.155767/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.155767/0/ -iterations 1000 -distance 50 [bnuhe_user04@cn77042:/fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer/sub-OAS30001/mri/] [2025-06-23 22:32:24] 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.155767/0/ ./tmp.mri_nu_correct.mni.155767/nu0.mnc ./tmp.mri_nu_correct.mni.155767/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 38 CV of field change: 0.000960676 mri_convert ./tmp.mri_nu_correct.mni.155767/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.155767/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.155767/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz... Mon Jun 23 22:33:21 CST 2025 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at Mon Jun 23 22:33:21 CST 2025 Ended at Mon Jun 23 22:33:42 CST 2025 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Mon Jun 23 22:33:44 CST 2025 /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer/sub-OAS30001/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6152, pval=0.2817 >= threshold=0.0050) awk -f /opt/freesurfer/bin/extract_talairach_avi_QA.awk /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer/sub-OAS30001/mri/transforms/talairach_avi.log tal_QC_AZS /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer/sub-OAS30001/mri/transforms/talairach_avi.log TalAviQA: 0.97894 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Mon Jun 23 22:33:45 CST 2025 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer/sub-OAS30001/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 cn77042 4.18.0-348.cn.x86_64 #1 SMP Wed Sep 14 10:27:16 CST 2022 x86_64 x86_64 x86_64 GNU/Linux Mon Jun 23 22:33:45 CST 2025 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /bin/bc tmpdir is ./tmp.mri_nu_correct.mni.156527 /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer/sub-OAS30001/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.156527/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.156527/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.156527/nu0.mnc... -------------------------------------------------------- Iteration 1 Mon Jun 23 22:33:46 CST 2025 nu_correct -clobber ./tmp.mri_nu_correct.mni.156527/nu0.mnc ./tmp.mri_nu_correct.mni.156527/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.156527/0/ [bnuhe_user04@cn77042:/fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer/sub-OAS30001/mri/] [2025-06-23 22:33:46] 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.156527/0/ ./tmp.mri_nu_correct.mni.156527/nu0.mnc ./tmp.mri_nu_correct.mni.156527/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 31 CV of field change: 0.000967996 -------------------------------------------------------- Iteration 2 Mon Jun 23 22:34:16 CST 2025 nu_correct -clobber ./tmp.mri_nu_correct.mni.156527/nu1.mnc ./tmp.mri_nu_correct.mni.156527/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.156527/1/ [bnuhe_user04@cn77042:/fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer/sub-OAS30001/mri/] [2025-06-23 22:34:16] 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.156527/1/ ./tmp.mri_nu_correct.mni.156527/nu1.mnc ./tmp.mri_nu_correct.mni.156527/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 Number of iterations: 12 CV of field change: 0.000947056 mri_binarize --i ./tmp.mri_nu_correct.mni.156527/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.156527/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer/sub-OAS30001/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.156527/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.156527/ones.mgz sysname Linux hostname cn77042 machine x86_64 user bnuhe_user04 input ./tmp.mri_nu_correct.mni.156527/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.156527/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.156527/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.156527/sum.junk --avgwf ./tmp.mri_nu_correct.mni.156527/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.156527/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.156527/sum.junk --avgwf ./tmp.mri_nu_correct.mni.156527/input.mean.dat sysname Linux hostname cn77042 machine x86_64 user bnuhe_user04 UseRobust 0 Loading ./tmp.mri_nu_correct.mni.156527/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.156527/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.156527/ones.mgz --i ./tmp.mri_nu_correct.mni.156527/nu2.mnc --sum ./tmp.mri_nu_correct.mni.156527/sum.junk --avgwf ./tmp.mri_nu_correct.mni.156527/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.156527/ones.mgz --i ./tmp.mri_nu_correct.mni.156527/nu2.mnc --sum ./tmp.mri_nu_correct.mni.156527/sum.junk --avgwf ./tmp.mri_nu_correct.mni.156527/output.mean.dat sysname Linux hostname cn77042 machine x86_64 user bnuhe_user04 UseRobust 0 Loading ./tmp.mri_nu_correct.mni.156527/ones.mgz Loading ./tmp.mri_nu_correct.mni.156527/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.156527/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.156527/nu2.mnc ./tmp.mri_nu_correct.mni.156527/nu2.mnc mul 1.02499879625124225376 Saving result to './tmp.mri_nu_correct.mni.156527/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.156527/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.156527/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.156527/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 4 seconds. mapping (21, 185) to ( 3, 110) Mon Jun 23 22:34:54 CST 2025 mri_nu_correct.mni done mri_add_xform_to_header -c /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer/sub-OAS30001/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Mon Jun 23 22:34:54 CST 2025 /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer/sub-OAS30001/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 1.10150 0.02113 -0.11534 -4.66419; 0.01410 1.07989 0.41267 -27.80986; 0.10542 -0.45760 1.16747 17.01317; 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 = 16 Starting OpenSpline(): npoints = 16 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 64 (64), valley at 52 (52) csf peak at 32, setting threshold to 53 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 53 (53), valley at 23 (23) csf peak at 27, setting threshold to 44 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 12 seconds. Started at Mon Jun 23 22:31:58 CST 2025 Ended at Mon Jun 23 22:36:07 CST 2025 #@#%# recon-all-run-time-hours 0.069 recon-all -s sub-OAS30001 finished without error at Mon Jun 23 22:36:07 CST 2025 New invocation of recon-all Mon Jun 23 22:36:15 CST 2025 /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer/sub-OAS30001 /opt/freesurfer/bin/recon-all -openmp 8 -subjid sub-OAS30001 -sd /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer -gcareg subjid sub-OAS30001 setenv SUBJECTS_DIR /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /opt/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux cn77042 4.18.0-348.cn.x86_64 #1 SMP Wed Sep 14 10:27:16 CST 2022 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 131072 memorylocked unlimited maxproc 1022271 maxlocks unlimited maxsignal 1022271 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 263245652 6752456 250428000 2201692 6065196 243972812 Swap: 0 0 0 ######################################## 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: 2025/06/23-14:36:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:36:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:36:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2025/06/23-14:36:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:36:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:36:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2025/06/23-14:36:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2025/06/23-14:36:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2025/06/23-14:36:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2025/06/23-14:36:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2025/06/23-14:36:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2025/06/23-14:36:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:36:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:36:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2025/06/23-14:36:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:36:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:36:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:36:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:36:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:36:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:36:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2025/06/23-14:36:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:36:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:36:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:36:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2025/06/23-14:36:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:36:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2025/06/23-14:36:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:36:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:36:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:36:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:36:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:36:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:36:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:36:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:36:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:36:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:36:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:36:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 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 Mon Jun 23 22:36:15 CST 2025 /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer/sub-OAS30001/mri mri_em_register -rusage /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer/sub-OAS30001/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 = 8 == 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'... 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=26.9 skull bounding box = (63, 80, 38) --> (186, 201, 179) using (104, 120, 109) as brain centroid... mean wm in atlas = 107, using box (89,105,92) --> (119, 134,126) to find MRI wm before smoothing, mri peak at 107 robust fit to distribution - 107 +- 4.1 after smoothing, mri peak at 107, scaling input intensities by 1.000 scaling channel 0 by 1 initial log_p = -4.263 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.102682 @ (9.091, -9.091, -9.091) max log p = -4.020347 @ (-4.545, -13.636, -4.545) max log p = -3.989951 @ (-2.273, 6.818, 2.273) max log p = -3.967559 @ (1.136, 1.136, 1.136) max log p = -3.967559 @ (0.000, 0.000, 0.000) max log p = -3.967559 @ (0.000, 0.000, 0.000) Found translation: (3.4, -14.8, -10.2): log p = -3.968 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.549, old_max_log_p =-3.968 (thresh=-4.0) 1.05465 -0.13412 -0.03594 18.80607; 0.16136 1.18391 0.31723 -96.02302; 0.00000 -0.27823 1.03837 30.13471; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.548, old_max_log_p =-3.549 (thresh=-3.5) 1.13375 -0.14417 -0.03863 10.71123; 0.15998 1.13747 0.45005 -104.01087; -0.02106 -0.43038 0.98808 58.88299; 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=-3.379, old_max_log_p =-3.548 (thresh=-3.5) 1.09563 -0.10310 -0.02661 6.52455; 0.12433 1.17678 0.42638 -100.43608; -0.01338 -0.39316 1.00222 51.21534; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.378, old_max_log_p =-3.379 (thresh=-3.4) 1.09460 -0.11591 0.00620 4.81458; 0.12433 1.17678 0.42638 -100.43608; -0.04922 -0.38958 1.00255 57.05262; 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=-3.350, old_max_log_p =-3.378 (thresh=-3.4) 1.09844 -0.11646 0.00612 4.87030; 0.12407 1.17353 0.43457 -100.37985; -0.05022 -0.39872 0.99786 58.43575; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.350, old_max_log_p =-3.350 (thresh=-3.3) 1.09844 -0.11646 0.00612 4.87030; 0.12407 1.17353 0.43457 -100.37985; -0.05022 -0.39872 0.99786 58.43575; 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 1.09844 -0.11646 0.00612 4.87030; 0.12407 1.17353 0.43457 -100.37985; -0.05022 -0.39872 0.99786 58.43575; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.09844 -0.11646 0.00612 4.87030; 0.12407 1.17353 0.43457 -100.37985; -0.05022 -0.39872 0.99786 58.43575; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.09844 -0.11646 0.00612 4.87030; 0.12407 1.17353 0.43457 -100.37985; -0.05022 -0.39872 0.99786 58.43575; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.350 (old=-4.263) transform before final EM align: 1.09844 -0.11646 0.00612 4.87030; 0.12407 1.17353 0.43457 -100.37985; -0.05022 -0.39872 0.99786 58.43575; 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 1.09844 -0.11646 0.00612 4.87030; 0.12407 1.17353 0.43457 -100.37985; -0.05022 -0.39872 0.99786 58.43575; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 1.09844 -0.11646 0.00612 4.87030; 0.12407 1.17353 0.43457 -100.37985; -0.05022 -0.39872 0.99786 58.43575; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = 3.8 tol 0.000000 final transform: 1.09844 -0.11646 0.00612 4.87030; 0.12407 1.17353 0.43457 -100.37985; -0.05022 -0.39872 0.99786 58.43575; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 1273.826744 mri_em_register stimesec 1.522434 mri_em_register ru_maxrss 598768 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 651034 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 140152 mri_em_register ru_oublock 24 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 350 mri_em_register ru_nivcsw 1528 registration took 2 minutes and 55 seconds. Started at Mon Jun 23 22:36:15 CST 2025 Ended at Mon Jun 23 22:39:10 CST 2025 #@#%# recon-all-run-time-hours 0.049 recon-all -s sub-OAS30001 finished without error at Mon Jun 23 22:39:10 CST 2025 New invocation of recon-all Mon Jun 23 22:39:12 CST 2025 /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer/sub-OAS30001 /opt/freesurfer/bin/recon-all -autorecon2-volonly -openmp 8 -subjid sub-OAS30001 -sd /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer -nogcareg subjid sub-OAS30001 setenv SUBJECTS_DIR /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /opt/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux cn77042 4.18.0-348.cn.x86_64 #1 SMP Wed Sep 14 10:27:16 CST 2022 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 131072 memorylocked unlimited maxproc 1022271 maxlocks unlimited maxsignal 1022271 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 263245652 6368564 250741608 2201692 6135480 244321572 Swap: 0 0 0 ######################################## 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: 2025/06/23-14:39:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:39:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:39:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2025/06/23-14:39:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:39:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:39:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2025/06/23-14:39:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2025/06/23-14:39:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2025/06/23-14:39:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2025/06/23-14:39:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2025/06/23-14:39:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2025/06/23-14:39:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:39:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:39:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2025/06/23-14:39:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:39:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:39:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:39:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:39:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:39:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:39:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2025/06/23-14:39:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:39:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:39:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:39:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2025/06/23-14:39:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:39:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2025/06/23-14:39:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:39:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:39:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:39:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:39:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:39:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:39:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:39:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:39:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:39:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:39:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2025/06/23-14:39:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: bnuhe_user04 Machine: cn77042 Platform: Linux PlatformVersion: 4.18.0-348.cn.x86_64 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 ####################################### #-------------------------------------- #@# CA Normalize Mon Jun 23 22:39:13 CST 2025 /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer/sub-OAS30001/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... resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=26.9 skull bounding box = (63, 80, 38) --> (186, 201, 179) using (104, 120, 109) as brain centroid... mean wm in atlas = 107, using box (89,105,92) --> (119, 134,126) to find MRI wm before smoothing, mri peak at 107 robust fit to distribution - 107 +- 4.1 after smoothing, mri peak at 107, scaling input intensities by 1.000 scaling channel 0 by 1 using 246344 sample points... INFO: compute sample coordinates transform 1.09844 -0.11646 0.00612 4.87030; 0.12407 1.17353 0.43457 -100.37985; -0.05022 -0.39872 0.99786 58.43575; 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 (123, 79, 39) --> (185, 180, 189) Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 132.0 3 of 8437 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (65, 81, 38) --> (125, 177, 189) Right_Cerebral_White_Matter: limiting intensities to 95.0 --> 132.0 2 of 8016 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (128, 158, 69) --> (174, 190, 119) Left_Cerebellum_White_Matter: limiting intensities to 98.0 --> 132.0 0 of 731 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (89, 158, 66) --> (129, 194, 119) Right_Cerebellum_White_Matter: limiting intensities to 97.0 --> 132.0 0 of 585 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (111, 143, 99) --> (144, 199, 128) Brain_Stem: limiting intensities to 94.0 --> 132.0 0 of 923 (0.0%) samples deleted using 18692 total control points for intensity normalization... bias field = 0.953 +- 0.069 25 of 18687 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (123, 79, 39) --> (185, 180, 189) Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 6 of 8583 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (65, 81, 38) --> (125, 177, 189) Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0 2 of 8209 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (128, 158, 69) --> (174, 190, 119) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 8 of 795 (1.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (89, 158, 66) --> (129, 194, 119) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 28 of 611 (4.6%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (111, 143, 99) --> (144, 199, 128) Brain_Stem: limiting intensities to 88.0 --> 132.0 46 of 1043 (4.4%) samples deleted using 19241 total control points for intensity normalization... bias field = 1.007 +- 0.047 88 of 19091 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (123, 79, 39) --> (185, 180, 189) Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 4 of 8623 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (65, 81, 38) --> (125, 177, 189) Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0 1 of 8255 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (128, 158, 69) --> (174, 190, 119) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 89 of 795 (11.2%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (89, 158, 66) --> (129, 194, 119) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 195 of 619 (31.5%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (111, 143, 99) --> (144, 199, 128) Brain_Stem: limiting intensities to 88.0 --> 132.0 251 of 1063 (23.6%) samples deleted using 19355 total control points for intensity normalization... bias field = 1.004 +- 0.037 96 of 18617 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 0 seconds. #-------------------------------------- #@# CA Reg Mon Jun 23 22:40:12 CST 2025 /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer/sub-OAS30001/mri mri_ca_register -rusage /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer/sub-OAS30001/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 = 8 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/opt/freesurfer/average/RB_all_2016-05-10.vc700.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.49 (predicted orig area = 5.4) 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=0.834, neg=0, invalid=762 0001: dt=203.837594, rms=0.738 (11.541%), neg=0, invalid=762 0002: dt=180.292683, rms=0.713 (3.347%), neg=0, invalid=762 0003: dt=264.971475, rms=0.700 (1.849%), neg=0, invalid=762 0004: dt=137.356725, rms=0.694 (0.905%), neg=0, invalid=762 0005: dt=517.888000, rms=0.685 (1.290%), neg=0, invalid=762 0006: dt=112.149533, rms=0.680 (0.738%), neg=0, invalid=762 0007: dt=517.888000, rms=0.674 (0.783%), neg=0, invalid=762 0008: dt=129.472000, rms=0.672 (0.388%), neg=0, invalid=762 0009: dt=221.952000, rms=0.670 (0.198%), neg=0, invalid=762 0010: dt=221.952000, rms=0.669 (0.255%), neg=0, invalid=762 0011: dt=221.952000, rms=0.666 (0.442%), neg=0, invalid=762 0012: dt=221.952000, rms=0.664 (0.315%), neg=0, invalid=762 0013: dt=221.952000, rms=0.660 (0.528%), neg=0, invalid=762 0014: dt=221.952000, rms=0.658 (0.321%), neg=0, invalid=762 0015: dt=221.952000, rms=0.656 (0.263%), neg=0, invalid=762 0016: dt=221.952000, rms=0.654 (0.285%), neg=0, invalid=762 0017: dt=221.952000, rms=0.653 (0.194%), neg=0, invalid=762 0018: dt=221.952000, rms=0.651 (0.262%), neg=0, invalid=762 0019: dt=221.952000, rms=0.650 (0.166%), neg=0, invalid=762 0020: dt=221.952000, rms=0.649 (0.168%), neg=0, invalid=762 0021: dt=221.952000, rms=0.648 (0.199%), neg=0, invalid=762 0022: dt=221.952000, rms=0.647 (0.172%), neg=0, invalid=762 0023: dt=221.952000, rms=0.645 (0.214%), neg=0, invalid=762 0024: dt=221.952000, rms=0.644 (0.155%), neg=0, invalid=762 0025: dt=221.952000, rms=0.643 (0.189%), neg=0, invalid=762 0026: dt=221.952000, rms=0.642 (0.197%), neg=0, invalid=762 0027: dt=221.952000, rms=0.641 (0.135%), neg=0, invalid=762 0028: dt=221.952000, rms=0.640 (0.176%), neg=0, invalid=762 0029: dt=221.952000, rms=0.639 (0.166%), neg=0, invalid=762 0030: dt=221.952000, rms=0.638 (0.122%), neg=0, invalid=762 0031: dt=221.952000, rms=0.637 (0.101%), neg=0, invalid=762 0032: dt=129.472000, rms=0.637 (0.040%), neg=0, invalid=762 0033: dt=129.472000, rms=0.637 (0.003%), neg=0, invalid=762 0034: dt=129.472000, rms=0.637 (0.011%), neg=0, invalid=762 0035: dt=129.472000, rms=0.637 (0.028%), neg=0, invalid=762 0036: dt=129.472000, rms=0.637 (0.036%), neg=0, invalid=762 0037: dt=129.472000, rms=0.637 (0.017%), neg=0, invalid=762 0038: dt=129.472000, rms=0.636 (0.033%), neg=0, invalid=762 0039: dt=129.472000, rms=0.636 (0.010%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.637, neg=0, invalid=762 0040: dt=221.952000, rms=0.635 (0.258%), neg=0, invalid=762 0041: dt=295.936000, rms=0.635 (0.072%), neg=0, invalid=762 0042: dt=295.936000, rms=0.634 (0.065%), neg=0, invalid=762 0043: dt=295.936000, rms=0.634 (0.070%), neg=0, invalid=762 0044: dt=295.936000, rms=0.633 (0.135%), neg=0, invalid=762 0045: dt=295.936000, rms=0.633 (0.099%), neg=0, invalid=762 0046: dt=295.936000, rms=0.632 (0.052%), neg=0, invalid=762 0047: dt=92.480000, rms=0.632 (0.029%), neg=0, invalid=762 0048: dt=92.480000, rms=0.632 (0.008%), neg=0, invalid=762 0049: dt=92.480000, rms=0.632 (0.013%), neg=0, invalid=762 0050: dt=92.480000, rms=0.632 (0.012%), neg=0, invalid=762 0051: dt=92.480000, rms=0.632 (0.014%), neg=0, invalid=762 0052: dt=92.480000, rms=0.632 (0.022%), neg=0, invalid=762 0053: dt=92.480000, rms=0.632 (0.005%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.639, neg=0, invalid=762 0054: dt=113.734940, rms=0.634 (0.750%), neg=0, invalid=762 0055: dt=221.788018, rms=0.624 (1.537%), neg=0, invalid=762 0056: dt=57.600000, rms=0.620 (0.657%), neg=0, invalid=762 0057: dt=414.720000, rms=0.614 (1.030%), neg=0, invalid=762 0058: dt=68.050633, rms=0.609 (0.815%), neg=0, invalid=762 0059: dt=88.368201, rms=0.607 (0.304%), neg=0, invalid=762 0060: dt=82.944000, rms=0.606 (0.182%), neg=0, invalid=762 0061: dt=82.944000, rms=0.604 (0.220%), neg=0, invalid=762 0062: dt=82.944000, rms=0.602 (0.311%), neg=0, invalid=762 0063: dt=82.944000, rms=0.600 (0.448%), neg=0, invalid=762 0064: dt=82.944000, rms=0.597 (0.481%), neg=0, invalid=762 0065: dt=82.944000, rms=0.594 (0.546%), neg=0, invalid=762 0066: dt=82.944000, rms=0.591 (0.453%), neg=0, invalid=762 0067: dt=82.944000, rms=0.588 (0.474%), neg=0, invalid=762 0068: dt=82.944000, rms=0.586 (0.415%), neg=0, invalid=762 0069: dt=82.944000, rms=0.583 (0.411%), neg=0, invalid=762 0070: dt=82.944000, rms=0.581 (0.325%), neg=0, invalid=762 0071: dt=82.944000, rms=0.580 (0.289%), neg=0, invalid=762 0072: dt=82.944000, rms=0.578 (0.244%), neg=0, invalid=762 0073: dt=82.944000, rms=0.577 (0.269%), neg=0, invalid=762 0074: dt=82.944000, rms=0.575 (0.205%), neg=0, invalid=762 0075: dt=82.944000, rms=0.574 (0.179%), neg=0, invalid=762 0076: dt=82.944000, rms=0.573 (0.174%), neg=0, invalid=762 0077: dt=82.944000, rms=0.572 (0.174%), neg=0, invalid=762 0078: dt=82.944000, rms=0.572 (0.094%), neg=0, invalid=762 0079: dt=82.944000, rms=0.571 (0.080%), neg=0, invalid=762 0080: dt=103.680000, rms=0.571 (0.071%), neg=0, invalid=762 0081: dt=103.680000, rms=0.571 (-0.131%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.572, neg=0, invalid=762 0082: dt=77.037037, rms=0.570 (0.345%), neg=0, invalid=762 0083: dt=103.680000, rms=0.569 (0.192%), neg=0, invalid=762 0084: dt=103.680000, rms=0.569 (-0.068%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.596, neg=0, invalid=762 0085: dt=4.800000, rms=0.595 (0.184%), neg=0, invalid=762 0086: dt=2.000000, rms=0.595 (0.006%), neg=0, invalid=762 0087: dt=2.000000, rms=0.595 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.596, neg=0, invalid=762 0088: dt=2.800000, rms=0.595 (0.152%), neg=0, invalid=762 0089: dt=2.800000, rms=0.595 (0.010%), neg=0, invalid=762 0090: dt=2.800000, rms=0.595 (0.001%), neg=0, invalid=762 0091: dt=2.800000, rms=0.595 (-0.053%), neg=0, invalid=762 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.660, neg=0, invalid=762 0092: dt=4.635294, rms=0.645 (2.208%), neg=0, invalid=762 0093: dt=2.231884, rms=0.644 (0.098%), neg=0, invalid=762 0094: dt=2.231884, rms=0.644 (-0.046%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.645, neg=0, invalid=762 0095: dt=0.720000, rms=0.644 (0.101%), neg=0, invalid=762 0096: dt=0.144000, rms=0.644 (0.001%), neg=0, invalid=762 0097: dt=0.144000, rms=0.644 (0.001%), neg=0, invalid=762 0098: dt=0.144000, rms=0.644 (-0.005%), neg=0, invalid=762 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.708, neg=0, invalid=762 0099: dt=1.024000, rms=0.705 (0.383%), neg=0, invalid=762 0100: dt=1.792000, rms=0.702 (0.416%), neg=0, invalid=762 0101: dt=1.024000, rms=0.702 (0.066%), neg=0, invalid=762 0102: dt=1.024000, rms=0.701 (0.109%), neg=0, invalid=762 0103: dt=1.024000, rms=0.701 (-0.012%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.702, neg=0, invalid=762 0104: dt=1.536000, rms=0.700 (0.254%), neg=0, invalid=762 0105: dt=0.000000, rms=0.700 (-0.002%), neg=0, invalid=762 0106: dt=0.100000, rms=0.700 (-0.002%), 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=0.651, neg=0, invalid=762 0107: dt=0.920027, rms=0.631 (3.036%), neg=0, invalid=762 0108: dt=0.096000, rms=0.630 (0.184%), neg=0, invalid=762 0109: dt=0.096000, rms=0.630 (-0.133%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.631, neg=0, invalid=762 0110: dt=0.024000, rms=0.630 (0.113%), neg=0, invalid=762 0111: dt=0.000000, rms=0.630 (-0.000%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.20278 (17) Left_Lateral_Ventricle (4): linear fit = 0.92 x + 0.0 (1087 voxels, overlap=0.511) Left_Lateral_Ventricle (4): linear fit = 0.92 x + 0.0 (1087 voxels, peak = 18), gca=18.3 gca peak = 0.15565 (16) mri peak = 0.11987 (21) Right_Lateral_Ventricle (43): linear fit = 1.10 x + 0.0 (679 voxels, overlap=0.818) Right_Lateral_Ventricle (43): linear fit = 1.10 x + 0.0 (679 voxels, peak = 18), gca=17.5 gca peak = 0.26829 (96) mri peak = 0.14698 (99) Right_Pallidum (52): linear fit = 1.03 x + 0.0 (573 voxels, overlap=0.909) Right_Pallidum (52): linear fit = 1.03 x + 0.0 (573 voxels, peak = 99), gca=99.4 gca peak = 0.20183 (93) mri peak = 0.14737 (99) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (614 voxels, overlap=0.632) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (614 voxels, peak = 97), gca=97.2 gca peak = 0.21683 (55) mri peak = 0.09453 (67) Right_Hippocampus (53): linear fit = 1.21 x + 0.0 (638 voxels, overlap=0.024) Right_Hippocampus (53): linear fit = 1.21 x + 0.0 (638 voxels, peak = 66), gca=66.3 gca peak = 0.30730 (58) mri peak = 0.10248 (68) Left_Hippocampus (17): linear fit = 1.18 x + 0.0 (608 voxels, overlap=0.017) Left_Hippocampus (17): linear fit = 1.18 x + 0.0 (608 voxels, peak = 69), gca=68.7 gca peak = 0.11430 (101) mri peak = 0.10284 (107) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (45714 voxels, overlap=0.549) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (45714 voxels, peak = 107), gca=106.6 gca peak = 0.12076 (102) mri peak = 0.11476 (105) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (47474 voxels, overlap=0.436) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (47474 voxels, peak = 108), gca=107.6 gca peak = 0.14995 (59) mri peak = 0.03728 (62) Left_Cerebral_Cortex (3): linear fit = 1.12 x + 0.0 (16044 voxels, overlap=0.684) Left_Cerebral_Cortex (3): linear fit = 1.12 x + 0.0 (16044 voxels, peak = 66), gca=66.4 gca peak = 0.15082 (58) mri peak = 0.04276 (67) Right_Cerebral_Cortex (42): linear fit = 1.16 x + 0.0 (17314 voxels, overlap=0.245) Right_Cerebral_Cortex (42): linear fit = 1.16 x + 0.0 (17314 voxels, peak = 68), gca=67.6 gca peak = 0.14161 (67) mri peak = 0.12560 (83) Right_Caudate (50): linear fit = 1.22 x + 0.0 (622 voxels, overlap=0.008) Right_Caudate (50): linear fit = 1.22 x + 0.0 (622 voxels, peak = 81), gca=81.4 gca peak = 0.15243 (71) mri peak = 0.18168 (83) Left_Caudate (11): linear fit = 1.12 x + 0.0 (644 voxels, overlap=0.096) Left_Caudate (11): linear fit = 1.12 x + 0.0 (644 voxels, peak = 80), gca=79.9 gca peak = 0.13336 (57) mri peak = 0.04702 (60) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (19522 voxels, overlap=0.745) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (19522 voxels, peak = 64), gca=63.6 gca peak = 0.13252 (56) mri peak = 0.04316 (62) Right_Cerebellum_Cortex (47): linear fit = 1.07 x + 0.0 (22903 voxels, overlap=0.833) Right_Cerebellum_Cortex (47): linear fit = 1.07 x + 0.0 (22903 voxels, peak = 60), gca=59.6 gca peak = 0.18181 (84) mri peak = 0.13336 (90) Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (7044 voxels, overlap=0.253) Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (7044 voxels, peak = 91), gca=91.1 gca peak = 0.20573 (83) mri peak = 0.15132 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (6238 voxels, overlap=0.456) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (6238 voxels, peak = 88), gca=88.4 gca peak = 0.21969 (57) mri peak = 0.15432 (69) Left_Amygdala (18): linear fit = 1.18 x + 0.0 (324 voxels, overlap=0.024) Left_Amygdala (18): linear fit = 1.18 x + 0.0 (324 voxels, peak = 68), gca=67.5 gca peak = 0.39313 (56) mri peak = 0.14706 (67) Right_Amygdala (54): linear fit = 1.13 x + 0.0 (366 voxels, overlap=0.049) Right_Amygdala (54): linear fit = 1.13 x + 0.0 (366 voxels, peak = 64), gca=63.6 gca peak = 0.14181 (85) mri peak = 0.09372 (90) Left_Thalamus_Proper (10): linear fit = 1.03 x + 0.0 (4023 voxels, overlap=0.802) Left_Thalamus_Proper (10): linear fit = 1.03 x + 0.0 (4023 voxels, peak = 88), gca=88.0 gca peak = 0.11978 (83) mri peak = 0.09600 (89) Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (3348 voxels, overlap=0.693) Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (3348 voxels, peak = 87), gca=86.7 gca peak = 0.13399 (79) mri peak = 0.09003 (90) Left_Putamen (12): linear fit = 1.12 x + 0.0 (1804 voxels, overlap=0.254) Left_Putamen (12): linear fit = 1.12 x + 0.0 (1804 voxels, peak = 89), gca=88.9 gca peak = 0.14159 (79) mri peak = 0.09829 (84) Right_Putamen (51): linear fit = 1.10 x + 0.0 (1720 voxels, overlap=0.566) Right_Putamen (51): linear fit = 1.10 x + 0.0 (1720 voxels, peak = 87), gca=86.5 gca peak = 0.10025 (80) mri peak = 0.12337 (88) Brain_Stem (16): linear fit = 1.12 x + 0.0 (9116 voxels, overlap=0.203) Brain_Stem (16): linear fit = 1.12 x + 0.0 (9116 voxels, peak = 89), gca=89.2 gca peak = 0.13281 (86) mri peak = 0.12843 (95) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (735 voxels, overlap=0.186) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (735 voxels, peak = 94), gca=94.2 gca peak = 0.12801 (89) mri peak = 0.11507 (94) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (863 voxels, overlap=0.087) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (863 voxels, peak = 97), gca=97.5 gca peak = 0.20494 (23) mri peak = 0.40000 (18) gca peak = 0.15061 (21) mri peak = 0.44643 (21) Fourth_Ventricle (15): linear fit = 0.98 x + 0.0 (341 voxels, overlap=0.449) Fourth_Ventricle (15): linear fit = 0.98 x + 0.0 (341 voxels, peak = 20), gca=20.5 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18056 (32) gca peak Left_Thalamus = 0.64095 (94) gca peak Third_Ventricle = 0.20494 (23) gca peak CSF = 0.20999 (34) gca peak Left_Accumbens_area = 0.39030 (62) gca peak Left_undetermined = 0.95280 (25) gca peak Left_vessel = 0.67734 (53) gca peak Left_choroid_plexus = 0.09433 (44) gca peak Right_Inf_Lat_Vent = 0.23544 (26) gca peak Right_Accumbens_area = 0.30312 (64) gca peak Right_vessel = 0.46315 (51) gca peak Right_choroid_plexus = 0.14086 (44) gca peak Fifth_Ventricle = 0.51669 (36) gca peak WM_hypointensities = 0.09722 (76) gca peak non_WM_hypointensities = 0.11899 (47) gca peak Optic_Chiasm = 0.39033 (72) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 1.17 x + 0.0 estimating mean wm scale to be 1.05 x + 0.0 estimating mean csf scale to be 1.00 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=0.640, neg=0, invalid=762 0112: dt=84.768212, rms=0.629 (1.780%), neg=0, invalid=762 0113: dt=133.370629, rms=0.626 (0.443%), neg=0, invalid=762 0114: dt=517.888000, rms=0.619 (1.181%), neg=0, invalid=762 0115: dt=129.472000, rms=0.618 (0.119%), neg=0, invalid=762 0116: dt=517.888000, rms=0.614 (0.705%), neg=0, invalid=762 0117: dt=32.368000, rms=0.614 (0.038%), neg=0, invalid=762 0118: dt=32.368000, rms=0.613 (0.009%), neg=0, invalid=762 0119: dt=32.368000, rms=0.613 (-0.003%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.614, neg=0, invalid=762 0120: dt=221.952000, rms=0.610 (0.586%), neg=0, invalid=762 0121: dt=92.480000, rms=0.610 (0.089%), neg=0, invalid=762 0122: dt=517.888000, rms=0.609 (0.164%), neg=0, invalid=762 0123: dt=129.472000, rms=0.608 (0.178%), neg=0, invalid=762 0124: dt=295.936000, rms=0.607 (0.078%), neg=0, invalid=762 0125: dt=110.976000, rms=0.607 (0.089%), neg=0, invalid=762 0126: dt=295.936000, rms=0.606 (0.076%), neg=0, invalid=762 0127: dt=92.480000, rms=0.606 (0.068%), neg=0, invalid=762 0128: dt=517.888000, rms=0.605 (0.142%), neg=0, invalid=762 0129: dt=92.480000, rms=0.605 (0.059%), neg=0, invalid=762 0130: dt=887.808000, rms=0.604 (0.147%), neg=0, invalid=762 0131: dt=92.480000, rms=0.603 (0.116%), neg=0, invalid=762 0132: dt=369.920000, rms=0.603 (0.062%), neg=0, invalid=762 0133: dt=92.480000, rms=0.602 (0.050%), neg=0, invalid=762 0134: dt=517.888000, rms=0.602 (0.066%), neg=0, invalid=762 0135: dt=92.480000, rms=0.602 (0.057%), neg=0, invalid=762 0136: dt=517.888000, rms=0.601 (0.072%), neg=0, invalid=762 0137: dt=92.480000, rms=0.601 (0.050%), neg=0, invalid=762 0138: dt=517.888000, rms=0.600 (0.053%), neg=0, invalid=762 0139: dt=110.976000, rms=0.600 (0.056%), neg=0, invalid=762 0140: dt=129.472000, rms=0.600 (0.014%), neg=0, invalid=762 0141: dt=129.472000, rms=0.600 (0.034%), neg=0, invalid=762 0142: dt=129.472000, rms=0.600 (0.040%), neg=0, invalid=762 0143: dt=129.472000, rms=0.599 (0.053%), neg=0, invalid=762 0144: dt=129.472000, rms=0.599 (0.064%), neg=0, invalid=762 0145: dt=129.472000, rms=0.598 (0.083%), neg=0, invalid=762 0146: dt=129.472000, rms=0.598 (0.085%), neg=0, invalid=762 0147: dt=129.472000, rms=0.597 (0.091%), neg=0, invalid=762 0148: dt=129.472000, rms=0.597 (0.086%), neg=0, invalid=762 0149: dt=129.472000, rms=0.596 (0.095%), neg=0, invalid=762 0150: dt=129.472000, rms=0.596 (0.096%), neg=0, invalid=762 0151: dt=129.472000, rms=0.595 (0.092%), neg=0, invalid=762 0152: dt=129.472000, rms=0.595 (0.085%), neg=0, invalid=762 0153: dt=129.472000, rms=0.594 (0.083%), neg=0, invalid=762 0154: dt=129.472000, rms=0.594 (0.084%), neg=0, invalid=762 0155: dt=129.472000, rms=0.593 (0.081%), neg=0, invalid=762 0156: dt=129.472000, rms=0.593 (0.079%), neg=0, invalid=762 0157: dt=129.472000, rms=0.592 (0.077%), neg=0, invalid=762 0158: dt=129.472000, rms=0.592 (0.070%), neg=0, invalid=762 0159: dt=129.472000, rms=0.591 (0.067%), neg=0, invalid=762 0160: dt=129.472000, rms=0.591 (0.070%), neg=0, invalid=762 0161: dt=129.472000, rms=0.591 (0.066%), neg=0, invalid=762 0162: dt=129.472000, rms=0.590 (0.064%), neg=0, invalid=762 0163: dt=129.472000, rms=0.590 (0.064%), neg=0, invalid=762 0164: dt=129.472000, rms=0.590 (0.061%), neg=0, invalid=762 0165: dt=129.472000, rms=0.589 (0.058%), neg=0, invalid=762 0166: dt=129.472000, rms=0.589 (0.054%), neg=0, invalid=762 0167: dt=129.472000, rms=0.589 (0.053%), neg=0, invalid=762 0168: dt=129.472000, rms=0.588 (0.046%), neg=0, invalid=762 0169: dt=129.472000, rms=0.588 (0.044%), neg=0, invalid=762 0170: dt=129.472000, rms=0.588 (0.047%), neg=0, invalid=762 0171: dt=129.472000, rms=0.587 (0.047%), neg=0, invalid=762 0172: dt=129.472000, rms=0.587 (0.042%), neg=0, invalid=762 0173: dt=129.472000, rms=0.587 (0.039%), neg=0, invalid=762 0174: dt=129.472000, rms=0.587 (0.041%), neg=0, invalid=762 0175: dt=129.472000, rms=0.587 (0.040%), neg=0, invalid=762 0176: dt=129.472000, rms=0.586 (0.036%), neg=0, invalid=762 0177: dt=129.472000, rms=0.586 (0.032%), neg=0, invalid=762 0178: dt=129.472000, rms=0.586 (0.032%), neg=0, invalid=762 0179: dt=129.472000, rms=0.586 (0.036%), neg=0, invalid=762 0180: dt=129.472000, rms=0.585 (0.042%), neg=0, invalid=762 0181: dt=129.472000, rms=0.585 (0.033%), neg=0, invalid=762 0182: dt=129.472000, rms=0.585 (0.024%), neg=0, invalid=762 0183: dt=129.472000, rms=0.585 (0.034%), neg=0, invalid=762 0184: dt=129.472000, rms=0.585 (0.027%), neg=0, invalid=762 0185: dt=129.472000, rms=0.585 (0.023%), neg=0, invalid=762 0186: dt=129.472000, rms=0.584 (0.030%), neg=0, invalid=762 0187: dt=129.472000, rms=0.584 (0.035%), neg=0, invalid=762 0188: dt=129.472000, rms=0.584 (0.024%), neg=0, invalid=762 0189: dt=129.472000, rms=0.584 (0.025%), neg=0, invalid=762 0190: dt=129.472000, rms=0.584 (0.024%), neg=0, invalid=762 0191: dt=129.472000, rms=0.584 (0.035%), neg=0, invalid=762 0192: dt=129.472000, rms=0.584 (0.020%), neg=0, invalid=762 0193: dt=129.472000, rms=0.583 (0.024%), neg=0, invalid=762 0194: dt=129.472000, rms=0.583 (0.028%), neg=0, invalid=762 0195: dt=129.472000, rms=0.583 (0.023%), neg=0, invalid=762 0196: dt=129.472000, rms=0.583 (0.020%), neg=0, invalid=762 0197: dt=517.888000, rms=0.583 (0.019%), neg=0, invalid=762 0198: dt=517.888000, rms=0.583 (-0.313%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.584, neg=0, invalid=762 0199: dt=65.939394, rms=0.582 (0.340%), neg=0, invalid=762 0200: dt=414.720000, rms=0.571 (1.883%), neg=0, invalid=762 0201: dt=68.824121, rms=0.567 (0.657%), neg=0, invalid=762 0202: dt=145.152000, rms=0.564 (0.660%), neg=0, invalid=762 0203: dt=56.510638, rms=0.561 (0.364%), neg=0, invalid=762 0204: dt=103.680000, rms=0.560 (0.266%), neg=0, invalid=762 0205: dt=36.288000, rms=0.559 (0.195%), neg=0, invalid=762 0206: dt=580.608000, rms=0.552 (1.152%), neg=0, invalid=762 0207: dt=36.288000, rms=0.551 (0.330%), neg=0, invalid=762 0208: dt=145.152000, rms=0.549 (0.231%), neg=0, invalid=762 0209: dt=82.944000, rms=0.549 (0.147%), neg=0, invalid=762 0210: dt=103.680000, rms=0.548 (0.147%), neg=0, invalid=762 0211: dt=36.288000, rms=0.547 (0.097%), neg=0, invalid=762 0212: dt=580.608000, rms=0.544 (0.673%), neg=0, invalid=762 0213: dt=36.288000, rms=0.543 (0.156%), neg=0, invalid=762 0214: dt=331.776000, rms=0.542 (0.208%), neg=0, invalid=762 0215: dt=36.288000, rms=0.540 (0.205%), neg=0, invalid=762 0216: dt=145.152000, rms=0.540 (0.110%), neg=0, invalid=762 0217: dt=82.944000, rms=0.539 (0.091%), neg=0, invalid=762 0218: dt=103.680000, rms=0.539 (0.092%), neg=0, invalid=762 0219: dt=62.208000, rms=0.538 (0.074%), neg=0, invalid=762 0220: dt=124.416000, rms=0.538 (0.116%), neg=0, invalid=762 0221: dt=9.072000, rms=0.538 (0.012%), neg=0, invalid=762 0222: dt=9.072000, rms=0.538 (0.010%), neg=0, invalid=762 0223: dt=4.536000, rms=0.538 (0.003%), neg=0, invalid=762 0224: dt=1.134000, rms=0.538 (0.001%), neg=0, invalid=762 0225: dt=0.141750, rms=0.538 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.538, neg=0, invalid=762 0226: dt=145.152000, rms=0.535 (0.667%), neg=0, invalid=762 0227: dt=36.288000, rms=0.534 (0.153%), neg=0, invalid=762 0228: dt=145.152000, rms=0.533 (0.158%), neg=0, invalid=762 0229: dt=145.152000, rms=0.532 (0.237%), neg=0, invalid=762 0230: dt=36.288000, rms=0.531 (0.092%), neg=0, invalid=762 0231: dt=145.152000, rms=0.531 (0.111%), neg=0, invalid=762 0232: dt=36.288000, rms=0.530 (0.070%), neg=0, invalid=762 0233: dt=9.072000, rms=0.530 (0.012%), neg=0, invalid=762 0234: dt=9.072000, rms=0.530 (0.011%), neg=0, invalid=762 0235: dt=4.536000, rms=0.530 (0.006%), neg=0, invalid=762 0236: dt=2.268000, rms=0.530 (0.003%), neg=0, invalid=762 0237: dt=0.567000, rms=0.530 (0.001%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.536, neg=0, invalid=762 0238: dt=0.010937, rms=0.535 (0.092%), neg=0, invalid=762 0239: dt=0.002734, rms=0.535 (0.000%), neg=0, invalid=762 0240: dt=0.000342, rms=0.535 (0.000%), neg=0, invalid=762 0241: dt=0.000085, rms=0.535 (0.000%), neg=0, invalid=762 0242: dt=0.000043, rms=0.535 (0.000%), neg=0, invalid=762 0243: dt=0.000000, rms=0.535 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.536, neg=0, invalid=762 0244: dt=44.800000, rms=0.522 (2.517%), neg=0, invalid=762 0245: dt=44.800000, rms=0.513 (1.682%), neg=0, invalid=762 0246: dt=44.800000, rms=0.507 (1.206%), neg=0, invalid=762 0247: dt=0.700000, rms=0.507 (0.016%), neg=0, invalid=762 0248: dt=0.350000, rms=0.507 (0.010%), neg=0, invalid=762 0249: dt=0.175000, rms=0.507 (0.004%), neg=0, invalid=762 0250: dt=0.087500, rms=0.507 (0.002%), neg=0, invalid=762 0251: dt=0.037500, rms=0.507 (0.001%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.522, neg=0, invalid=762 0252: dt=4.032000, rms=0.518 (0.877%), neg=0, invalid=762 0253: dt=4.032000, rms=0.515 (0.584%), neg=0, invalid=762 0254: dt=0.015750, rms=0.515 (0.003%), neg=0, invalid=762 0255: dt=0.015750, rms=0.515 (0.002%), neg=0, invalid=762 0256: dt=0.003938, rms=0.515 (0.000%), neg=0, invalid=762 0257: dt=0.001969, rms=0.515 (0.000%), neg=0, invalid=762 0258: dt=0.000984, rms=0.515 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.515, neg=0, invalid=762 0259: dt=0.000630, rms=0.515 (0.083%), neg=0, invalid=762 0260: dt=0.000000, rms=0.515 (0.000%), neg=0, invalid=762 0261: dt=0.000002, rms=0.515 (0.000%), neg=0, invalid=762 0262: dt=0.000002, rms=0.515 (0.000%), neg=0, invalid=762 0263: dt=0.000001, rms=0.515 (0.000%), neg=0, invalid=762 0264: dt=0.000000, rms=0.515 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.544, neg=0, invalid=762 0265: dt=1.792000, rms=0.542 (0.406%), neg=0, invalid=762 0266: dt=1.024000, rms=0.542 (0.036%), neg=0, invalid=762 0267: dt=1.024000, rms=0.542 (-0.009%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.542, neg=0, invalid=762 0268: dt=4.096000, rms=0.539 (0.572%), neg=0, invalid=762 0269: dt=0.000000, rms=0.539 (-0.000%), neg=0, invalid=762 0270: dt=0.100000, rms=0.539 (-0.002%), 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=0.505, neg=0, invalid=762 0271: dt=0.448000, rms=0.491 (2.763%), neg=0, invalid=762 0272: dt=0.448000, rms=0.488 (0.784%), neg=0, invalid=762 0273: dt=0.448000, rms=0.485 (0.485%), neg=0, invalid=762 0274: dt=0.448000, rms=0.484 (0.314%), neg=0, invalid=762 0275: dt=0.448000, rms=0.483 (0.243%), neg=0, invalid=762 0276: dt=0.448000, rms=0.482 (0.174%), neg=0, invalid=762 0277: dt=0.466667, rms=0.481 (0.159%), neg=0, invalid=762 0278: dt=0.448000, rms=0.480 (0.108%), neg=0, invalid=762 0279: dt=0.448000, rms=0.480 (0.103%), neg=0, invalid=762 0280: dt=0.448000, rms=0.480 (0.076%), neg=0, invalid=762 0281: dt=0.448000, rms=0.479 (0.076%), neg=0, invalid=762 0282: dt=0.448000, rms=0.479 (0.052%), neg=0, invalid=762 0283: dt=0.448000, rms=0.479 (0.059%), neg=0, invalid=762 0284: dt=0.448000, rms=0.478 (0.037%), neg=0, invalid=762 0285: dt=0.448000, rms=0.478 (0.043%), neg=0, invalid=762 0286: dt=0.448000, rms=0.478 (0.074%), neg=0, invalid=762 0287: dt=0.448000, rms=0.478 (0.082%), neg=0, invalid=762 0288: dt=0.448000, rms=0.477 (0.093%), neg=0, invalid=762 0289: dt=0.224000, rms=0.477 (0.009%), neg=0, invalid=762 0290: dt=0.224000, rms=0.477 (0.015%), neg=0, invalid=762 0291: dt=0.224000, rms=0.477 (0.001%), neg=0, invalid=762 0292: dt=0.448000, rms=0.477 (0.015%), neg=0, invalid=762 0293: dt=0.112000, rms=0.477 (0.000%), neg=0, invalid=762 0294: dt=0.112000, rms=0.477 (0.001%), neg=0, invalid=762 0295: dt=0.112000, rms=0.477 (0.004%), neg=0, invalid=762 0296: dt=0.112000, rms=0.477 (0.005%), neg=0, invalid=762 0297: dt=0.112000, rms=0.477 (0.006%), neg=0, invalid=762 0298: dt=0.112000, rms=0.477 (0.005%), neg=0, invalid=762 0299: dt=0.112000, rms=0.477 (0.009%), neg=0, invalid=762 0300: dt=0.112000, rms=0.477 (0.008%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.477, neg=0, invalid=762 0301: dt=0.320000, rms=0.474 (0.610%), neg=0, invalid=762 0302: dt=0.320000, rms=0.473 (0.173%), neg=0, invalid=762 0303: dt=0.320000, rms=0.473 (0.066%), neg=0, invalid=762 0304: dt=0.320000, rms=0.473 (0.026%), neg=0, invalid=762 0305: dt=0.320000, rms=0.473 (0.013%), neg=0, invalid=762 0306: dt=0.320000, rms=0.473 (0.019%), neg=0, invalid=762 0307: dt=0.320000, rms=0.473 (0.009%), neg=0, invalid=762 0308: dt=0.320000, rms=0.473 (-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=0.471, neg=0, invalid=762 0309: dt=0.000000, rms=0.470 (0.098%), neg=0, invalid=762 0310: dt=0.000000, rms=0.470 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.471, neg=0, invalid=762 0311: dt=129.472000, rms=0.470 (0.128%), neg=0, invalid=762 0312: dt=129.472000, rms=0.470 (0.023%), neg=0, invalid=762 0313: dt=129.472000, rms=0.470 (0.012%), neg=0, invalid=762 0314: dt=129.472000, rms=0.470 (0.027%), neg=0, invalid=762 0315: dt=129.472000, rms=0.470 (0.027%), neg=0, invalid=762 0316: dt=129.472000, rms=0.470 (0.035%), neg=0, invalid=762 0317: dt=129.472000, rms=0.470 (0.018%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.470, neg=0, invalid=762 0318: dt=20.736000, rms=0.469 (0.121%), neg=0, invalid=762 0319: dt=20.736000, rms=0.469 (0.017%), neg=0, invalid=762 0320: dt=20.736000, rms=0.469 (0.019%), neg=0, invalid=762 0321: dt=20.736000, rms=0.469 (0.017%), neg=0, invalid=762 0322: dt=20.736000, rms=0.469 (-0.004%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.470, neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0323: dt=109.751004, rms=0.466 (0.703%), neg=0, invalid=762 0324: dt=36.288000, rms=0.466 (0.152%), neg=0, invalid=762 0325: dt=36.288000, rms=0.465 (0.056%), neg=0, invalid=762 0326: dt=36.288000, rms=0.465 (0.092%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0327: dt=36.288000, rms=0.464 (0.140%), neg=0, invalid=762 0328: dt=36.288000, rms=0.463 (0.183%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 9 iterations, nbhd size=1, neg = 0 0329: dt=36.288000, rms=0.463 (0.186%), neg=0, invalid=762 0330: dt=36.288000, rms=0.462 (0.175%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 0331: dt=36.288000, rms=0.461 (0.148%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0332: dt=36.288000, rms=0.461 (0.112%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0333: dt=36.288000, rms=0.460 (0.093%), neg=0, invalid=762 0334: dt=331.776000, rms=0.460 (0.122%), neg=0, invalid=762 0335: dt=31.104000, rms=0.459 (0.058%), neg=0, invalid=762 0336: dt=31.104000, rms=0.459 (0.011%), neg=0, invalid=762 0337: dt=31.104000, rms=0.459 (0.013%), neg=0, invalid=762 0338: dt=31.104000, rms=0.459 (0.015%), neg=0, invalid=762 0339: dt=31.104000, rms=0.459 (0.038%), neg=0, invalid=762 0340: dt=31.104000, rms=0.459 (0.055%), neg=0, invalid=762 0341: dt=31.104000, rms=0.459 (0.054%), neg=0, invalid=762 0342: dt=31.104000, rms=0.458 (0.046%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.459, neg=0, invalid=762 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0343: dt=44.800000, rms=0.456 (0.808%), neg=0, invalid=762 iter 0, gcam->neg = 20 after 13 iterations, nbhd size=1, neg = 0 0344: dt=86.243070, rms=0.450 (1.195%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0345: dt=20.762923, rms=0.449 (0.364%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 4 iterations, nbhd size=0, neg = 0 0346: dt=44.800000, rms=0.448 (0.195%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 0347: dt=44.800000, rms=0.447 (0.253%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 12 iterations, nbhd size=1, neg = 0 0348: dt=44.800000, rms=0.444 (0.512%), neg=0, invalid=762 iter 0, gcam->neg = 15 after 14 iterations, nbhd size=1, neg = 0 0349: dt=44.800000, rms=0.443 (0.237%), neg=0, invalid=762 iter 0, gcam->neg = 36 after 22 iterations, nbhd size=1, neg = 0 0350: dt=44.800000, rms=0.441 (0.432%), neg=0, invalid=762 iter 0, gcam->neg = 35 after 19 iterations, nbhd size=1, neg = 0 0351: dt=44.800000, rms=0.440 (0.244%), neg=0, invalid=762 iter 0, gcam->neg = 57 after 19 iterations, nbhd size=1, neg = 0 0352: dt=44.800000, rms=0.439 (0.373%), neg=0, invalid=762 iter 0, gcam->neg = 56 after 19 iterations, nbhd size=1, neg = 0 0353: dt=44.800000, rms=0.438 (0.092%), neg=0, invalid=762 iter 0, gcam->neg = 62 after 30 iterations, nbhd size=1, neg = 0 0354: dt=44.800000, rms=0.438 (-0.015%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 18 iterations, nbhd size=1, neg = 0 0355: dt=22.686567, rms=0.437 (0.312%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0356: dt=25.600000, rms=0.436 (0.134%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0357: dt=25.600000, rms=0.436 (0.022%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 9 iterations, nbhd size=1, neg = 0 0358: dt=25.600000, rms=0.436 (0.032%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 10 iterations, nbhd size=0, neg = 0 0359: dt=25.600000, rms=0.436 (0.055%), neg=0, invalid=762 iter 0, gcam->neg = 12 after 8 iterations, nbhd size=0, neg = 0 0360: dt=25.600000, rms=0.436 (0.030%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 14 iterations, nbhd size=1, neg = 0 0361: dt=25.600000, rms=0.436 (0.032%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 19 iterations, nbhd size=2, neg = 0 0362: dt=25.600000, rms=0.436 (-0.042%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.436, neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0363: dt=55.074830, rms=0.433 (0.795%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0364: dt=20.263323, rms=0.432 (0.257%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0365: dt=38.400000, rms=0.431 (0.150%), neg=0, invalid=762 0366: dt=38.400000, rms=0.431 (0.084%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0367: dt=38.400000, rms=0.429 (0.262%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0368: dt=38.400000, rms=0.429 (0.006%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0369: dt=38.400000, rms=0.428 (0.222%), neg=0, invalid=762 0370: dt=38.400000, rms=0.428 (-0.033%), neg=0, invalid=762 0371: dt=25.600000, rms=0.428 (0.074%), neg=0, invalid=762 0372: dt=19.200000, rms=0.428 (0.035%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.436, neg=0, invalid=762 0373: dt=0.000000, rms=0.436 (0.108%), neg=0, invalid=762 0374: dt=0.000000, rms=0.436 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.436, neg=0, invalid=762 0375: dt=1.008000, rms=0.436 (0.113%), neg=0, invalid=762 0376: dt=0.252000, rms=0.436 (0.004%), neg=0, invalid=762 0377: dt=0.252000, rms=0.436 (0.001%), neg=0, invalid=762 0378: dt=0.252000, rms=0.436 (0.001%), neg=0, invalid=762 0379: dt=0.252000, rms=0.436 (-0.008%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.451, neg=0, invalid=762 0380: dt=1.280000, rms=0.449 (0.412%), neg=0, invalid=762 0381: dt=0.320000, rms=0.449 (0.012%), neg=0, invalid=762 0382: dt=0.320000, rms=0.449 (-0.005%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.450, neg=0, invalid=762 0383: dt=1.280000, rms=0.449 (0.241%), neg=0, invalid=762 0384: dt=0.320000, rms=0.449 (0.008%), neg=0, invalid=762 0385: dt=0.320000, rms=0.449 (-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=0.436, neg=0, invalid=762 iter 0, gcam->neg = 859 after 13 iterations, nbhd size=1, neg = 0 0386: dt=2.163997, rms=0.409 (6.236%), neg=0, invalid=762 0387: dt=0.028000, rms=0.408 (0.017%), neg=0, invalid=762 0388: dt=0.028000, rms=0.408 (0.001%), neg=0, invalid=762 0389: dt=0.028000, rms=0.408 (-0.028%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.409, neg=0, invalid=762 0390: dt=0.048000, rms=0.408 (0.170%), neg=0, invalid=762 0391: dt=0.001750, rms=0.408 (-0.001%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.395, neg=0, invalid=762 0392: dt=0.000000, rms=0.395 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.395, neg=0, invalid=762 0393: dt=27.744000, rms=0.395 (0.001%), neg=0, invalid=762 0394: dt=27.744000, rms=0.395 (0.000%), neg=0, invalid=762 0395: dt=27.744000, rms=0.395 (0.000%), neg=0, invalid=762 0396: dt=27.744000, rms=0.395 (-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=0.396, neg=0, invalid=762 0397: dt=0.000000, rms=0.396 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.396, neg=0, invalid=762 0398: dt=82.944000, rms=0.395 (0.050%), neg=0, invalid=762 0399: dt=145.152000, rms=0.395 (0.072%), neg=0, invalid=762 0400: dt=36.288000, rms=0.395 (0.015%), neg=0, invalid=762 0401: dt=36.288000, rms=0.395 (0.010%), neg=0, invalid=762 0402: dt=36.288000, rms=0.395 (0.018%), neg=0, invalid=762 0403: dt=36.288000, rms=0.395 (0.023%), neg=0, invalid=762 0404: dt=36.288000, rms=0.395 (0.026%), neg=0, invalid=762 0405: dt=36.288000, rms=0.395 (0.024%), neg=0, invalid=762 0406: dt=36.288000, rms=0.395 (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=0.395, neg=0, invalid=762 0407: dt=11.200000, rms=0.395 (0.089%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0408: dt=19.200000, rms=0.395 (0.072%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 7 iterations, nbhd size=1, neg = 0 0409: dt=19.200000, rms=0.394 (0.055%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 9 iterations, nbhd size=1, neg = 0 0410: dt=19.200000, rms=0.394 (0.042%), neg=0, invalid=762 iter 0, gcam->neg = 31 after 14 iterations, nbhd size=1, neg = 0 0411: dt=19.200000, rms=0.394 (-0.116%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.394, neg=0, invalid=762 iter 0, gcam->neg = 7 after 11 iterations, nbhd size=1, neg = 0 0412: dt=60.800000, rms=0.391 (0.860%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 10 iterations, nbhd size=1, neg = 0 0413: dt=25.247706, rms=0.390 (0.236%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0414: dt=25.247706, rms=0.389 (0.126%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=0, neg = 0 0415: dt=25.247706, rms=0.389 (0.162%), neg=0, invalid=762 iter 0, gcam->neg = 11 after 13 iterations, nbhd size=1, neg = 0 0416: dt=25.247706, rms=0.388 (0.168%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 10 iterations, nbhd size=1, neg = 0 0417: dt=25.247706, rms=0.387 (0.209%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 5 iterations, nbhd size=0, neg = 0 0418: dt=25.247706, rms=0.386 (0.229%), neg=0, invalid=762 iter 0, gcam->neg = 20 after 15 iterations, nbhd size=1, neg = 0 0419: dt=25.247706, rms=0.386 (0.171%), neg=0, invalid=762 iter 0, gcam->neg = 15 after 5 iterations, nbhd size=0, neg = 0 0420: dt=25.247706, rms=0.385 (0.157%), neg=0, invalid=762 iter 0, gcam->neg = 12 after 20 iterations, nbhd size=2, neg = 0 0421: dt=25.247706, rms=0.385 (0.043%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 14 iterations, nbhd size=1, neg = 0 0422: dt=25.247706, rms=0.384 (0.138%), neg=0, invalid=762 iter 0, gcam->neg = 13 after 10 iterations, nbhd size=1, neg = 0 0423: dt=25.247706, rms=0.384 (0.129%), neg=0, invalid=762 iter 0, gcam->neg = 22 after 14 iterations, nbhd size=1, neg = 0 0424: dt=25.247706, rms=0.383 (0.111%), neg=0, invalid=762 iter 0, gcam->neg = 13 after 19 iterations, nbhd size=1, neg = 0 0425: dt=25.247706, rms=0.383 (0.059%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0426: dt=25.600000, rms=0.383 (0.012%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0427: dt=25.600000, rms=0.383 (0.007%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 11 iterations, nbhd size=1, neg = 0 0428: dt=25.600000, rms=0.383 (-0.002%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.388, neg=0, invalid=762 0429: dt=1.008000, rms=0.388 (0.006%), neg=0, invalid=762 0430: dt=0.432000, rms=0.388 (0.001%), neg=0, invalid=762 0431: dt=0.432000, rms=0.388 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.388, neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0432: dt=4.032000, rms=0.388 (0.041%), neg=0, invalid=762 0433: dt=2.880000, rms=0.388 (0.009%), neg=0, invalid=762 0434: dt=2.880000, rms=0.388 (0.001%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 6 iterations, nbhd size=0, neg = 0 0435: dt=2.880000, rms=0.388 (-0.034%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.397, neg=0, invalid=762 0436: dt=0.000000, rms=0.397 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.397, neg=0, invalid=762 0437: dt=0.000000, rms=0.397 (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=0.382, neg=0, invalid=762 iter 0, gcam->neg = 598 after 18 iterations, nbhd size=1, neg = 0 0438: dt=1.024000, rms=0.375 (1.816%), neg=0, invalid=762 0439: dt=0.000040, rms=0.375 (0.000%), neg=0, invalid=762 0440: dt=0.000040, rms=0.375 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.375, neg=0, invalid=762 0441: dt=0.112000, rms=0.375 (0.062%), neg=0, invalid=762 0442: dt=0.112000, rms=0.375 (0.035%), neg=0, invalid=762 0443: dt=0.112000, rms=0.375 (0.033%), neg=0, invalid=762 0444: dt=0.112000, rms=0.375 (0.025%), neg=0, invalid=762 0445: dt=0.112000, rms=0.375 (-0.021%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 1 hours, 5 minutes and 27 seconds. mri_ca_register utimesec 4943.582988 mri_ca_register stimesec 16.343260 mri_ca_register ru_maxrss 1331976 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 16912184 mri_ca_register ru_majflt 0 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 8216 mri_ca_register ru_oublock 63400 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 70788 mri_ca_register ru_nivcsw 9065 FSRUNTIME@ mri_ca_register 1.0908 hours 8 threads #-------------------------------------- #@# SubCort Seg Mon Jun 23 23:45:40 CST 2025 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 cn77042 machine x86_64 setenv SUBJECTS_DIR /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer cd /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer/sub-OAS30001/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 = 8 == 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 5.36 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 = 0.15166 (17) Left_Lateral_Ventricle (4): linear fit = 0.87 x + 0.0 (1894 voxels, overlap=0.606) Left_Lateral_Ventricle (4): linear fit = 0.87 x + 0.0 (1894 voxels, peak = 17), gca=17.3 gca peak = 0.17677 (13) mri peak = 0.13766 (17) Right_Lateral_Ventricle (43): linear fit = 1.20 x + 0.0 (1293 voxels, overlap=0.658) Right_Lateral_Ventricle (43): linear fit = 1.20 x + 0.0 (1293 voxels, peak = 16), gca=15.5 gca peak = 0.28129 (95) mri peak = 0.18697 (99) Right_Pallidum (52): linear fit = 1.04 x + 0.0 (491 voxels, overlap=0.735) Right_Pallidum (52): linear fit = 1.04 x + 0.0 (491 voxels, peak = 99), gca=99.3 gca peak = 0.16930 (96) mri peak = 0.19724 (98) Left_Pallidum (13): linear fit = 1.03 x + 0.0 (521 voxels, overlap=0.492) Left_Pallidum (13): linear fit = 1.03 x + 0.0 (521 voxels, peak = 99), gca=99.4 gca peak = 0.24553 (55) mri peak = 0.13193 (70) Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (944 voxels, overlap=0.020) Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (944 voxels, peak = 67), gca=67.4 gca peak = 0.30264 (59) mri peak = 0.10916 (68) Left_Hippocampus (17): linear fit = 1.21 x + 0.0 (742 voxels, overlap=0.016) Left_Hippocampus (17): linear fit = 1.21 x + 0.0 (742 voxels, peak = 71), gca=71.1 gca peak = 0.07580 (103) mri peak = 0.11909 (107) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (27728 voxels, overlap=0.495) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (27728 voxels, peak = 106), gca=105.6 gca peak = 0.07714 (104) mri peak = 0.11198 (107) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (29927 voxels, overlap=0.465) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (29927 voxels, peak = 108), gca=107.6 gca peak = 0.09712 (58) mri peak = 0.04910 (67) Left_Cerebral_Cortex (3): linear fit = 1.13 x + 0.0 (21671 voxels, overlap=0.545) Left_Cerebral_Cortex (3): linear fit = 1.13 x + 0.0 (21671 voxels, peak = 66), gca=65.8 gca peak = 0.11620 (58) mri peak = 0.05028 (68) Right_Cerebral_Cortex (42): linear fit = 1.15 x + 0.0 (19646 voxels, overlap=0.432) Right_Cerebral_Cortex (42): linear fit = 1.15 x + 0.0 (19646 voxels, peak = 67), gca=67.0 gca peak = 0.30970 (66) mri peak = 0.20700 (83) Right_Caudate (50): linear fit = 1.21 x + 0.0 (666 voxels, overlap=0.015) Right_Caudate (50): linear fit = 1.21 x + 0.0 (666 voxels, peak = 80), gca=79.5 gca peak = 0.15280 (69) mri peak = 0.19214 (83) Left_Caudate (11): linear fit = 1.07 x + 0.0 (664 voxels, overlap=0.208) Left_Caudate (11): linear fit = 1.07 x + 0.0 (664 voxels, peak = 73), gca=73.5 gca peak = 0.13902 (56) mri peak = 0.05797 (64) Left_Cerebellum_Cortex (8): linear fit = 1.13 x + 0.0 (18990 voxels, overlap=0.721) Left_Cerebellum_Cortex (8): linear fit = 1.13 x + 0.0 (18990 voxels, peak = 64), gca=63.6 gca peak = 0.14777 (55) mri peak = 0.06592 (62) Right_Cerebellum_Cortex (47): linear fit = 1.12 x + 0.0 (19126 voxels, overlap=0.721) Right_Cerebellum_Cortex (47): linear fit = 1.12 x + 0.0 (19126 voxels, peak = 61), gca=61.3 gca peak = 0.16765 (84) mri peak = 0.15363 (90) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (6675 voxels, overlap=0.237) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (6675 voxels, peak = 90), gca=90.3 gca peak = 0.18739 (84) mri peak = 0.14781 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (8297 voxels, overlap=0.466) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (8297 voxels, peak = 89), gca=89.5 gca peak = 0.29869 (57) mri peak = 0.12535 (69) Left_Amygdala (18): linear fit = 1.22 x + 0.0 (359 voxels, overlap=0.053) Left_Amygdala (18): linear fit = 1.22 x + 0.0 (359 voxels, peak = 69), gca=69.3 gca peak = 0.33601 (57) mri peak = 0.13018 (67) Right_Amygdala (54): linear fit = 1.18 x + 0.0 (332 voxels, overlap=0.039) Right_Amygdala (54): linear fit = 1.18 x + 0.0 (332 voxels, peak = 68), gca=67.5 gca peak = 0.11131 (90) mri peak = 0.10657 (90) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (3615 voxels, overlap=0.786) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (3615 voxels, peak = 91), gca=91.3 gca peak = 0.11793 (83) mri peak = 0.11394 (88) Right_Thalamus_Proper (49): linear fit = 1.08 x + 0.0 (3772 voxels, overlap=0.679) Right_Thalamus_Proper (49): linear fit = 1.08 x + 0.0 (3772 voxels, peak = 89), gca=89.2 gca peak = 0.08324 (81) mri peak = 0.09914 (89) Left_Putamen (12): linear fit = 1.10 x + 0.0 (1397 voxels, overlap=0.353) Left_Putamen (12): linear fit = 1.10 x + 0.0 (1397 voxels, peak = 89), gca=88.7 gca peak = 0.10360 (77) mri peak = 0.11731 (84) Right_Putamen (51): linear fit = 1.11 x + 0.0 (1404 voxels, overlap=0.377) Right_Putamen (51): linear fit = 1.11 x + 0.0 (1404 voxels, peak = 85), gca=85.1 gca peak = 0.08424 (78) mri peak = 0.10800 (88) Brain_Stem (16): linear fit = 1.09 x + 0.0 (12839 voxels, overlap=0.414) Brain_Stem (16): linear fit = 1.09 x + 0.0 (12839 voxels, peak = 85), gca=84.6 gca peak = 0.12631 (89) mri peak = 0.11010 (95) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1235 voxels, overlap=0.321) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1235 voxels, peak = 97), gca=97.5 gca peak = 0.14500 (87) mri peak = 0.11769 (97) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (1308 voxels, overlap=0.152) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (1308 voxels, peak = 96), gca=96.1 gca peak = 0.14975 (24) mri peak = 0.23686 (21) gca peak = 0.19357 (14) mri peak = 0.26175 (21) Fourth_Ventricle (15): linear fit = 1.39 x + 0.0 (145 voxels, overlap=0.482) Fourth_Ventricle (15): linear fit = 1.39 x + 0.0 (145 voxels, peak = 20), gca=19.5 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 1.00000 (94) gca peak Third_Ventricle = 0.14975 (24) gca peak CSF = 0.23379 (36) gca peak Left_Accumbens_area = 0.70037 (62) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.24655 (23) gca peak Right_Accumbens_area = 0.45042 (65) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.65475 (32) gca peak WM_hypointensities = 0.07854 (76) gca peak non_WM_hypointensities = 0.08491 (43) gca peak Optic_Chiasm = 0.71127 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.19 x + 0.0 estimating mean wm scale to be 1.03 x + 0.0 estimating mean csf scale to be 1.15 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.17218 (16) mri peak = 0.15166 (17) Left_Lateral_Ventricle (4): linear fit = 0.93 x + 0.0 (1894 voxels, overlap=0.856) Left_Lateral_Ventricle (4): linear fit = 0.93 x + 0.0 (1894 voxels, peak = 15), gca=14.8 gca peak = 0.16342 (15) mri peak = 0.13766 (17) Right_Lateral_Ventricle (43): linear fit = 0.98 x + 0.0 (1293 voxels, overlap=0.610) Right_Lateral_Ventricle (43): linear fit = 0.98 x + 0.0 (1293 voxels, peak = 15), gca=14.6 gca peak = 0.29137 (100) mri peak = 0.18697 (99) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (491 voxels, overlap=1.002) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (491 voxels, peak = 100), gca=100.0 gca peak = 0.17344 (100) mri peak = 0.19724 (98) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (521 voxels, overlap=0.903) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (521 voxels, peak = 100), gca=100.0 gca peak = 0.25346 (68) mri peak = 0.13193 (70) Right_Hippocampus (53): linear fit = 0.96 x + 0.0 (944 voxels, overlap=0.981) Right_Hippocampus (53): linear fit = 0.96 x + 0.0 (944 voxels, peak = 66), gca=65.6 gca peak = 0.27407 (68) mri peak = 0.10916 (68) Left_Hippocampus (17): linear fit = 0.98 x + 0.0 (742 voxels, overlap=1.001) Left_Hippocampus (17): linear fit = 0.98 x + 0.0 (742 voxels, peak = 66), gca=66.3 gca peak = 0.07615 (105) mri peak = 0.11909 (107) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (27728 voxels, overlap=0.612) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (27728 voxels, peak = 106), gca=105.5 gca peak = 0.07663 (108) mri peak = 0.11198 (107) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (29927 voxels, overlap=0.630) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (29927 voxels, peak = 108), gca=108.0 gca peak = 0.08623 (66) mri peak = 0.04910 (67) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (21671 voxels, overlap=0.961) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (21671 voxels, peak = 66), gca=66.0 gca peak = 0.10161 (67) mri peak = 0.05028 (68) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (19646 voxels, overlap=0.955) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (19646 voxels, peak = 67), gca=67.0 gca peak = 0.21544 (80) mri peak = 0.20700 (83) Right_Caudate (50): linear fit = 1.01 x + 0.0 (666 voxels, overlap=0.999) Right_Caudate (50): linear fit = 1.01 x + 0.0 (666 voxels, peak = 81), gca=81.2 gca peak = 0.12686 (73) mri peak = 0.19214 (83) Left_Caudate (11): linear fit = 1.01 x + 0.0 (664 voxels, overlap=0.592) Left_Caudate (11): linear fit = 1.01 x + 0.0 (664 voxels, peak = 74), gca=74.1 gca peak = 0.12594 (63) mri peak = 0.05797 (64) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (18990 voxels, overlap=0.996) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (18990 voxels, peak = 63), gca=63.0 gca peak = 0.14151 (61) mri peak = 0.06592 (62) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (19126 voxels, overlap=0.988) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (19126 voxels, peak = 61), gca=61.0 gca peak = 0.16303 (91) mri peak = 0.15363 (90) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6675 voxels, overlap=0.856) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6675 voxels, peak = 91), gca=91.0 gca peak = 0.15240 (90) mri peak = 0.14781 (88) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (8297 voxels, overlap=0.868) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (8297 voxels, peak = 89), gca=88.7 gca peak = 0.27695 (69) mri peak = 0.12535 (69) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (359 voxels, overlap=1.008) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (359 voxels, peak = 69), gca=69.0 gca peak = 0.31323 (68) mri peak = 0.13018 (67) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (332 voxels, overlap=1.000) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (332 voxels, peak = 68), gca=68.0 gca peak = 0.10590 (90) mri peak = 0.10657 (90) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3615 voxels, overlap=0.831) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3615 voxels, peak = 90), gca=89.6 gca peak = 0.10395 (87) mri peak = 0.11394 (88) Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (3772 voxels, overlap=0.886) Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (3772 voxels, peak = 86), gca=85.7 gca peak = 0.07937 (85) mri peak = 0.09914 (89) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1397 voxels, overlap=0.776) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1397 voxels, peak = 85), gca=84.6 gca peak = 0.07581 (86) mri peak = 0.11731 (84) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1404 voxels, overlap=0.857) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1404 voxels, peak = 86), gca=86.0 gca peak = 0.08258 (85) mri peak = 0.10800 (88) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12839 voxels, overlap=0.694) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12839 voxels, peak = 85), gca=84.6 gca peak = 0.11389 (92) mri peak = 0.11010 (95) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1235 voxels, overlap=0.800) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1235 voxels, peak = 92), gca=91.5 gca peak = 0.14470 (94) mri peak = 0.11769 (97) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1308 voxels, overlap=0.861) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1308 voxels, peak = 94), gca=94.5 gca peak = 0.13197 (29) mri peak = 0.23686 (21) gca peak = 0.14735 (21) mri peak = 0.26175 (21) Fourth_Ventricle (15): linear fit = 0.98 x + 0.0 (145 voxels, overlap=0.650) Fourth_Ventricle (15): linear fit = 0.98 x + 0.0 (145 voxels, peak = 20), gca=20.5 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.14117 (32) gca peak Left_Thalamus = 0.64095 (105) gca peak Third_Ventricle = 0.13197 (29) gca peak CSF = 0.25410 (42) gca peak Left_Accumbens_area = 0.64157 (66) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75962 (52) gca peak Left_choroid_plexus = 0.11914 (35) gca peak Right_Inf_Lat_Vent = 0.20093 (28) gca peak Right_Accumbens_area = 0.29932 (78) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14531 (37) gca peak Fifth_Ventricle = 0.54107 (37) gca peak WM_hypointensities = 0.07310 (78) gca peak non_WM_hypointensities = 0.11678 (56) gca peak Optic_Chiasm = 0.69015 (75) not using caudate to estimate GM means estimating mean gm scale to be 0.99 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.96 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 34368 voxels changed in iteration 0 of unlikely voxel relabeling 166 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 28483 gm and wm labels changed (%27 to gray, %73 to white out of all changed labels) 434 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 45712 changed. image ll: -2.037, PF=0.500 pass 2: 11189 changed. image ll: -2.037, PF=0.500 pass 3: 3143 changed. 23365 voxels changed in iteration 0 of unlikely voxel relabeling 161 voxels changed in iteration 1 of unlikely voxel relabeling 6 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 4338 voxels changed in iteration 0 of unlikely voxel relabeling 41 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 4016 voxels changed in iteration 0 of unlikely voxel relabeling 42 voxels changed in iteration 1 of unlikely voxel relabeling 2 voxels changed in iteration 2 of unlikely voxel relabeling 5 voxels changed in iteration 3 of unlikely voxel relabeling 1 voxels changed in iteration 4 of unlikely voxel relabeling 3494 voxels changed in iteration 0 of unlikely voxel relabeling 20 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling MRItoUCHAR: min=0, max=85 MRItoUCHAR: converting to UCHAR writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 1179.534739 mri_ca_label stimesec 2.982985 mri_ca_label ru_maxrss 2117160 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 4189991 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 156616 mri_ca_label ru_oublock 400 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 653 mri_ca_label ru_nivcsw 492 auto-labeling took 19 minutes and 11 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer/sub-OAS30001/mri/transforms/cc_up.lta sub-OAS30001 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer/sub-OAS30001/mri/transforms/cc_up.lta reading aseg from /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer/sub-OAS30001/mri/aseg.auto_noCCseg.mgz reading norm from /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer/sub-OAS30001/mri/norm.mgz 30781 voxels in left wm, 26666 in right wm, xrange [119, 127] searching rotation angles z=[-2 12], y=[-9 5] searching scale 1 Z rot -2.3 searching scale 1 Z rot -2.1 searching scale 1 Z rot -1.8 searching scale 1 Z rot -1.6 searching scale 1 Z rot -1.3 searching scale 1 Z rot -1.1 searching scale 1 Z rot -0.8 searching scale 1 Z rot -0.6 searching scale 1 Z rot -0.3 searching scale 1 Z rot -0.1 searching scale 1 Z rot 0.2 searching scale 1 Z rot 0.4 searching scale 1 Z rot 0.7 searching scale 1 Z rot 0.9 searching scale 1 Z rot 1.2 searching scale 1 Z rot 1.4 searching scale 1 Z rot 1.7 searching scale 1 Z rot 1.9 searching scale 1 Z rot 2.2 searching scale 1 Z rot 2.4 searching scale 1 Z rot 2.7 searching scale 1 Z rot 2.9 searching scale 1 Z rot 3.2 searching scale 1 Z rot 3.4 searching scale 1 Z rot 3.7 searching scale 1 Z rot 3.9 searching scale 1 Z rot 4.2 searching scale 1 Z rot 4.4 searching scale 1 Z rot 4.7 searching scale 1 Z rot 4.9 searching scale 1 Z rot 5.2 searching scale 1 Z rot 5.4 searching scale 1 Z rot 5.7 searching scale 1 Z rot 5.9 searching scale 1 Z rot 6.2 searching scale 1 Z rot 6.4 searching scale 1 Z rot 6.7 searching scale 1 Z rot 6.9 searching scale 1 Z rot 7.2 searching scale 1 Z rot 7.4 searching scale 1 Z rot 7.7 searching scale 1 Z rot 7.9 searching scale 1 Z rot 8.2 searching scale 1 Z rot 8.4 searching scale 1 Z rot 8.7 searching scale 1 Z rot 8.9 searching scale 1 Z rot 9.2 searching scale 1 Z rot 9.4 searching scale 1 Z rot 9.7 searching scale 1 Z rot 9.9 searching scale 1 Z rot 10.2 searching scale 1 Z rot 10.4 searching scale 1 Z rot 10.7 searching scale 1 Z rot 10.9 searching scale 1 Z rot 11.2 searching scale 1 Z rot 11.4 global minimum found at slice 122.3, rotations (-1.56, 4.65) final transformation (x=122.3, yr=-1.559, zr=4.654): 0.99633 -0.08114 -0.02711 18.52285; 0.08111 0.99670 -0.00221 0.69747; 0.02720 -0.00000 0.99963 20.71097; 0.00000 0.00000 0.00000 1.00000; updating x range to be [126, 131] in xformed coordinates best xformed slice 128 cc center is found at 128 118 104 eigenvectors: -0.00149 0.00756 0.99997; -0.27085 -0.96260 0.00687; 0.96262 -0.27083 0.00348; error in mid anterior detected - correcting... writing aseg with callosum to /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer/sub-OAS30001/mri/aseg.auto.mgz... corpus callosum segmentation took 0.4 minutes #-------------------------------------- #@# Merge ASeg Tue Jun 24 00:05:13 CST 2025 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Tue Jun 24 00:05:13 CST 2025 /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer/sub-OAS30001/mri mri_normalize -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz assuming input volume is MGH (Van der Kouwe) MP-RAGE using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.presurf.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 272 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 73 (73), valley at 34 (34) csf peak at 37, setting threshold to 61 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 76 (76), valley at 35 (35) csf peak at 38, setting threshold to 63 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 1 minutes and 33 seconds. #-------------------------------------------- #@# Mask BFS Tue Jun 24 00:06:47 CST 2025 /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer/sub-OAS30001/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1185215 voxels in mask (pct= 7.06) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Tue Jun 24 00:06:48 CST 2025 mri_segment -mprage brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (103.0): 102.5 +- 6.9 [79.0 --> 125.0] GM (75.0) : 73.4 +- 10.6 [30.0 --> 95.0] setting bottom of white matter range to 83.9 setting top of gray matter range to 94.5 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... 2103 sparsely connected voxels removed... thickening thin strands.... 20 segments, 2280 filled 5 bright non-wm voxels segmented. 1412 diagonally connected voxels added... white matter segmentation took 0.8 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 0.26 minutes reading wm segmentation from wm.seg.mgz... 2 voxels added to wm to prevent paths from MTL structures to cortex 2121 additional wm voxels added 0 additional wm voxels added SEG EDIT: 35356 voxels turned on, 42755 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 104 new 104 115,126,128 old 104 new 104 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 11 found - 11 modified | TOTAL: 11 pass 2 (xy+): 0 found - 11 modified | TOTAL: 11 pass 1 (xy-): 9 found - 9 modified | TOTAL: 20 pass 2 (xy-): 0 found - 9 modified | TOTAL: 20 pass 1 (yz+): 6 found - 6 modified | TOTAL: 26 pass 2 (yz+): 0 found - 6 modified | TOTAL: 26 pass 1 (yz-): 10 found - 10 modified | TOTAL: 36 pass 2 (yz-): 0 found - 10 modified | TOTAL: 36 pass 1 (xz+): 6 found - 6 modified | TOTAL: 42 pass 2 (xz+): 0 found - 6 modified | TOTAL: 42 pass 1 (xz-): 7 found - 7 modified | TOTAL: 49 pass 2 (xz-): 0 found - 7 modified | TOTAL: 49 Iteration Number : 1 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 (+++): 4 found - 4 modified | TOTAL: 6 pass 2 (+++): 0 found - 4 modified | TOTAL: 6 Iteration Number : 1 pass 1 (++): 47 found - 47 modified | TOTAL: 47 pass 2 (++): 0 found - 47 modified | TOTAL: 47 pass 1 (+-): 53 found - 53 modified | TOTAL: 100 pass 2 (+-): 0 found - 53 modified | TOTAL: 100 pass 1 (--): 51 found - 51 modified | TOTAL: 151 pass 2 (--): 0 found - 51 modified | TOTAL: 151 pass 1 (-+): 45 found - 45 modified | TOTAL: 196 pass 2 (-+): 0 found - 45 modified | TOTAL: 196 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 1 found - 1 modified | TOTAL: 2 pass 2 (yz+): 0 found - 1 modified | TOTAL: 2 pass 1 (yz-): 2 found - 2 modified | TOTAL: 4 pass 2 (yz-): 0 found - 2 modified | TOTAL: 4 pass 1 (xz+): 0 found - 0 modified | TOTAL: 4 pass 1 (xz-): 0 found - 0 modified | TOTAL: 4 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 2 found - 2 modified | TOTAL: 2 pass 2 (++): 0 found - 2 modified | TOTAL: 2 pass 1 (+-): 1 found - 1 modified | TOTAL: 3 pass 2 (+-): 0 found - 1 modified | TOTAL: 3 pass 1 (--): 1 found - 1 modified | TOTAL: 4 pass 2 (--): 0 found - 1 modified | TOTAL: 4 pass 1 (-+): 0 found - 0 modified | TOTAL: 4 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 1 found - 1 modified | TOTAL: 1 pass 2 (xz+): 0 found - 1 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 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 = 260 (out of 453014: 0.057393) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Tue Jun 24 00:07:56 CST 2025 /fs2/home/bnuhe_user04/250623OASIS_output/sourcedata/freesurfer/sub-OAS30001/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 1.09844 -0.11646 0.00612 4.87029; 0.12407 1.17353 0.43457 -100.37985; -0.05022 -0.39872 0.99786 58.43575; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.09844 -0.11646 0.00612 4.87029; 0.12407 1.17353 0.43457 -100.37985; -0.05022 -0.39872 0.99786 58.43575; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1414 (min = 350, max = 1400), aspect = 0.53 (min = 0.10, max = 0.75) need search nearby using seed (126, 112, 93), TAL = (2.0, -35.0, 16.0) talairach voxel to voxel transform 0.90001 0.07617 -0.03869 5.52340; -0.09750 0.73404 -0.31908 92.80334; 0.00634 0.29714 0.87270 -21.20128; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (126, 112, 93) --> (2.0, -35.0, 16.0) done. writing output to filled.mgz... filling took 0.3 minutes talairach cc position changed to (2.00, -35.00, 16.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, -35.00, 16.00) SRC: (107.66, 134.81, 93.92) search lh wm seed point around talairach space (-16.00, -35.00, 16.00), SRC: (140.06, 131.30, 94.15) 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 Mon Jun 23 22:39:12 CST 2025 Ended at Tue Jun 24 00:08:15 CST 2025 #@#%# recon-all-run-time-hours 1.484 recon-all -s sub-OAS30001 finished without error at Tue Jun 24 00:08:16 CST 2025