Thu Oct 10 23:58:15 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz /usr/local/freesurfer/bin/recon-all -s sub-A00039639_ses-DS2_T1w.nii.gz -i /fleni/databases/databases/child_mind_institute/sub-A00039639/ses-DS2/anat/sub-A00039639_ses-DS2_T1w.nii.gz -all -parallel subjid sub-A00039639_ses-DS2_T1w.nii.gz setenv SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux fisicos-ub2 5.0.0-29-generic #31~18.04.1-Ubuntu SMP Thu Sep 12 18:29:21 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 4096 memorylocked 16384 kbytes maxproc 128196 maxlocks unlimited maxsignal 128196 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 32866180 3529208 22021920 71872 7315052 28854820 Swap: 2097148 708992 1388156 ######################################## 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: 2019/10/11-02:58:15-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic 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: 2019/10/11-02:58:15-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic 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: 2019/10/11-02:58:15-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/10/11-02:58:15-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/11-02:58:15-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/11-02:58:15-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/10/11-02:58:15-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/10/11-02:58:15-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/10/11-02:58:15-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/10/11-02:58:15-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/10/11-02:58:16-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/10/11-02:58:16-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/11-02:58:16-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/11-02:58:16-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/10/11-02:58:16-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/11-02:58:16-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/11-02:58:16-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/11-02:58:16-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/11-02:58:16-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/11-02:58:16-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/11-02:58:16-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/10/11-02:58:16-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/11-02:58:16-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/11-02:58:17-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/11-02:58:17-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/10/11-02:58:17-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/11-02:58:17-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2019/10/11-02:58:17-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/11-02:58:17-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/11-02:58:17-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/11-02:58:17-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/11-02:58:17-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic 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: 2019/10/11-02:58:17-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic 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: 2019/10/11-02:58:18-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/11-02:58:18-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/11-02:58:18-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/11-02:58:18-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/11-02:58:18-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/11-02:58:18-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: fisicos Machine: fisicos-ub2 Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/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 /usr/local/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz mri_convert /fleni/databases/databases/child_mind_institute/sub-A00039639/ses-DS2/anat/sub-A00039639_ses-DS2_T1w.nii.gz /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/orig/001.mgz mri_convert.bin /fleni/databases/databases/child_mind_institute/sub-A00039639/ses-DS2/anat/sub-A00039639_ses-DS2_T1w.nii.gz /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /fleni/databases/databases/child_mind_institute/sub-A00039639/ses-DS2/anat/sub-A00039639_ses-DS2_T1w.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, 1, 0) k_ras = (-0, -0, 1) writing to /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Thu Oct 10 23:58:19 -03 2019 Found 1 runs /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/orig/001.mgz /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/rawavg.mgz /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz mri_convert /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/rawavg.mgz /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/orig.mgz --conform mri_convert.bin /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/rawavg.mgz /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, 1, 0) k_ras = (-0, -0, 1) changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/orig.mgz... mri_add_xform_to_header -c /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/transforms/talairach.xfm /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/orig.mgz /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Oct 10 23:58:25 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri /usr/local/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 fisicos-ub2 5.0.0-29-generic #31~18.04.1-Ubuntu SMP Thu Sep 12 18:29:21 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux Thu Oct 10 23:58:26 -03 2019 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.25336 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.25336/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.25336/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.25336/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Oct 10 23:58:27 -03 2019 nu_correct -clobber ./tmp.mri_nu_correct.mni.25336/nu0.mnc ./tmp.mri_nu_correct.mni.25336/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.25336/0/ -iterations 1000 -distance 50 [fisicos@fisicos-ub2:/mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/] [2019-10-10 23:58:27] running: /usr/local/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.25336/0/ ./tmp.mri_nu_correct.mni.25336/nu0.mnc ./tmp.mri_nu_correct.mni.25336/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done 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: 62 CV of field change: 0.000989311 mri_convert ./tmp.mri_nu_correct.mni.25336/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.25336/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.25336/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... Thu Oct 10 23:59:04 -03 2019 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at Thu Oct 10 23:59:04 -03 2019 Ended at Thu Oct 10 23:59:22 -03 2019 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Thu Oct 10 23:59:24 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7489, pval=0.6675 >= threshold=0.0050) awk -f /usr/local/freesurfer/bin/extract_talairach_avi_QA.awk /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/transforms/talairach_avi.log tal_QC_AZS /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/transforms/talairach_avi.log TalAviQA: 0.98013 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Thu Oct 10 23:59:24 -03 2019 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri /usr/local/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 fisicos-ub2 5.0.0-29-generic #31~18.04.1-Ubuntu SMP Thu Sep 12 18:29:21 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux Thu Oct 10 23:59:24 -03 2019 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.27606 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.27606/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.27606/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.27606/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Oct 10 23:59:25 -03 2019 nu_correct -clobber ./tmp.mri_nu_correct.mni.27606/nu0.mnc ./tmp.mri_nu_correct.mni.27606/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.27606/0/ [fisicos@fisicos-ub2:/mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/] [2019-10-10 23:59:25] running: /usr/local/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.27606/0/ ./tmp.mri_nu_correct.mni.27606/nu0.mnc ./tmp.mri_nu_correct.mni.27606/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 43 CV of field change: 0.00095564 -------------------------------------------------------- Iteration 2 Thu Oct 10 23:59:47 -03 2019 nu_correct -clobber ./tmp.mri_nu_correct.mni.27606/nu1.mnc ./tmp.mri_nu_correct.mni.27606/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.27606/1/ [fisicos@fisicos-ub2:/mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/] [2019-10-10 23:59:47] running: /usr/local/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.27606/1/ ./tmp.mri_nu_correct.mni.27606/nu1.mnc ./tmp.mri_nu_correct.mni.27606/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 19 CV of field change: 0.000992436 mri_binarize --i ./tmp.mri_nu_correct.mni.27606/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.27606/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.27606/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.27606/ones.mgz sysname Linux hostname fisicos-ub2 machine x86_64 user fisicos input ./tmp.mri_nu_correct.mni.27606/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.27606/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.27606/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.27606/sum.junk --avgwf ./tmp.mri_nu_correct.mni.27606/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.27606/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.27606/sum.junk --avgwf ./tmp.mri_nu_correct.mni.27606/input.mean.dat sysname Linux hostname fisicos-ub2 machine x86_64 user fisicos UseRobust 0 Loading ./tmp.mri_nu_correct.mni.27606/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.27606/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.27606/ones.mgz --i ./tmp.mri_nu_correct.mni.27606/nu2.mnc --sum ./tmp.mri_nu_correct.mni.27606/sum.junk --avgwf ./tmp.mri_nu_correct.mni.27606/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.27606/ones.mgz --i ./tmp.mri_nu_correct.mni.27606/nu2.mnc --sum ./tmp.mri_nu_correct.mni.27606/sum.junk --avgwf ./tmp.mri_nu_correct.mni.27606/output.mean.dat sysname Linux hostname fisicos-ub2 machine x86_64 user fisicos UseRobust 0 Loading ./tmp.mri_nu_correct.mni.27606/ones.mgz Loading ./tmp.mri_nu_correct.mni.27606/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.27606/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.27606/nu2.mnc ./tmp.mri_nu_correct.mni.27606/nu2.mnc mul .99133370548725875716 Saving result to './tmp.mri_nu_correct.mni.27606/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.27606/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.27606/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.27606/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 ( 7, 92) to ( 3, 110) Fri Oct 11 00:00:21 -03 2019 mri_nu_correct.mni done mri_add_xform_to_header -c /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Fri Oct 11 00:00:21 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/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 1.02572 -0.01746 -0.06602 -0.03184; 0.02554 0.96343 0.25188 -22.33872; 0.04315 -0.25867 1.12929 -17.82315; 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 87 (87), valley at 48 (48) csf peak at 30, setting threshold to 68 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 85 (85), valley at 43 (43) csf peak at 30, setting threshold to 66 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 2 seconds. #-------------------------------------------- #@# Skull Stripping Fri Oct 11 00:01:23 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri mri_em_register -rusage /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 == Number of threads available to mri_em_register for OpenMP = 4 == reading 1 input volumes... logging results to talairach_with_skull.log reading '/usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca'... average std = 22.9 using min determinant for regularization = 52.6 0 singular and 9002 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 8.7 or > 569.1 total sample mean = 77.6 (1399 zeros) ************************************************ spacing=8, using 3243 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3243, passno 0, spacing 8 resetting wm mean[0]: 100 --> 108 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=18.0 skull bounding box = (43, 20, 13) --> (210, 171, 220) using (99, 70, 117) as brain centroid... mean wm in atlas = 108, using box (78,51,91) --> (119, 88,142) to find MRI wm before smoothing, mri peak at 105 robust fit to distribution - 105 +- 4.4 after smoothing, mri peak at 105, scaling input intensities by 1.029 scaling channel 0 by 1.02857 initial log_p = -4.703 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.576464 @ (9.091, 27.273, -9.091) max log p = -4.473172 @ (-13.636, -4.545, 4.545) max log p = -4.387371 @ (6.818, 2.273, 2.273) max log p = -4.359442 @ (-1.136, -3.409, 3.409) max log p = -4.358785 @ (-0.568, 1.705, -0.568) max log p = -4.358785 @ (0.000, 0.000, 0.000) Found translation: (0.6, 23.3, 0.6): log p = -4.359 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.277, old_max_log_p =-4.359 (thresh=-4.4) 0.99144 -0.05744 0.13868 -8.78471; 0.00000 1.14215 0.47309 -40.41553; -0.13053 -0.43632 1.05337 55.52850; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.244, old_max_log_p =-4.277 (thresh=-4.3) 0.99985 -0.01995 -0.00688 2.63816; 0.01704 1.18933 0.33155 -31.62299; 0.00102 -0.26694 1.03114 22.56172; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.196, old_max_log_p =-4.244 (thresh=-4.2) 0.99985 -0.01995 -0.00688 2.63816; 0.01831 1.27853 0.35642 -44.65779; 0.00095 -0.24692 0.95381 29.18883; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.196, old_max_log_p =-4.196 (thresh=-4.2) 0.99985 -0.01995 -0.00688 2.63816; 0.01831 1.27853 0.35642 -44.65779; 0.00095 -0.24692 0.95381 29.18883; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.170, old_max_log_p =-4.196 (thresh=-4.2) 1.01684 -0.05499 -0.01443 5.06567; 0.04729 1.22911 0.34504 -41.19345; 0.00358 -0.24365 0.95471 30.24710; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.155, old_max_log_p =-4.170 (thresh=-4.2) 0.99740 -0.06045 0.01684 4.59367; 0.04803 1.25961 0.31950 -41.84241; -0.02762 -0.19762 0.94735 29.80711; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.155, old_max_log_p =-4.155 (thresh=-4.2) 0.99740 -0.06045 0.01684 4.59367; 0.04803 1.25961 0.31950 -41.84241; -0.02762 -0.19762 0.94735 29.80711; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.138, old_max_log_p =-4.155 (thresh=-4.2) 0.99688 -0.03985 0.02230 1.72212; 0.03112 1.25962 0.34354 -41.97106; -0.02876 -0.22929 0.94253 33.12318; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 8 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.138, old_max_log_p =-4.138 (thresh=-4.1) 0.99688 -0.03985 0.02230 1.72212; 0.03112 1.25962 0.34354 -41.97106; -0.02876 -0.22929 0.94253 33.12318; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3243 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.99688 -0.03985 0.02230 1.72212; 0.03112 1.25962 0.34354 -41.97106; -0.02876 -0.22929 0.94253 33.12318; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 0.99688 -0.03985 0.02230 1.72212; 0.03112 1.25962 0.34354 -41.97106; -0.02876 -0.22929 0.94253 33.12318; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.99688 -0.03985 0.02230 1.72212; 0.03112 1.25962 0.34354 -41.97106; -0.02876 -0.22929 0.94253 33.12318; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -4.138 (old=-4.703) transform before final EM align: 0.99688 -0.03985 0.02230 1.72212; 0.03112 1.25962 0.34354 -41.97106; -0.02876 -0.22929 0.94253 33.12318; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 364799 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.99688 -0.03985 0.02230 1.72212; 0.03112 1.25962 0.34354 -41.97106; -0.02876 -0.22929 0.94253 33.12318; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 0.99688 -0.03985 0.02230 1.72212; 0.03112 1.25962 0.34354 -41.97106; -0.02876 -0.22929 0.94253 33.12318; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 013: -log(p) = 4.5 tol 0.000000 final transform: 0.99688 -0.03985 0.02230 1.72212; 0.03112 1.25962 0.34354 -41.97106; -0.02876 -0.22929 0.94253 33.12318; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 800.743595 mri_em_register stimesec 0.907813 mri_em_register ru_maxrss 614348 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 161771 mri_em_register ru_majflt 6 mri_em_register ru_nswap 0 mri_em_register ru_inblock 150296 mri_em_register ru_oublock 16 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 136 mri_em_register ru_nivcsw 8547 registration took 3 minutes and 40 seconds. mri_watershed -rusage /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/touch/rusage.mri_watershed.dat -T1 -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=126 y=94 z=108 r=72 first estimation of the main basin volume: 1604324 voxels Looking for seedpoints 2 found in the cerebellum 18 found in the rest of the brain global maximum in x=105, y=80, z=74, Imax=255 CSF=21, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percent done. Analyze... main basin size=9403997883 voxels, voxel volume =1.000 = 9403997883 mmm3 = 9403998.208 cm3 done. PostAnalyze...Basin Prior 11 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=125,y=97, z=105, r=10061 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=39 , nb = 44830 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=12 , nb = -1035941441 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=12 , nb = -1068349164 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=45 , nb = 1075853235 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=46 , nb = 1078582608 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1075387533 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 39, 41, 43, 78 after analyzing : 39, 42, 43, 51 RIGHT_CER before analyzing : 12, 21, 53, 86 after analyzing : 12, 42, 53, 53 LEFT_CER before analyzing : 12, 18, 46, 87 after analyzing : 12, 36, 46, 48 RIGHT_BRAIN before analyzing : 45, 45, 45, 78 after analyzing : 28, 45, 45, 53 LEFT_BRAIN before analyzing : 46, 43, 42, 76 after analyzing : 27, 43, 43, 51 OTHER before analyzing : 4, 3, 0, 92 after analyzing : 3, 17, 25, 35 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...61 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.010 curvature mean = 71.795, std = 7.542 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 1.73, sigma = 2.64 after rotation: sse = 1.73, sigma = 2.64 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 1.87, its var is 2.73 before Erosion-Dilatation 0.22% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...41 iterations mri_strip_skull: done peeling brain Brain Size = 1758414 voxels, voxel volume = 1.000 mm3 = 1758414 mmm3 = 1758.414 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 16.549451 mri_watershed stimesec 0.172431 mri_watershed ru_maxrss 837508 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 207728 mri_watershed ru_majflt 0 mri_watershed ru_nswap 0 mri_watershed ru_inblock 0 mri_watershed ru_oublock 2752 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 4133 mri_watershed ru_nivcsw 169 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Fri Oct 11 00:05:14 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri mri_em_register -rusage /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /usr/local/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 = 4 == reading 1 input volumes... logging results to talairach.log reading '/usr/local/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 = (57, 37, 26) --> (196, 170, 196) using (103, 81, 111) as brain centroid... mean wm in atlas = 107, using box (86,65,90) --> (120, 97,131) to find MRI wm before smoothing, mri peak at 105 robust fit to distribution - 105 +- 4.7 after smoothing, mri peak at 105, scaling input intensities by 1.019 scaling channel 0 by 1.01905 initial log_p = -4.422 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.171487 @ (9.091, 27.273, 9.091) max log p = -3.961171 @ (-4.545, -4.545, -13.636) max log p = -3.810783 @ (-6.818, 2.273, 2.273) max log p = -3.776587 @ (1.136, -1.136, -1.136) max log p = -3.776587 @ (0.000, 0.000, 0.000) max log p = -3.763905 @ (0.852, -0.852, -0.852) Found translation: (-0.3, 23.0, -4.3): log p = -3.764 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.641, old_max_log_p =-3.764 (thresh=-3.8) 1.00000 0.00000 0.00000 -0.28409; 0.00000 1.03837 0.27823 -11.20635; 0.00000 -0.23941 0.89348 37.97418; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.617, old_max_log_p =-3.641 (thresh=-3.6) 0.99144 -0.13553 -0.03632 17.83578; 0.13053 1.02949 0.27585 -26.66952; 0.00000 -0.23941 0.89348 37.97418; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.617, old_max_log_p =-3.617 (thresh=-3.6) 0.99144 -0.13553 -0.03632 17.83578; 0.13053 1.02949 0.27585 -26.66952; 0.00000 -0.23941 0.89348 37.97418; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.529, old_max_log_p =-3.617 (thresh=-3.6) 0.97969 -0.00891 0.05039 -1.96160; -0.00202 1.10691 0.25535 -15.48599; -0.05950 -0.20791 0.95402 32.44679; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.529, old_max_log_p =-3.529 (thresh=-3.5) 0.97969 -0.00891 0.05039 -1.96160; -0.00202 1.10691 0.25535 -15.48599; -0.05950 -0.20791 0.95402 32.44679; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.505, old_max_log_p =-3.529 (thresh=-3.5) 0.98199 -0.00921 0.05037 -2.23671; -0.00176 1.10691 0.25533 -15.06390; -0.05944 -0.20746 0.95178 32.16426; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.504, old_max_log_p =-3.505 (thresh=-3.5) 0.98242 -0.01675 0.04059 -0.52147; 0.00726 1.11136 0.24034 -15.51853; -0.05142 -0.18939 0.95621 28.45443; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2830 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.98242 -0.01675 0.04059 -0.52147; 0.00726 1.11136 0.24034 -15.51853; -0.05142 -0.18939 0.95621 28.45443; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 0.98242 -0.01675 0.04059 -0.52147; 0.00726 1.11136 0.24034 -15.51853; -0.05142 -0.18939 0.95621 28.45443; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.98242 -0.01675 0.04059 -0.52147; 0.00726 1.11136 0.24034 -15.51853; -0.05142 -0.18939 0.95621 28.45443; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.504 (old=-4.422) transform before final EM align: 0.98242 -0.01675 0.04059 -0.52147; 0.00726 1.11136 0.24034 -15.51853; -0.05142 -0.18939 0.95621 28.45443; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 315557 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.98242 -0.01675 0.04059 -0.52147; 0.00726 1.11136 0.24034 -15.51853; -0.05142 -0.18939 0.95621 28.45443; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 0.98242 -0.01675 0.04059 -0.52147; 0.00726 1.11136 0.24034 -15.51853; -0.05142 -0.18939 0.95621 28.45443; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = 4.0 tol 0.000000 final transform: 0.98242 -0.01675 0.04059 -0.52147; 0.00726 1.11136 0.24034 -15.51853; -0.05142 -0.18939 0.95621 28.45443; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 438.308928 mri_em_register stimesec 0.619995 mri_em_register ru_maxrss 603988 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 166547 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 0 mri_em_register ru_oublock 16 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 42 mri_em_register ru_nivcsw 529 registration took 2 minutes and 1 seconds. #-------------------------------------- #@# CA Normalize Fri Oct 11 00:07:15 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/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 '/usr/local/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 = (57, 37, 26) --> (196, 170, 196) using (103, 81, 111) as brain centroid... mean wm in atlas = 107, using box (86,65,90) --> (120, 97,131) to find MRI wm before smoothing, mri peak at 105 robust fit to distribution - 105 +- 4.7 after smoothing, mri peak at 105, scaling input intensities by 1.019 scaling channel 0 by 1.01905 using 246344 sample points... INFO: compute sample coordinates transform 0.98242 -0.01675 0.04059 -0.52147; 0.00726 1.11136 0.24034 -15.51853; -0.05142 -0.18939 0.95621 28.45443; 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 (126, 38, 29) --> (194, 142, 198) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0 0 of 3222 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (61, 39, 26) --> (127, 140, 197) Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0 3 of 3974 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (129, 120, 57) --> (179, 158, 112) Left_Cerebellum_White_Matter: limiting intensities to 105.0 --> 132.0 0 of 81 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (83, 120, 53) --> (128, 157, 111) Right_Cerebellum_White_Matter: limiting intensities to 106.0 --> 132.0 0 of 53 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (110, 107, 92) --> (145, 170, 123) Brain_Stem: limiting intensities to 90.0 --> 132.0 0 of 162 (0.0%) samples deleted using 7492 total control points for intensity normalization... bias field = 0.951 +- 0.053 117 of 7489 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (126, 38, 29) --> (194, 142, 198) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 2 of 3985 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (61, 39, 26) --> (127, 140, 197) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 4 of 5036 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (129, 120, 57) --> (179, 158, 112) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 4 of 145 (2.8%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (83, 120, 53) --> (128, 157, 111) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 14 of 147 (9.5%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (110, 107, 92) --> (145, 170, 123) Brain_Stem: limiting intensities to 88.0 --> 132.0 162 of 288 (56.2%) samples deleted using 9601 total control points for intensity normalization... bias field = 1.032 +- 0.047 57 of 9337 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (126, 38, 29) --> (194, 142, 198) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 3 of 4010 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (61, 39, 26) --> (127, 140, 197) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 5 of 5092 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (129, 120, 57) --> (179, 158, 112) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 13 of 184 (7.1%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (83, 120, 53) --> (128, 157, 111) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 41 of 184 (22.3%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (110, 107, 92) --> (145, 170, 123) Brain_Stem: limiting intensities to 88.0 --> 132.0 282 of 392 (71.9%) samples deleted using 9862 total control points for intensity normalization... bias field = 1.025 +- 0.044 40 of 9357 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 0 minutes and 47 seconds. #-------------------------------------- #@# CA Reg Fri Oct 11 00:08:02 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri mri_ca_register -rusage /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /usr/local/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 = 4 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.09 (predicted orig area = 7.3) 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=0.838, neg=0, invalid=762 0001: dt=236.606061, rms=0.773 (7.767%), neg=0, invalid=762 0002: dt=148.742004, rms=0.754 (2.451%), neg=0, invalid=762 0003: dt=369.920000, rms=0.745 (1.187%), neg=0, invalid=762 0004: dt=129.472000, rms=0.739 (0.755%), neg=0, invalid=762 0005: dt=443.904000, rms=0.736 (0.464%), neg=0, invalid=762 0006: dt=153.212121, rms=0.733 (0.476%), neg=0, invalid=762 0007: dt=129.472000, rms=0.732 (0.119%), neg=0, invalid=762 0008: dt=129.472000, rms=0.730 (0.176%), neg=0, invalid=762 0009: dt=129.472000, rms=0.728 (0.307%), neg=0, invalid=762 0010: dt=129.472000, rms=0.726 (0.355%), neg=0, invalid=762 0011: dt=129.472000, rms=0.723 (0.404%), neg=0, invalid=762 0012: dt=129.472000, rms=0.719 (0.442%), neg=0, invalid=762 0013: dt=129.472000, rms=0.717 (0.289%), neg=0, invalid=762 0014: dt=129.472000, rms=0.716 (0.127%), neg=0, invalid=762 0015: dt=129.472000, rms=0.716 (0.060%), neg=0, invalid=762 0016: dt=129.472000, rms=0.715 (0.109%), neg=0, invalid=762 0017: dt=129.472000, rms=0.714 (0.133%), neg=0, invalid=762 0018: dt=129.472000, rms=0.713 (0.165%), neg=0, invalid=762 0019: dt=129.472000, rms=0.712 (0.197%), neg=0, invalid=762 0020: dt=129.472000, rms=0.711 (0.162%), neg=0, invalid=762 0021: dt=129.472000, rms=0.710 (0.112%), neg=0, invalid=762 0022: dt=129.472000, rms=0.709 (0.072%), neg=0, invalid=762 0023: dt=517.888000, rms=0.707 (0.245%), neg=0, invalid=762 0024: dt=129.472000, rms=0.707 (0.038%), neg=0, invalid=762 0025: dt=129.472000, rms=0.707 (0.028%), neg=0, invalid=762 0026: dt=129.472000, rms=0.707 (0.044%), neg=0, invalid=762 0027: dt=129.472000, rms=0.706 (0.063%), neg=0, invalid=762 0028: dt=129.472000, rms=0.706 (0.077%), neg=0, invalid=762 0029: dt=129.472000, rms=0.705 (0.087%), neg=0, invalid=762 0030: dt=129.472000, rms=0.704 (0.094%), neg=0, invalid=762 0031: dt=129.472000, rms=0.704 (0.096%), neg=0, invalid=762 0032: dt=129.472000, rms=0.703 (0.070%), neg=0, invalid=762 0033: dt=129.472000, rms=0.703 (0.049%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.704, neg=0, invalid=762 0034: dt=295.936000, rms=0.701 (0.425%), neg=0, invalid=762 0035: dt=129.472000, rms=0.700 (0.042%), neg=0, invalid=762 0036: dt=129.472000, rms=0.700 (0.051%), neg=0, invalid=762 0037: dt=129.472000, rms=0.700 (0.063%), neg=0, invalid=762 0038: dt=129.472000, rms=0.699 (0.074%), neg=0, invalid=762 0039: dt=129.472000, rms=0.698 (0.096%), neg=0, invalid=762 0040: dt=129.472000, rms=0.698 (0.093%), neg=0, invalid=762 0041: dt=129.472000, rms=0.697 (0.094%), neg=0, invalid=762 0042: dt=129.472000, rms=0.696 (0.093%), neg=0, invalid=762 0043: dt=1183.744000, rms=0.696 (0.093%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.702, neg=0, invalid=762 0044: dt=145.152000, rms=0.696 (0.925%), neg=0, invalid=762 0045: dt=209.661721, rms=0.682 (1.931%), neg=0, invalid=762 0046: dt=36.288000, rms=0.680 (0.412%), neg=0, invalid=762 0047: dt=36.288000, rms=0.679 (0.112%), neg=0, invalid=762 0048: dt=36.288000, rms=0.678 (0.085%), neg=0, invalid=762 0049: dt=36.288000, rms=0.677 (0.154%), neg=0, invalid=762 0050: dt=36.288000, rms=0.675 (0.284%), neg=0, invalid=762 0051: dt=36.288000, rms=0.672 (0.461%), neg=0, invalid=762 0052: dt=36.288000, rms=0.668 (0.541%), neg=0, invalid=762 0053: dt=36.288000, rms=0.665 (0.508%), neg=0, invalid=762 0054: dt=36.288000, rms=0.662 (0.423%), neg=0, invalid=762 0055: dt=36.288000, rms=0.660 (0.337%), neg=0, invalid=762 0056: dt=36.288000, rms=0.658 (0.278%), neg=0, invalid=762 0057: dt=36.288000, rms=0.656 (0.276%), neg=0, invalid=762 0058: dt=36.288000, rms=0.655 (0.280%), neg=0, invalid=762 0059: dt=36.288000, rms=0.653 (0.255%), neg=0, invalid=762 0060: dt=36.288000, rms=0.653 (0.046%), neg=0, invalid=762 0061: dt=36.288000, rms=0.652 (0.067%), neg=0, invalid=762 0062: dt=36.288000, rms=0.652 (0.069%), neg=0, invalid=762 0063: dt=36.288000, rms=0.651 (0.097%), neg=0, invalid=762 0064: dt=36.288000, rms=0.650 (0.106%), neg=0, invalid=762 0065: dt=36.288000, rms=0.650 (0.073%), neg=0, invalid=762 0066: dt=103.680000, rms=0.650 (0.032%), neg=0, invalid=762 0067: dt=103.680000, rms=0.649 (0.113%), neg=0, invalid=762 0068: dt=103.680000, rms=0.648 (0.094%), neg=0, invalid=762 0069: dt=103.680000, rms=0.648 (0.100%), neg=0, invalid=762 0070: dt=103.680000, rms=0.646 (0.273%), neg=0, invalid=762 0071: dt=103.680000, rms=0.644 (0.227%), neg=0, invalid=762 0072: dt=103.680000, rms=0.643 (0.202%), neg=0, invalid=762 0073: dt=103.680000, rms=0.642 (0.183%), neg=0, invalid=762 0074: dt=103.680000, rms=0.641 (0.157%), neg=0, invalid=762 0075: dt=103.680000, rms=0.639 (0.254%), neg=0, invalid=762 0076: dt=103.680000, rms=0.638 (0.187%), neg=0, invalid=762 0077: dt=103.680000, rms=0.637 (0.222%), neg=0, invalid=762 0078: dt=103.680000, rms=0.635 (0.231%), neg=0, invalid=762 0079: dt=103.680000, rms=0.635 (-0.041%), neg=0, invalid=762 0080: dt=9.072000, rms=0.635 (0.001%), neg=0, invalid=762 0081: dt=0.015187, rms=0.635 (-0.003%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.636, neg=0, invalid=762 0082: dt=104.907216, rms=0.633 (0.486%), neg=0, invalid=762 0083: dt=15.552000, rms=0.633 (0.012%), neg=0, invalid=762 0084: dt=15.552000, rms=0.633 (0.002%), neg=0, invalid=762 0085: dt=15.552000, rms=0.633 (0.003%), neg=0, invalid=762 0086: dt=15.552000, rms=0.633 (-0.005%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.665, neg=0, invalid=762 0087: dt=11.200000, rms=0.663 (0.329%), neg=0, invalid=762 0088: dt=9.600000, rms=0.663 (0.073%), neg=0, invalid=762 0089: dt=9.600000, rms=0.662 (0.048%), neg=0, invalid=762 0090: dt=9.600000, rms=0.662 (-0.003%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.663, neg=0, invalid=762 0091: dt=11.200000, rms=0.662 (0.200%), neg=0, invalid=762 0092: dt=8.000000, rms=0.662 (0.017%), neg=0, invalid=762 0093: dt=8.000000, rms=0.662 (0.008%), neg=0, invalid=762 0094: dt=8.000000, rms=0.662 (-0.042%), neg=0, invalid=762 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.711, neg=0, invalid=762 0095: dt=4.861538, rms=0.705 (0.963%), neg=0, invalid=762 0096: dt=5.428571, rms=0.703 (0.214%), neg=0, invalid=762 0097: dt=5.428571, rms=0.703 (0.061%), neg=0, invalid=762 0098: dt=5.428571, rms=0.703 (-0.139%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.703, neg=0, invalid=762 0099: dt=0.000000, rms=0.703 (0.115%), neg=0, invalid=762 0100: dt=0.000000, rms=0.703 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.748, neg=0, invalid=762 0101: dt=0.000000, rms=0.747 (0.102%), neg=0, invalid=762 0102: dt=0.000000, rms=0.747 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.748, neg=0, invalid=762 0103: dt=0.096000, rms=0.747 (0.105%), neg=0, invalid=762 0104: dt=0.064000, rms=0.747 (0.000%), neg=0, invalid=762 0105: dt=0.064000, rms=0.747 (-0.000%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.675, neg=0, invalid=762 0106: dt=0.811562, rms=0.658 (2.488%), neg=0, invalid=762 0107: dt=0.080000, rms=0.657 (0.128%), neg=0, invalid=762 0108: dt=0.080000, rms=0.657 (-0.084%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.658, neg=0, invalid=762 0109: dt=0.028000, rms=0.657 (0.149%), neg=0, invalid=762 0110: dt=0.006000, rms=0.657 (-0.001%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.13197 (30) Left_Lateral_Ventricle (4): linear fit = 1.48 x + 0.0 (1516 voxels, overlap=0.282) Left_Lateral_Ventricle (4): linear fit = 1.48 x + 0.0 (1516 voxels, peak = 30), gca=29.5 gca peak = 0.15565 (16) mri peak = 0.12811 (30) Right_Lateral_Ventricle (43): linear fit = 1.84 x + 0.0 (949 voxels, overlap=0.170) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (949 voxels, peak = 29), gca=24.0 gca peak = 0.26829 (96) mri peak = 0.09826 (103) Right_Pallidum (52): linear fit = 1.09 x + 0.0 (1089 voxels, overlap=0.295) Right_Pallidum (52): linear fit = 1.09 x + 0.0 (1089 voxels, peak = 104), gca=104.2 gca peak = 0.20183 (93) mri peak = 0.06257 (104) Left_Pallidum (13): linear fit = 1.09 x + 0.0 (929 voxels, overlap=0.930) Left_Pallidum (13): linear fit = 1.09 x + 0.0 (929 voxels, peak = 101), gca=100.9 gca peak = 0.21683 (55) mri peak = 0.09077 (77) Right_Hippocampus (53): linear fit = 1.32 x + 0.0 (1155 voxels, overlap=0.022) Right_Hippocampus (53): linear fit = 1.32 x + 0.0 (1155 voxels, peak = 72), gca=72.3 gca peak = 0.30730 (58) mri peak = 0.09853 (76) Left_Hippocampus (17): linear fit = 1.28 x + 0.0 (1115 voxels, overlap=0.018) Left_Hippocampus (17): linear fit = 1.28 x + 0.0 (1115 voxels, peak = 75), gca=74.5 gca peak = 0.11430 (101) mri peak = 0.10275 (103) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (75940 voxels, overlap=0.748) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (75940 voxels, peak = 105), gca=104.5 gca peak = 0.12076 (102) mri peak = 0.09240 (104) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (78642 voxels, overlap=0.719) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (78642 voxels, peak = 107), gca=106.6 gca peak = 0.14995 (59) mri peak = 0.03778 (77) Left_Cerebral_Cortex (3): linear fit = 1.33 x + 0.0 (30745 voxels, overlap=0.001) Left_Cerebral_Cortex (3): linear fit = 1.33 x + 0.0 (30745 voxels, peak = 78), gca=78.2 gca peak = 0.15082 (58) mri peak = 0.04099 (77) Right_Cerebral_Cortex (42): linear fit = 1.33 x + 0.0 (35262 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.33 x + 0.0 (35262 voxels, peak = 77), gca=76.9 gca peak = 0.14161 (67) mri peak = 0.11083 (87) Right_Caudate (50): linear fit = 1.27 x + 0.0 (618 voxels, overlap=0.016) Right_Caudate (50): linear fit = 1.27 x + 0.0 (618 voxels, peak = 85), gca=85.4 gca peak = 0.15243 (71) mri peak = 0.09907 (88) Left_Caudate (11): linear fit = 1.21 x + 0.0 (1186 voxels, overlap=0.012) Left_Caudate (11): linear fit = 1.21 x + 0.0 (1186 voxels, peak = 86), gca=85.6 gca peak = 0.13336 (57) mri peak = 0.03897 (74) Left_Cerebellum_Cortex (8): linear fit = 1.30 x + 0.0 (27688 voxels, overlap=0.000) Left_Cerebellum_Cortex (8): linear fit = 1.30 x + 0.0 (27688 voxels, peak = 74), gca=74.4 gca peak = 0.13252 (56) mri peak = 0.04839 (72) Right_Cerebellum_Cortex (47): linear fit = 1.35 x + 0.0 (31296 voxels, overlap=0.001) Right_Cerebellum_Cortex (47): linear fit = 1.35 x + 0.0 (31296 voxels, peak = 75), gca=75.3 gca peak = 0.18181 (84) mri peak = 0.06857 (95) Left_Cerebellum_White_Matter (7): linear fit = 1.12 x + 0.0 (10616 voxels, overlap=0.002) Left_Cerebellum_White_Matter (7): linear fit = 1.12 x + 0.0 (10616 voxels, peak = 94), gca=94.5 gca peak = 0.20573 (83) mri peak = 0.07679 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.09 x + 0.0 (9424 voxels, overlap=0.807) Right_Cerebellum_White_Matter (46): linear fit = 1.09 x + 0.0 (9424 voxels, peak = 90), gca=90.1 gca peak = 0.21969 (57) mri peak = 0.10998 (75) Left_Amygdala (18): linear fit = 1.29 x + 0.0 (492 voxels, overlap=0.053) Left_Amygdala (18): linear fit = 1.29 x + 0.0 (492 voxels, peak = 74), gca=73.8 gca peak = 0.39313 (56) mri peak = 0.09662 (74) Right_Amygdala (54): linear fit = 1.32 x + 0.0 (628 voxels, overlap=0.039) Right_Amygdala (54): linear fit = 1.32 x + 0.0 (628 voxels, peak = 74), gca=73.6 gca peak = 0.14181 (85) mri peak = 0.08092 (100) Left_Thalamus_Proper (10): linear fit = 1.16 x + 0.0 (6204 voxels, overlap=0.060) Left_Thalamus_Proper (10): linear fit = 1.16 x + 0.0 (6204 voxels, peak = 99), gca=99.0 gca peak = 0.11978 (83) mri peak = 0.07555 (94) Right_Thalamus_Proper (49): linear fit = 1.17 x + 0.0 (4359 voxels, overlap=0.185) Right_Thalamus_Proper (49): linear fit = 1.17 x + 0.0 (4359 voxels, peak = 98), gca=97.5 gca peak = 0.13399 (79) mri peak = 0.07973 (92) Left_Putamen (12): linear fit = 1.15 x + 0.0 (2697 voxels, overlap=0.009) Left_Putamen (12): linear fit = 1.15 x + 0.0 (2697 voxels, peak = 91), gca=91.2 gca peak = 0.14159 (79) mri peak = 0.08542 (91) Right_Putamen (51): linear fit = 1.14 x + 0.0 (2873 voxels, overlap=0.120) Right_Putamen (51): linear fit = 1.14 x + 0.0 (2873 voxels, peak = 90), gca=90.5 gca peak = 0.10025 (80) mri peak = 0.10111 (83) Brain_Stem (16): linear fit = 1.10 x + 0.0 (14466 voxels, overlap=0.402) Brain_Stem (16): linear fit = 1.10 x + 0.0 (14466 voxels, peak = 88), gca=87.6 gca peak = 0.13281 (86) mri peak = 0.08216 (94) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1347 voxels, overlap=0.431) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1347 voxels, peak = 93), gca=93.3 gca peak = 0.12801 (89) mri peak = 0.07978 (96) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1555 voxels, overlap=0.392) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1555 voxels, peak = 97), gca=97.5 gca peak = 0.20494 (23) mri peak = 0.24138 (30) gca peak = 0.15061 (21) mri peak = 0.11487 (24) Fourth_Ventricle (15): linear fit = 1.30 x + 0.0 (263 voxels, overlap=0.310) Fourth_Ventricle (15): linear fit = 1.30 x + 0.0 (263 voxels, peak = 27), gca=27.4 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18056 (32) gca peak Left_Thalamus = 0.64095 (94) gca peak Third_Ventricle = 0.20494 (23) gca peak CSF = 0.20999 (34) gca peak Left_Accumbens_area = 0.39030 (62) gca peak Left_undetermined = 0.95280 (25) gca peak Left_vessel = 0.67734 (53) gca peak Left_choroid_plexus = 0.09433 (44) gca peak Right_Inf_Lat_Vent = 0.23544 (26) gca peak Right_Accumbens_area = 0.30312 (64) gca peak Right_vessel = 0.46315 (51) gca peak Right_choroid_plexus = 0.14086 (44) gca peak Fifth_Ventricle = 0.51669 (36) gca peak WM_hypointensities = 0.09722 (76) gca peak non_WM_hypointensities = 0.11899 (47) gca peak Optic_Chiasm = 0.39033 (72) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 1.31 x + 0.0 estimating mean wm scale to be 1.04 x + 0.0 estimating mean csf scale to be 1.43 x + 0.0 Right_Pallidum too bright - rescaling by 0.983 (from 1.085) to 102.4 (was 104.2) saving intensity scales to talairach.label_intensities.txt **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.674, neg=0, invalid=762 0111: dt=80.475248, rms=0.653 (3.210%), neg=0, invalid=762 0112: dt=32.368000, rms=0.652 (0.100%), neg=0, invalid=762 0113: dt=32.368000, rms=0.652 (0.052%), neg=0, invalid=762 0114: dt=32.368000, rms=0.651 (0.038%), neg=0, invalid=762 0115: dt=32.368000, rms=0.651 (0.030%), neg=0, invalid=762 0116: dt=32.368000, rms=0.651 (0.019%), neg=0, invalid=762 0117: dt=32.368000, rms=0.651 (-0.014%), neg=0, invalid=762 0118: dt=129.472000, rms=0.650 (0.122%), neg=0, invalid=762 0119: dt=517.888000, rms=0.646 (0.624%), neg=0, invalid=762 0120: dt=1183.744000, rms=0.640 (1.014%), neg=0, invalid=762 0121: dt=129.472000, rms=0.637 (0.433%), neg=0, invalid=762 0122: dt=73.984000, rms=0.637 (0.009%), neg=0, invalid=762 0123: dt=73.984000, rms=0.637 (0.029%), neg=0, invalid=762 0124: dt=73.984000, rms=0.636 (0.051%), neg=0, invalid=762 0125: dt=73.984000, rms=0.636 (0.072%), neg=0, invalid=762 0126: dt=73.984000, rms=0.635 (0.109%), neg=0, invalid=762 0127: dt=73.984000, rms=0.634 (0.154%), neg=0, invalid=762 0128: dt=73.984000, rms=0.633 (0.197%), neg=0, invalid=762 0129: dt=73.984000, rms=0.632 (0.220%), neg=0, invalid=762 0130: dt=73.984000, rms=0.630 (0.216%), neg=0, invalid=762 0131: dt=73.984000, rms=0.629 (0.197%), neg=0, invalid=762 0132: dt=73.984000, rms=0.628 (0.177%), neg=0, invalid=762 0133: dt=73.984000, rms=0.627 (0.146%), neg=0, invalid=762 0134: dt=73.984000, rms=0.626 (0.127%), neg=0, invalid=762 0135: dt=73.984000, rms=0.625 (0.115%), neg=0, invalid=762 0136: dt=73.984000, rms=0.625 (0.109%), neg=0, invalid=762 0137: dt=73.984000, rms=0.624 (0.107%), neg=0, invalid=762 0138: dt=73.984000, rms=0.623 (0.112%), neg=0, invalid=762 0139: dt=73.984000, rms=0.623 (0.110%), neg=0, invalid=762 0140: dt=73.984000, rms=0.622 (0.102%), neg=0, invalid=762 0141: dt=73.984000, rms=0.621 (0.097%), neg=0, invalid=762 0142: dt=73.984000, rms=0.621 (0.090%), neg=0, invalid=762 0143: dt=73.984000, rms=0.620 (0.087%), neg=0, invalid=762 0144: dt=73.984000, rms=0.620 (0.082%), neg=0, invalid=762 0145: dt=73.984000, rms=0.619 (0.081%), neg=0, invalid=762 0146: dt=73.984000, rms=0.619 (0.085%), neg=0, invalid=762 0147: dt=73.984000, rms=0.618 (0.079%), neg=0, invalid=762 0148: dt=73.984000, rms=0.618 (0.075%), neg=0, invalid=762 0149: dt=73.984000, rms=0.617 (0.068%), neg=0, invalid=762 0150: dt=73.984000, rms=0.617 (0.063%), neg=0, invalid=762 0151: dt=73.984000, rms=0.617 (0.060%), neg=0, invalid=762 0152: dt=73.984000, rms=0.616 (0.059%), neg=0, invalid=762 0153: dt=73.984000, rms=0.616 (0.057%), neg=0, invalid=762 0154: dt=73.984000, rms=0.616 (0.057%), neg=0, invalid=762 0155: dt=73.984000, rms=0.615 (0.059%), neg=0, invalid=762 0156: dt=73.984000, rms=0.615 (0.058%), neg=0, invalid=762 0157: dt=73.984000, rms=0.615 (0.059%), neg=0, invalid=762 0158: dt=73.984000, rms=0.614 (0.057%), neg=0, invalid=762 0159: dt=73.984000, rms=0.614 (0.056%), neg=0, invalid=762 0160: dt=73.984000, rms=0.614 (0.053%), neg=0, invalid=762 0161: dt=73.984000, rms=0.613 (0.055%), neg=0, invalid=762 0162: dt=73.984000, rms=0.613 (0.052%), neg=0, invalid=762 0163: dt=73.984000, rms=0.613 (0.049%), neg=0, invalid=762 0164: dt=73.984000, rms=0.612 (0.044%), neg=0, invalid=762 0165: dt=73.984000, rms=0.612 (0.044%), neg=0, invalid=762 0166: dt=73.984000, rms=0.612 (0.043%), neg=0, invalid=762 0167: dt=73.984000, rms=0.612 (0.040%), neg=0, invalid=762 0168: dt=73.984000, rms=0.611 (0.036%), neg=0, invalid=762 0169: dt=73.984000, rms=0.611 (0.036%), neg=0, invalid=762 0170: dt=73.984000, rms=0.611 (0.036%), neg=0, invalid=762 0171: dt=73.984000, rms=0.611 (0.035%), neg=0, invalid=762 0172: dt=73.984000, rms=0.610 (0.036%), neg=0, invalid=762 0173: dt=73.984000, rms=0.610 (0.037%), neg=0, invalid=762 0174: dt=73.984000, rms=0.610 (0.033%), neg=0, invalid=762 0175: dt=73.984000, rms=0.610 (0.031%), neg=0, invalid=762 0176: dt=73.984000, rms=0.610 (0.026%), neg=0, invalid=762 0177: dt=73.984000, rms=0.609 (0.026%), neg=0, invalid=762 0178: dt=73.984000, rms=0.609 (0.024%), neg=0, invalid=762 0179: dt=73.984000, rms=0.609 (0.025%), neg=0, invalid=762 0180: dt=73.984000, rms=0.609 (0.025%), neg=0, invalid=762 0181: dt=73.984000, rms=0.609 (0.026%), neg=0, invalid=762 0182: dt=73.984000, rms=0.609 (0.027%), neg=0, invalid=762 0183: dt=73.984000, rms=0.609 (0.028%), neg=0, invalid=762 0184: dt=73.984000, rms=0.608 (0.024%), neg=0, invalid=762 0185: dt=73.984000, rms=0.608 (0.023%), neg=0, invalid=762 0186: dt=517.888000, rms=0.608 (0.006%), neg=0, invalid=762 0187: dt=517.888000, rms=0.608 (-0.069%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.609, neg=0, invalid=762 0188: dt=369.920000, rms=0.607 (0.325%), neg=0, invalid=762 0189: dt=92.480000, rms=0.606 (0.060%), neg=0, invalid=762 0190: dt=27.744000, rms=0.606 (-0.000%), neg=0, invalid=762 0191: dt=27.744000, rms=0.606 (0.000%), neg=0, invalid=762 0192: dt=27.744000, rms=0.606 (-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=0.608, neg=0, invalid=762 0193: dt=92.952381, rms=0.606 (0.311%), neg=0, invalid=762 0194: dt=414.720000, rms=0.596 (1.631%), neg=0, invalid=762 0195: dt=46.990991, rms=0.592 (0.601%), neg=0, invalid=762 0196: dt=124.416000, rms=0.592 (0.140%), neg=0, invalid=762 0197: dt=145.152000, rms=0.588 (0.530%), neg=0, invalid=762 0198: dt=36.288000, rms=0.588 (0.097%), neg=0, invalid=762 0199: dt=145.152000, rms=0.587 (0.175%), neg=0, invalid=762 0200: dt=145.152000, rms=0.585 (0.344%), neg=0, invalid=762 0201: dt=36.288000, rms=0.584 (0.116%), neg=0, invalid=762 0202: dt=124.416000, rms=0.584 (0.105%), neg=0, invalid=762 0203: dt=103.680000, rms=0.582 (0.220%), neg=0, invalid=762 0204: dt=36.288000, rms=0.582 (0.096%), neg=0, invalid=762 0205: dt=145.152000, rms=0.581 (0.161%), neg=0, invalid=762 0206: dt=36.288000, rms=0.580 (0.087%), neg=0, invalid=762 0207: dt=36.288000, rms=0.580 (0.060%), neg=0, invalid=762 0208: dt=25.920000, rms=0.580 (0.034%), neg=0, invalid=762 0209: dt=1.620000, rms=0.580 (0.001%), neg=0, invalid=762 0210: dt=0.810000, rms=0.580 (0.001%), neg=0, invalid=762 0211: dt=0.202500, rms=0.580 (0.000%), neg=0, invalid=762 0212: dt=0.008859, rms=0.580 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.580, neg=0, invalid=762 0213: dt=145.152000, rms=0.576 (0.726%), neg=0, invalid=762 0214: dt=103.680000, rms=0.575 (0.131%), neg=0, invalid=762 0215: dt=145.152000, rms=0.574 (0.218%), neg=0, invalid=762 0216: dt=36.288000, rms=0.573 (0.103%), neg=0, invalid=762 0217: dt=103.680000, rms=0.573 (0.082%), neg=0, invalid=762 0218: dt=82.944000, rms=0.572 (0.135%), neg=0, invalid=762 0219: dt=82.944000, rms=0.571 (0.088%), neg=0, invalid=762 0220: dt=145.152000, rms=0.571 (0.149%), neg=0, invalid=762 0221: dt=62.208000, rms=0.570 (0.083%), neg=0, invalid=762 0222: dt=145.152000, rms=0.570 (0.103%), neg=0, invalid=762 0223: dt=62.208000, rms=0.569 (0.079%), neg=0, invalid=762 0224: dt=145.152000, rms=0.569 (0.103%), neg=0, invalid=762 0225: dt=36.288000, rms=0.568 (0.052%), neg=0, invalid=762 0226: dt=497.664000, rms=0.567 (0.186%), neg=0, invalid=762 0227: dt=36.288000, rms=0.566 (0.193%), neg=0, invalid=762 0228: dt=124.416000, rms=0.566 (0.083%), neg=0, invalid=762 0229: dt=36.288000, rms=0.565 (0.044%), neg=0, invalid=762 0230: dt=36.288000, rms=0.565 (0.028%), neg=0, invalid=762 0231: dt=36.288000, rms=0.565 (0.041%), neg=0, invalid=762 0232: dt=36.288000, rms=0.565 (0.060%), neg=0, invalid=762 0233: dt=36.288000, rms=0.564 (0.080%), neg=0, invalid=762 0234: dt=36.288000, rms=0.564 (0.091%), neg=0, invalid=762 0235: dt=36.288000, rms=0.563 (0.102%), neg=0, invalid=762 0236: dt=36.288000, rms=0.562 (0.112%), neg=0, invalid=762 0237: dt=36.288000, rms=0.562 (0.115%), neg=0, invalid=762 0238: dt=36.288000, rms=0.561 (0.117%), neg=0, invalid=762 0239: dt=36.288000, rms=0.560 (0.124%), neg=0, invalid=762 0240: dt=36.288000, rms=0.560 (0.132%), neg=0, invalid=762 0241: dt=36.288000, rms=0.559 (0.126%), neg=0, invalid=762 0242: dt=36.288000, rms=0.558 (0.132%), neg=0, invalid=762 0243: dt=36.288000, rms=0.558 (0.130%), neg=0, invalid=762 0244: dt=36.288000, rms=0.557 (0.123%), neg=0, invalid=762 0245: dt=36.288000, rms=0.556 (0.119%), neg=0, invalid=762 0246: dt=36.288000, rms=0.556 (0.120%), neg=0, invalid=762 0247: dt=36.288000, rms=0.555 (0.112%), neg=0, invalid=762 0248: dt=36.288000, rms=0.554 (0.112%), neg=0, invalid=762 0249: dt=36.288000, rms=0.554 (0.109%), neg=0, invalid=762 0250: dt=36.288000, rms=0.553 (0.103%), neg=0, invalid=762 0251: dt=36.288000, rms=0.553 (0.098%), neg=0, invalid=762 0252: dt=36.288000, rms=0.552 (0.091%), neg=0, invalid=762 0253: dt=36.288000, rms=0.552 (0.085%), neg=0, invalid=762 0254: dt=36.288000, rms=0.551 (0.090%), neg=0, invalid=762 0255: dt=36.288000, rms=0.551 (0.081%), neg=0, invalid=762 0256: dt=36.288000, rms=0.550 (0.082%), neg=0, invalid=762 0257: dt=36.288000, rms=0.550 (0.084%), neg=0, invalid=762 0258: dt=36.288000, rms=0.549 (0.074%), neg=0, invalid=762 0259: dt=36.288000, rms=0.549 (0.075%), neg=0, invalid=762 0260: dt=36.288000, rms=0.549 (0.065%), neg=0, invalid=762 0261: dt=36.288000, rms=0.548 (0.063%), neg=0, invalid=762 0262: dt=36.288000, rms=0.548 (0.068%), neg=0, invalid=762 0263: dt=36.288000, rms=0.548 (0.066%), neg=0, invalid=762 0264: dt=36.288000, rms=0.547 (0.061%), neg=0, invalid=762 0265: dt=36.288000, rms=0.547 (0.064%), neg=0, invalid=762 0266: dt=36.288000, rms=0.546 (0.062%), neg=0, invalid=762 0267: dt=36.288000, rms=0.546 (0.049%), neg=0, invalid=762 0268: dt=36.288000, rms=0.546 (0.048%), neg=0, invalid=762 0269: dt=36.288000, rms=0.546 (0.053%), neg=0, invalid=762 0270: dt=36.288000, rms=0.545 (0.048%), neg=0, invalid=762 0271: dt=36.288000, rms=0.545 (0.051%), neg=0, invalid=762 0272: dt=36.288000, rms=0.545 (0.048%), neg=0, invalid=762 0273: dt=36.288000, rms=0.545 (0.047%), neg=0, invalid=762 0274: dt=36.288000, rms=0.544 (0.047%), neg=0, invalid=762 0275: dt=36.288000, rms=0.544 (0.044%), neg=0, invalid=762 0276: dt=36.288000, rms=0.544 (0.042%), neg=0, invalid=762 0277: dt=36.288000, rms=0.544 (0.045%), neg=0, invalid=762 0278: dt=36.288000, rms=0.543 (0.046%), neg=0, invalid=762 0279: dt=36.288000, rms=0.543 (0.042%), neg=0, invalid=762 0280: dt=36.288000, rms=0.543 (0.040%), neg=0, invalid=762 0281: dt=36.288000, rms=0.543 (0.038%), neg=0, invalid=762 0282: dt=36.288000, rms=0.543 (0.036%), neg=0, invalid=762 0283: dt=36.288000, rms=0.542 (0.029%), neg=0, invalid=762 0284: dt=36.288000, rms=0.542 (0.035%), neg=0, invalid=762 0285: dt=36.288000, rms=0.542 (0.035%), neg=0, invalid=762 0286: dt=36.288000, rms=0.542 (0.035%), neg=0, invalid=762 0287: dt=36.288000, rms=0.542 (0.034%), neg=0, invalid=762 0288: dt=36.288000, rms=0.541 (0.033%), neg=0, invalid=762 0289: dt=36.288000, rms=0.541 (0.030%), neg=0, invalid=762 0290: dt=36.288000, rms=0.541 (0.023%), neg=0, invalid=762 0291: dt=36.288000, rms=0.541 (0.024%), neg=0, invalid=762 0292: dt=36.288000, rms=0.541 (0.026%), neg=0, invalid=762 0293: dt=36.288000, rms=0.541 (0.022%), neg=0, invalid=762 0294: dt=36.288000, rms=0.541 (0.032%), neg=0, invalid=762 0295: dt=36.288000, rms=0.540 (0.027%), neg=0, invalid=762 0296: dt=36.288000, rms=0.540 (0.023%), neg=0, invalid=762 0297: dt=36.288000, rms=0.540 (0.026%), neg=0, invalid=762 0298: dt=36.288000, rms=0.540 (0.025%), neg=0, invalid=762 0299: dt=36.288000, rms=0.540 (0.020%), neg=0, invalid=762 0300: dt=36.288000, rms=0.540 (0.007%), neg=0, invalid=762 0301: dt=36.288000, rms=0.540 (0.002%), neg=0, invalid=762 0302: dt=36.288000, rms=0.540 (0.009%), neg=0, invalid=762 0303: dt=36.288000, rms=0.540 (0.005%), neg=0, invalid=762 0304: dt=36.288000, rms=0.540 (0.006%), neg=0, invalid=762 0305: dt=36.288000, rms=0.540 (0.010%), neg=0, invalid=762 0306: dt=36.288000, rms=0.540 (0.007%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.547, neg=0, invalid=762 0307: dt=19.200000, rms=0.546 (0.175%), neg=0, invalid=762 0308: dt=44.800000, rms=0.545 (0.186%), neg=0, invalid=762 0309: dt=44.800000, rms=0.543 (0.506%), neg=0, invalid=762 0310: dt=44.800000, rms=0.541 (0.373%), neg=0, invalid=762 0311: dt=38.400000, rms=0.539 (0.366%), neg=0, invalid=762 0312: dt=2.800000, rms=0.538 (0.021%), neg=0, invalid=762 0313: dt=1.400000, rms=0.538 (0.010%), neg=0, invalid=762 0314: dt=0.700000, rms=0.538 (0.006%), neg=0, invalid=762 0315: dt=0.175000, rms=0.538 (0.000%), neg=0, invalid=762 0316: dt=0.000000, rms=0.538 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.539, neg=0, invalid=762 0317: dt=89.660377, rms=0.533 (1.047%), neg=0, invalid=762 0318: dt=30.190813, rms=0.531 (0.330%), neg=0, invalid=762 0319: dt=102.193548, rms=0.530 (0.278%), neg=0, invalid=762 0320: dt=32.000000, rms=0.528 (0.407%), neg=0, invalid=762 0321: dt=44.800000, rms=0.526 (0.277%), neg=0, invalid=762 0322: dt=44.800000, rms=0.525 (0.142%), neg=0, invalid=762 0323: dt=38.400000, rms=0.524 (0.183%), neg=0, invalid=762 0324: dt=38.400000, rms=0.524 (0.123%), neg=0, invalid=762 0325: dt=38.400000, rms=0.523 (0.139%), neg=0, invalid=762 0326: dt=32.000000, rms=0.522 (0.115%), neg=0, invalid=762 0327: dt=44.800000, rms=0.522 (0.120%), neg=0, invalid=762 0328: dt=32.000000, rms=0.521 (0.117%), neg=0, invalid=762 0329: dt=38.400000, rms=0.521 (0.092%), neg=0, invalid=762 0330: dt=38.400000, rms=0.520 (0.116%), neg=0, invalid=762 0331: dt=32.000000, rms=0.520 (0.076%), neg=0, invalid=762 0332: dt=44.800000, rms=0.519 (0.099%), neg=0, invalid=762 0333: dt=32.000000, rms=0.519 (0.077%), neg=0, invalid=762 0334: dt=44.800000, rms=0.518 (0.099%), neg=0, invalid=762 0335: dt=32.000000, rms=0.518 (0.061%), neg=0, invalid=762 0336: dt=38.400000, rms=0.518 (0.087%), neg=0, invalid=762 0337: dt=25.600000, rms=0.517 (0.048%), neg=0, invalid=762 0338: dt=25.600000, rms=0.517 (0.070%), neg=0, invalid=762 0339: dt=25.600000, rms=0.517 (0.083%), neg=0, invalid=762 0340: dt=25.600000, rms=0.516 (0.133%), neg=0, invalid=762 0341: dt=25.600000, rms=0.515 (0.133%), neg=0, invalid=762 0342: dt=25.600000, rms=0.514 (0.205%), neg=0, invalid=762 0343: dt=25.600000, rms=0.513 (0.185%), neg=0, invalid=762 0344: dt=25.600000, rms=0.512 (0.201%), neg=0, invalid=762 0345: dt=25.600000, rms=0.511 (0.193%), neg=0, invalid=762 0346: dt=25.600000, rms=0.510 (0.205%), neg=0, invalid=762 0347: dt=25.600000, rms=0.509 (0.210%), neg=0, invalid=762 0348: dt=25.600000, rms=0.508 (0.178%), neg=0, invalid=762 0349: dt=25.600000, rms=0.507 (0.180%), neg=0, invalid=762 0350: dt=25.600000, rms=0.506 (0.160%), neg=0, invalid=762 0351: dt=25.600000, rms=0.506 (0.173%), neg=0, invalid=762 0352: dt=25.600000, rms=0.505 (0.141%), neg=0, invalid=762 0353: dt=25.600000, rms=0.504 (0.135%), neg=0, invalid=762 0354: dt=25.600000, rms=0.504 (0.112%), neg=0, invalid=762 0355: dt=25.600000, rms=0.503 (0.110%), neg=0, invalid=762 0356: dt=25.600000, rms=0.502 (0.104%), neg=0, invalid=762 0357: dt=25.600000, rms=0.502 (0.081%), neg=0, invalid=762 0358: dt=25.600000, rms=0.502 (0.084%), neg=0, invalid=762 0359: dt=25.600000, rms=0.501 (0.071%), neg=0, invalid=762 0360: dt=25.600000, rms=0.501 (0.082%), neg=0, invalid=762 0361: dt=25.600000, rms=0.501 (0.066%), neg=0, invalid=762 0362: dt=25.600000, rms=0.500 (0.058%), neg=0, invalid=762 0363: dt=12.800000, rms=0.500 (0.010%), neg=0, invalid=762 0364: dt=12.800000, rms=0.500 (0.007%), neg=0, invalid=762 0365: dt=2.800000, rms=0.500 (0.002%), neg=0, invalid=762 0366: dt=0.700000, rms=0.500 (0.000%), neg=0, invalid=762 0367: dt=0.350000, rms=0.500 (0.000%), neg=0, invalid=762 0368: dt=0.175000, rms=0.500 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.518, neg=0, invalid=762 0369: dt=0.000000, rms=0.518 (0.066%), neg=0, invalid=762 0370: dt=0.000000, rms=0.518 (0.000%), neg=0, invalid=762 0371: dt=0.150000, rms=0.518 (-0.023%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.518, neg=0, invalid=762 0372: dt=0.000000, rms=0.518 (0.066%), neg=0, invalid=762 0373: dt=0.000000, rms=0.518 (0.000%), neg=0, invalid=762 0374: dt=0.150000, rms=0.518 (-0.020%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.554, neg=0, invalid=762 0375: dt=1.024000, rms=0.552 (0.361%), neg=0, invalid=762 0376: dt=0.080000, rms=0.552 (0.002%), neg=0, invalid=762 0377: dt=0.080000, rms=0.552 (0.001%), neg=0, invalid=762 0378: dt=0.080000, rms=0.552 (-0.010%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.552, neg=0, invalid=762 0379: dt=0.448000, rms=0.552 (0.130%), neg=0, invalid=762 0380: dt=0.320000, rms=0.551 (0.011%), neg=0, invalid=762 0381: dt=0.320000, rms=0.551 (-0.004%), 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=0.508, neg=0, invalid=762 0382: dt=0.448000, rms=0.495 (2.678%), neg=0, invalid=762 0383: dt=0.448000, rms=0.492 (0.556%), neg=0, invalid=762 0384: dt=0.448000, rms=0.490 (0.306%), neg=0, invalid=762 0385: dt=0.448000, rms=0.490 (0.167%), neg=0, invalid=762 0386: dt=0.448000, rms=0.489 (0.124%), neg=0, invalid=762 0387: dt=0.448000, rms=0.489 (0.083%), neg=0, invalid=762 0388: dt=0.448000, rms=0.488 (0.068%), neg=0, invalid=762 0389: dt=0.448000, rms=0.488 (0.049%), neg=0, invalid=762 0390: dt=0.448000, rms=0.488 (0.044%), neg=0, invalid=762 0391: dt=0.448000, rms=0.487 (0.069%), neg=0, invalid=762 0392: dt=0.448000, rms=0.487 (0.080%), neg=0, invalid=762 0393: dt=0.448000, rms=0.487 (0.073%), neg=0, invalid=762 0394: dt=0.448000, rms=0.487 (0.000%), neg=0, invalid=762 0395: dt=0.448000, rms=0.487 (-0.004%), neg=0, invalid=762 0396: dt=0.080000, rms=0.487 (0.000%), neg=0, invalid=762 0397: dt=0.064000, rms=0.487 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.487, neg=0, invalid=762 0398: dt=0.448000, rms=0.482 (1.119%), neg=0, invalid=762 0399: dt=0.448000, rms=0.481 (0.224%), neg=0, invalid=762 0400: dt=0.448000, rms=0.480 (0.100%), neg=0, invalid=762 0401: dt=0.448000, rms=0.480 (0.050%), neg=0, invalid=762 0402: dt=0.448000, rms=0.480 (0.025%), neg=0, invalid=762 0403: dt=0.448000, rms=0.479 (0.048%), neg=0, invalid=762 0404: dt=0.448000, rms=0.479 (0.040%), neg=0, invalid=762 0405: dt=0.448000, rms=0.479 (0.007%), neg=0, invalid=762 0406: dt=0.448000, rms=0.479 (-0.007%), neg=0, invalid=762 0407: dt=-0.000049, rms=0.479 (0.000%), neg=0, invalid=762 0408: dt=0.000000, rms=0.479 (0.000%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) ********************* ALLOWING NEGATIVE NODES IN DEFORMATION******************************** **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.478, neg=0, invalid=762 0409: dt=0.000000, rms=0.477 (0.085%), neg=0, invalid=762 0410: dt=0.000000, rms=0.477 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.478, neg=0, invalid=762 0411: dt=0.000000, rms=0.477 (0.085%), neg=0, invalid=762 0412: dt=0.000000, rms=0.477 (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=0.478, neg=0, invalid=762 0413: dt=0.000000, rms=0.477 (0.085%), neg=0, invalid=762 0414: dt=0.000000, rms=0.477 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.478, neg=0, invalid=762 0415: dt=145.152000, rms=0.476 (0.433%), neg=0, invalid=762 0416: dt=82.944000, rms=0.475 (0.162%), neg=0, invalid=762 0417: dt=82.944000, rms=0.475 (-0.063%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.475, neg=0, invalid=762 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0418: dt=24.465116, rms=0.473 (0.420%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0419: dt=38.400000, rms=0.472 (0.298%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 9 iterations, nbhd size=1, neg = 0 0420: dt=25.600000, rms=0.471 (0.190%), neg=0, invalid=762 0421: dt=25.600000, rms=0.470 (0.168%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 8 iterations, nbhd size=1, neg = 0 0422: dt=25.600000, rms=0.470 (0.156%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 13 iterations, nbhd size=1, neg = 0 0423: dt=25.600000, rms=0.469 (0.097%), neg=0, invalid=762 iter 0, gcam->neg = 12 after 9 iterations, nbhd size=1, neg = 0 0424: dt=25.600000, rms=0.469 (0.035%), neg=0, invalid=762 0425: dt=38.400000, rms=0.469 (0.105%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 7 iterations, nbhd size=1, neg = 0 0426: dt=25.600000, rms=0.468 (0.055%), neg=0, invalid=762 0427: dt=25.600000, rms=0.468 (0.062%), neg=0, invalid=762 0428: dt=25.600000, rms=0.468 (0.069%), neg=0, invalid=762 0429: dt=25.600000, rms=0.467 (0.074%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0430: dt=25.600000, rms=0.467 (0.095%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0431: dt=25.600000, rms=0.467 (0.067%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 0432: dt=25.600000, rms=0.466 (0.075%), neg=0, invalid=762 0433: dt=25.600000, rms=0.466 (0.075%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.466, neg=0, invalid=762 0434: dt=57.043478, rms=0.461 (1.179%), neg=0, invalid=762 0435: dt=24.975610, rms=0.459 (0.393%), neg=0, invalid=762 0436: dt=44.800000, rms=0.458 (0.247%), neg=0, invalid=762 0437: dt=44.800000, rms=0.458 (0.047%), neg=0, invalid=762 0438: dt=44.800000, rms=0.456 (0.418%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0439: dt=44.800000, rms=0.456 (0.014%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0440: dt=44.800000, rms=0.454 (0.304%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 3 iterations, nbhd size=0, neg = 0 0441: dt=44.800000, rms=0.454 (-0.278%), neg=0, invalid=762 0442: dt=25.600000, rms=0.454 (0.100%), neg=0, invalid=762 0443: dt=19.200000, rms=0.453 (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=0.458, neg=0, invalid=762 0444: dt=0.063000, rms=0.458 (0.085%), neg=0, invalid=762 0445: dt=0.002813, rms=0.458 (0.000%), neg=0, invalid=762 0446: dt=0.002813, rms=0.458 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.458, neg=0, invalid=762 0447: dt=7.272727, rms=0.457 (0.170%), neg=0, invalid=762 0448: dt=10.202899, rms=0.457 (0.093%), neg=0, invalid=762 0449: dt=10.202899, rms=0.456 (0.152%), neg=0, invalid=762 0450: dt=10.202899, rms=0.455 (0.223%), neg=0, invalid=762 0451: dt=10.202899, rms=0.454 (0.280%), neg=0, invalid=762 0452: dt=10.202899, rms=0.452 (0.418%), neg=0, invalid=762 0453: dt=10.202899, rms=0.449 (0.547%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 5 iterations, nbhd size=0, neg = 0 0454: dt=10.202899, rms=0.447 (0.528%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 3 iterations, nbhd size=0, neg = 0 0455: dt=10.202899, rms=0.445 (0.366%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 7 iterations, nbhd size=1, neg = 0 0456: dt=10.202899, rms=0.445 (0.142%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 2 iterations, nbhd size=0, neg = 0 0457: dt=10.202899, rms=0.445 (-0.016%), neg=0, invalid=762 0458: dt=0.000844, rms=0.445 (0.000%), neg=0, invalid=762 0459: dt=0.000000, rms=0.445 (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=0.450, neg=0, invalid=762 0460: dt=0.000000, rms=0.450 (0.092%), neg=0, invalid=762 0461: dt=0.000000, rms=0.450 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.450, neg=0, invalid=762 0462: dt=0.000000, rms=0.450 (0.092%), neg=0, invalid=762 0463: dt=0.000000, rms=0.450 (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=0.442, neg=0, invalid=762 iter 0, gcam->neg = 588 after 14 iterations, nbhd size=1, neg = 0 0464: dt=1.883644, rms=0.419 (5.130%), neg=0, invalid=762 0465: dt=0.016000, rms=0.419 (0.008%), neg=0, invalid=762 0466: dt=0.016000, rms=0.419 (-0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.419, neg=0, invalid=762 0467: dt=0.096000, rms=0.419 (0.175%), neg=0, invalid=762 0468: dt=0.001750, rms=0.419 (0.001%), neg=0, invalid=762 0469: dt=0.001750, rms=0.419 (-0.000%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.408, neg=0, invalid=762 0470: dt=0.000000, rms=0.408 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.408, neg=0, invalid=762 0471: dt=0.000000, rms=0.408 (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=0.408, neg=0, invalid=762 0472: dt=0.000000, rms=0.408 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.408, neg=0, invalid=762 0473: dt=9.072000, rms=0.408 (0.005%), neg=0, invalid=762 0474: dt=9.072000, rms=0.408 (0.002%), neg=0, invalid=762 0475: dt=9.072000, rms=0.408 (0.000%), neg=0, invalid=762 0476: dt=9.072000, rms=0.408 (-0.004%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.409, neg=0, invalid=762 0477: dt=2.800000, rms=0.409 (0.006%), neg=0, invalid=762 0478: dt=0.700000, rms=0.409 (0.000%), neg=0, invalid=762 0479: dt=0.700000, rms=0.409 (0.000%), neg=0, invalid=762 0480: dt=0.700000, rms=0.409 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.409, neg=0, invalid=762 0481: dt=80.727273, rms=0.407 (0.370%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0482: dt=32.000000, rms=0.406 (0.276%), neg=0, invalid=762 0483: dt=44.800000, rms=0.405 (0.117%), neg=0, invalid=762 0484: dt=44.800000, rms=0.405 (0.067%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0485: dt=44.800000, rms=0.404 (0.192%), neg=0, invalid=762 0486: dt=44.800000, rms=0.404 (0.111%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0487: dt=44.800000, rms=0.403 (0.188%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 1 iterations, nbhd size=0, neg = 0 0488: dt=44.800000, rms=0.403 (0.111%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0489: dt=44.800000, rms=0.402 (0.141%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0490: dt=44.800000, rms=0.402 (0.112%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 2 iterations, nbhd size=0, neg = 0 0491: dt=44.800000, rms=0.401 (0.071%), neg=0, invalid=762 0492: dt=25.600000, rms=0.401 (0.035%), neg=0, invalid=762 0493: dt=25.600000, rms=0.401 (0.006%), neg=0, invalid=762 0494: dt=25.600000, rms=0.401 (0.005%), neg=0, invalid=762 0495: dt=25.600000, rms=0.401 (0.012%), neg=0, invalid=762 0496: dt=25.600000, rms=0.401 (0.006%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.405, neg=0, invalid=762 0497: dt=0.000000, rms=0.405 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.405, neg=0, invalid=762 0498: dt=8.551724, rms=0.404 (0.090%), neg=0, invalid=762 0499: dt=16.128000, rms=0.404 (0.094%), neg=0, invalid=762 iter 0, gcam->neg = 13 after 9 iterations, nbhd size=1, neg = 0 0500: dt=60.000000, rms=0.403 (0.297%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0501: dt=11.104478, rms=0.402 (0.128%), neg=0, invalid=762 0502: dt=11.104478, rms=0.402 (0.046%), neg=0, invalid=762 0503: dt=11.104478, rms=0.402 (0.069%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0504: dt=11.104478, rms=0.401 (0.105%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0505: dt=11.104478, rms=0.401 (0.059%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 3 iterations, nbhd size=0, neg = 0 0506: dt=11.104478, rms=0.401 (0.045%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0507: dt=13.824000, rms=0.401 (0.017%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.405, neg=0, invalid=762 0508: dt=0.000040, rms=0.405 (0.000%), neg=0, invalid=762 0509: dt=0.000000, rms=0.405 (0.000%), neg=0, invalid=762 0510: dt=0.100000, rms=0.405 (-0.057%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.405, neg=0, invalid=762 0511: dt=0.000000, rms=0.405 (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=0.398, neg=0, invalid=762 iter 0, gcam->neg = 371 after 15 iterations, nbhd size=1, neg = 0 0512: dt=1.285800, rms=0.390 (1.993%), neg=0, invalid=762 0513: dt=0.000020, rms=0.390 (0.000%), neg=0, invalid=762 0514: dt=0.000020, rms=0.390 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.390, neg=0, invalid=762 0515: dt=0.112000, rms=0.389 (0.061%), neg=0, invalid=762 0516: dt=0.080000, rms=0.389 (0.018%), neg=0, invalid=762 0517: dt=0.080000, rms=0.389 (0.008%), neg=0, invalid=762 0518: dt=0.080000, rms=0.389 (-0.027%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 1 hours, 8 minutes and 18 seconds. mri_ca_register utimesec 4877.689973 mri_ca_register stimesec 4.515901 mri_ca_register ru_maxrss 1337328 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 6145859 mri_ca_register ru_majflt 0 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 0 mri_ca_register ru_oublock 63576 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 7538 mri_ca_register ru_nivcsw 7916 FSRUNTIME@ mri_ca_register 1.1384 hours 4 threads #-------------------------------------- #@# SubCort Seg Fri Oct 11 01:16:20 -03 2019 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz sysname Linux hostname fisicos-ub2 machine x86_64 setenv SUBJECTS_DIR /mnt/disco1/subjects cd /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz == Number of threads available to mri_ca_label for OpenMP = 4 == relabeling unlikely voxels with window_size = 9 and prior threshold 0.30 using Gibbs prior factor = 0.500 renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes reading classifier array from /usr/local/freesurfer/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 7.33 Atlas used for the 3D morph was /usr/local/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 = 0.13524 (30) Left_Lateral_Ventricle (4): linear fit = 1.47 x + 0.0 (2456 voxels, overlap=0.258) Left_Lateral_Ventricle (4): linear fit = 1.47 x + 0.0 (2456 voxels, peak = 29), gca=29.3 gca peak = 0.17677 (13) mri peak = 0.13931 (30) Right_Lateral_Ventricle (43): linear fit = 2.08 x + 0.0 (2619 voxels, overlap=0.176) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (2619 voxels, peak = 27), gca=19.5 gca peak = 0.28129 (95) mri peak = 0.12645 (102) Right_Pallidum (52): linear fit = 1.09 x + 0.0 (857 voxels, overlap=0.020) Right_Pallidum (52): linear fit = 1.09 x + 0.0 (857 voxels, peak = 103), gca=103.1 gca peak = 0.16930 (96) mri peak = 0.13212 (104) Left_Pallidum (13): linear fit = 1.10 x + 0.0 (872 voxels, overlap=0.190) Left_Pallidum (13): linear fit = 1.10 x + 0.0 (872 voxels, peak = 105), gca=105.1 gca peak = 0.24553 (55) mri peak = 0.09360 (75) Right_Hippocampus (53): linear fit = 1.34 x + 0.0 (1174 voxels, overlap=0.020) Right_Hippocampus (53): linear fit = 1.34 x + 0.0 (1174 voxels, peak = 73), gca=73.4 gca peak = 0.30264 (59) mri peak = 0.08509 (72) Left_Hippocampus (17): linear fit = 1.29 x + 0.0 (1013 voxels, overlap=0.022) Left_Hippocampus (17): linear fit = 1.29 x + 0.0 (1013 voxels, peak = 76), gca=76.4 gca peak = 0.07580 (103) mri peak = 0.11646 (103) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (50120 voxels, overlap=0.691) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (50120 voxels, peak = 104), gca=103.5 gca peak = 0.07714 (104) mri peak = 0.09669 (104) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (50014 voxels, overlap=0.659) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (50014 voxels, peak = 106), gca=105.6 gca peak = 0.09712 (58) mri peak = 0.04247 (77) Left_Cerebral_Cortex (3): linear fit = 1.33 x + 0.0 (37304 voxels, overlap=0.022) Left_Cerebral_Cortex (3): linear fit = 1.33 x + 0.0 (37304 voxels, peak = 77), gca=76.9 gca peak = 0.11620 (58) mri peak = 0.04624 (77) Right_Cerebral_Cortex (42): linear fit = 1.29 x + 0.0 (35096 voxels, overlap=0.001) Right_Cerebral_Cortex (42): linear fit = 1.29 x + 0.0 (35096 voxels, peak = 75), gca=75.1 gca peak = 0.30970 (66) mri peak = 0.14500 (87) Right_Caudate (50): linear fit = 1.28 x + 0.0 (1069 voxels, overlap=0.020) Right_Caudate (50): linear fit = 1.28 x + 0.0 (1069 voxels, peak = 85), gca=84.8 gca peak = 0.15280 (69) mri peak = 0.11891 (87) Left_Caudate (11): linear fit = 1.17 x + 0.0 (1164 voxels, overlap=0.019) Left_Caudate (11): linear fit = 1.17 x + 0.0 (1164 voxels, peak = 81), gca=81.1 gca peak = 0.13902 (56) mri peak = 0.05325 (72) Left_Cerebellum_Cortex (8): linear fit = 1.29 x + 0.0 (30271 voxels, overlap=0.014) Left_Cerebellum_Cortex (8): linear fit = 1.29 x + 0.0 (30271 voxels, peak = 73), gca=72.5 gca peak = 0.14777 (55) mri peak = 0.06250 (74) Right_Cerebellum_Cortex (47): linear fit = 1.33 x + 0.0 (32817 voxels, overlap=0.001) Right_Cerebellum_Cortex (47): linear fit = 1.33 x + 0.0 (32817 voxels, peak = 73), gca=72.9 gca peak = 0.16765 (84) mri peak = 0.11514 (95) Left_Cerebellum_White_Matter (7): linear fit = 1.12 x + 0.0 (7865 voxels, overlap=0.003) Left_Cerebellum_White_Matter (7): linear fit = 1.12 x + 0.0 (7865 voxels, peak = 94), gca=94.5 gca peak = 0.18739 (84) mri peak = 0.11727 (91) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (6793 voxels, overlap=0.672) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (6793 voxels, peak = 90), gca=90.3 gca peak = 0.29869 (57) mri peak = 0.11607 (75) Left_Amygdala (18): linear fit = 1.30 x + 0.0 (561 voxels, overlap=0.057) Left_Amygdala (18): linear fit = 1.30 x + 0.0 (561 voxels, peak = 74), gca=74.4 gca peak = 0.33601 (57) mri peak = 0.09704 (76) Right_Amygdala (54): linear fit = 1.30 x + 0.0 (658 voxels, overlap=0.046) Right_Amygdala (54): linear fit = 1.30 x + 0.0 (658 voxels, peak = 74), gca=74.4 gca peak = 0.11131 (90) mri peak = 0.08312 (100) Left_Thalamus_Proper (10): linear fit = 1.13 x + 0.0 (5185 voxels, overlap=0.283) Left_Thalamus_Proper (10): linear fit = 1.13 x + 0.0 (5185 voxels, peak = 102), gca=102.2 gca peak = 0.11793 (83) mri peak = 0.10492 (96) Right_Thalamus_Proper (49): linear fit = 1.14 x + 0.0 (5003 voxels, overlap=0.058) Right_Thalamus_Proper (49): linear fit = 1.14 x + 0.0 (5003 voxels, peak = 95), gca=95.0 gca peak = 0.08324 (81) mri peak = 0.10961 (90) Left_Putamen (12): linear fit = 1.15 x + 0.0 (2151 voxels, overlap=0.023) Left_Putamen (12): linear fit = 1.15 x + 0.0 (2151 voxels, peak = 94), gca=93.6 gca peak = 0.10360 (77) mri peak = 0.09207 (91) Right_Putamen (51): linear fit = 1.12 x + 0.0 (2494 voxels, overlap=0.239) Right_Putamen (51): linear fit = 1.12 x + 0.0 (2494 voxels, peak = 87), gca=86.6 gca peak = 0.08424 (78) mri peak = 0.09099 (83) Brain_Stem (16): linear fit = 1.07 x + 0.0 (15672 voxels, overlap=0.476) Brain_Stem (16): linear fit = 1.07 x + 0.0 (15672 voxels, peak = 83), gca=83.1 gca peak = 0.12631 (89) mri peak = 0.08395 (97) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1651 voxels, overlap=0.208) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1651 voxels, peak = 100), gca=100.1 gca peak = 0.14500 (87) mri peak = 0.10637 (101) Left_VentralDC (28): linear fit = 1.14 x + 0.0 (1680 voxels, overlap=0.085) Left_VentralDC (28): linear fit = 1.14 x + 0.0 (1680 voxels, peak = 100), gca=99.6 gca peak = 0.14975 (24) mri peak = 0.14958 (31) Third_Ventricle (14): linear fit = 1.22 x + 0.0 (312 voxels, overlap=0.439) Third_Ventricle (14): linear fit = 1.22 x + 0.0 (312 voxels, peak = 29), gca=29.2 gca peak = 0.19357 (14) mri peak = 0.13713 (29) Fourth_Ventricle (15): linear fit = 1.76 x + 0.0 (296 voxels, overlap=0.194) Fourth_Ventricle (15): linear fit = 1.76 x + 0.0 (296 voxels, peak = 25), gca=24.7 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 1.00000 (94) gca peak Fourth_Ventricle = 0.19357 (14) 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 1.31 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 1.39 x + 0.0 Left_Putamen too bright - rescaling by 1.006 (from 1.155) to 94.1 (was 93.6) Left_Pallidum too bright - rescaling by 0.965 (from 1.095) to 101.4 (was 105.1) Right_Pallidum too bright - rescaling by 0.984 (from 1.085) to 101.4 (was 103.1) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.13690 (27) mri peak = 0.13524 (30) Left_Lateral_Ventricle (4): linear fit = 0.99 x + 0.0 (2456 voxels, overlap=0.811) Left_Lateral_Ventricle (4): linear fit = 0.99 x + 0.0 (2456 voxels, peak = 27), gca=26.6 gca peak = 0.13981 (19) mri peak = 0.13931 (30) Right_Lateral_Ventricle (43): linear fit = 1.40 x + 0.0 (2619 voxels, overlap=0.370) Right_Lateral_Ventricle (43): linear fit = 1.40 x + 0.0 (2619 voxels, peak = 27), gca=26.7 gca peak = 0.29360 (102) mri peak = 0.12645 (102) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (857 voxels, overlap=1.002) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (857 voxels, peak = 104), gca=103.5 gca peak = 0.16985 (102) mri peak = 0.13212 (104) Left_Pallidum (13): linear fit = 1.03 x + 0.0 (872 voxels, overlap=0.722) Left_Pallidum (13): linear fit = 1.03 x + 0.0 (872 voxels, peak = 106), gca=105.6 gca peak = 0.22461 (74) mri peak = 0.09360 (75) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1174 voxels, overlap=1.001) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1174 voxels, peak = 74), gca=74.0 gca peak = 0.27088 (73) mri peak = 0.08509 (72) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (1013 voxels, overlap=1.004) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (1013 voxels, peak = 72), gca=71.9 gca peak = 0.07896 (103) mri peak = 0.11646 (103) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (50120 voxels, overlap=0.710) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (50120 voxels, peak = 103), gca=103.0 gca peak = 0.07821 (106) mri peak = 0.09669 (104) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (50014 voxels, overlap=0.725) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (50014 voxels, peak = 106), gca=106.0 gca peak = 0.07413 (77) mri peak = 0.04247 (77) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (37304 voxels, overlap=0.949) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (37304 voxels, peak = 76), gca=75.8 gca peak = 0.09084 (75) mri peak = 0.04624 (77) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (35096 voxels, overlap=0.945) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (35096 voxels, peak = 75), gca=75.0 gca peak = 0.28455 (85) mri peak = 0.14500 (87) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1069 voxels, overlap=0.999) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1069 voxels, peak = 85), gca=85.0 gca peak = 0.14946 (91) mri peak = 0.11891 (87) Left_Caudate (11): linear fit = 0.98 x + 0.0 (1164 voxels, overlap=0.997) Left_Caudate (11): linear fit = 0.98 x + 0.0 (1164 voxels, peak = 89), gca=88.7 gca peak = 0.11022 (72) mri peak = 0.05325 (72) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (30271 voxels, overlap=0.978) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (30271 voxels, peak = 72), gca=72.0 gca peak = 0.11385 (73) mri peak = 0.06250 (74) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (32817 voxels, overlap=0.959) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (32817 voxels, peak = 72), gca=71.9 gca peak = 0.15219 (95) mri peak = 0.11514 (95) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (7865 voxels, overlap=0.897) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (7865 voxels, peak = 95), gca=94.5 gca peak = 0.14971 (90) mri peak = 0.11727 (91) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6793 voxels, overlap=0.963) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6793 voxels, peak = 90), gca=89.6 gca peak = 0.28656 (76) mri peak = 0.11607 (75) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (561 voxels, overlap=1.015) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (561 voxels, peak = 76), gca=76.0 gca peak = 0.31032 (74) mri peak = 0.09704 (76) Right_Amygdala (54): linear fit = 1.01 x + 0.0 (658 voxels, overlap=1.008) Right_Amygdala (54): linear fit = 1.01 x + 0.0 (658 voxels, peak = 75), gca=75.1 gca peak = 0.10617 (100) mri peak = 0.08312 (100) Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (5185 voxels, overlap=0.890) Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (5185 voxels, peak = 98), gca=98.5 gca peak = 0.09598 (95) mri peak = 0.10492 (96) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (5003 voxels, overlap=0.852) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (5003 voxels, peak = 96), gca=96.4 gca peak = 0.07534 (94) mri peak = 0.10961 (90) Left_Putamen (12): linear fit = 0.99 x + 0.0 (2151 voxels, overlap=0.695) Left_Putamen (12): linear fit = 0.99 x + 0.0 (2151 voxels, peak = 93), gca=92.6 gca peak = 0.08298 (84) mri peak = 0.09207 (91) Right_Putamen (51): linear fit = 1.02 x + 0.0 (2494 voxels, overlap=0.843) Right_Putamen (51): linear fit = 1.02 x + 0.0 (2494 voxels, peak = 86), gca=86.1 gca peak = 0.07352 (83) mri peak = 0.09099 (83) Brain_Stem (16): linear fit = 0.99 x + 0.0 (15672 voxels, overlap=0.723) Brain_Stem (16): linear fit = 0.99 x + 0.0 (15672 voxels, peak = 82), gca=81.8 gca peak = 0.10032 (99) mri peak = 0.08395 (97) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1651 voxels, overlap=0.815) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1651 voxels, peak = 99), gca=99.0 gca peak = 0.16195 (98) mri peak = 0.10637 (101) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1680 voxels, overlap=0.881) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1680 voxels, peak = 98), gca=97.5 gca peak = 0.16540 (31) mri peak = 0.14958 (31) Third_Ventricle (14): linear fit = 1.04 x + 0.0 (312 voxels, overlap=0.845) Third_Ventricle (14): linear fit = 1.04 x + 0.0 (312 voxels, peak = 32), gca=32.4 gca peak = 0.14737 (21) mri peak = 0.13713 (29) Fourth_Ventricle (15): linear fit = 1.29 x + 0.0 (296 voxels, overlap=0.471) Fourth_Ventricle (15): linear fit = 1.29 x + 0.0 (296 voxels, peak = 27), gca=27.2 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.17746 (35) gca peak Left_Thalamus = 0.36646 (104) gca peak CSF = 0.17474 (51) gca peak Left_Accumbens_area = 0.63261 (73) gca peak Left_undetermined = 0.96707 (34) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.11834 (35) gca peak Right_Inf_Lat_Vent = 0.24572 (31) gca peak Right_Accumbens_area = 0.29708 (83) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14504 (37) gca peak Fifth_Ventricle = 0.51669 (43) gca peak WM_hypointensities = 0.08074 (77) gca peak non_WM_hypointensities = 0.12165 (55) gca peak Optic_Chiasm = 0.68702 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.18 x + 0.0 Left_Pallidum too bright - rescaling by 0.960 (from 1.035) to 101.4 (was 105.6) Right_Pallidum too bright - rescaling by 0.979 (from 1.015) to 101.4 (was 103.5) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 72855 voxels changed in iteration 0 of unlikely voxel relabeling 318 voxels changed in iteration 1 of unlikely voxel relabeling 12 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 73139 gm and wm labels changed (%28 to gray, %72 to white out of all changed labels) 534 hippocampal voxels changed. 5 amygdala voxels changed. pass 1: 80231 changed. image ll: -2.139, PF=0.500 pass 2: 21296 changed. image ll: -2.138, PF=0.500 pass 3: 6226 changed. pass 4: 2303 changed. 66767 voxels changed in iteration 0 of unlikely voxel relabeling 363 voxels changed in iteration 1 of unlikely voxel relabeling 17 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 6999 voxels changed in iteration 0 of unlikely voxel relabeling 114 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 5683 voxels changed in iteration 0 of unlikely voxel relabeling 62 voxels changed in iteration 1 of unlikely voxel relabeling 1 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 5357 voxels changed in iteration 0 of unlikely voxel relabeling 30 voxels changed in iteration 1 of unlikely voxel relabeling 2 voxels changed in iteration 2 of unlikely voxel relabeling 2 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 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 1962.362854 mri_ca_label stimesec 0.443999 mri_ca_label ru_maxrss 2100296 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 732171 mri_ca_label ru_majflt 8 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 1616 mri_ca_label ru_oublock 512 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 247 mri_ca_label ru_nivcsw 5932 auto-labeling took 32 minutes and 17 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/transforms/cc_up.lta sub-A00039639_ses-DS2_T1w.nii.gz will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/transforms/cc_up.lta reading aseg from /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/aseg.auto_noCCseg.mgz reading norm from /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/norm.mgz 55494 voxels in left wm, 33756 in right wm, xrange [122, 132] searching rotation angles z=[-4 10], y=[-6 8] searching scale 1 Z rot -4.2 searching scale 1 Z rot -3.9 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.4 searching scale 1 Z rot -3.2 searching scale 1 Z rot -2.9 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.4 searching scale 1 Z rot -2.2 searching scale 1 Z rot -1.9 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.4 searching scale 1 Z rot -1.2 searching scale 1 Z rot -0.9 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.4 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.1 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.6 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.1 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.6 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.1 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.6 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.1 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.6 searching scale 1 Z rot 3.8 searching scale 1 Z rot 4.1 searching scale 1 Z rot 4.3 searching scale 1 Z rot 4.6 searching scale 1 Z rot 4.8 searching scale 1 Z rot 5.1 searching scale 1 Z rot 5.3 searching scale 1 Z rot 5.6 searching scale 1 Z rot 5.8 searching scale 1 Z rot 6.1 searching scale 1 Z rot 6.3 searching scale 1 Z rot 6.6 searching scale 1 Z rot 6.8 searching scale 1 Z rot 7.1 searching scale 1 Z rot 7.3 searching scale 1 Z rot 7.6 searching scale 1 Z rot 7.8 searching scale 1 Z rot 8.1 searching scale 1 Z rot 8.3 searching scale 1 Z rot 8.6 searching scale 1 Z rot 8.8 searching scale 1 Z rot 9.1 searching scale 1 Z rot 9.3 searching scale 1 Z rot 9.6 global minimum found at slice 125.8, rotations (1.46, 2.80) final transformation (x=125.8, yr=1.461, zr=2.805): 0.99848 -0.04893 0.02546 4.10034; 0.04891 0.99880 0.00125 38.83093; -0.02549 0.00000 0.99968 37.23600; 0.00000 0.00000 0.00000 1.00000; updating x range to be [125, 129] in xformed coordinates best xformed slice 127 cc center is found at 127 83 94 eigenvectors: 0.00010 -0.00116 1.00000; -0.08897 -0.99603 -0.00114; 0.99603 -0.08897 -0.00020; writing aseg with callosum to /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/aseg.auto.mgz... corpus callosum segmentation took 0.5 minutes #-------------------------------------- #@# Merge ASeg Fri Oct 11 01:49:06 -03 2019 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Fri Oct 11 01:49:06 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/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... 394 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 84 (84), valley at 50 (50) csf peak at 29, setting threshold to 65 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 83 (83), valley at 51 (51) csf peak at 29, setting threshold to 65 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 Fri Oct 11 01:50:40 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1719003 voxels in mask (pct= 10.25) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Fri Oct 11 01:50:40 -03 2019 mri_segment -mprage brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (103.0): 103.1 +- 6.2 [79.0 --> 125.0] GM (76.0) : 72.8 +- 13.7 [30.0 --> 95.0] setting bottom of white matter range to 86.5 setting top of gray matter range to 100.2 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... 7841 sparsely connected voxels removed... thickening thin strands.... 20 segments, 4630 filled 3767 bright non-wm voxels segmented. 4702 diagonally connected voxels added... white matter segmentation took 1.0 minutes writing output to wm.seg.mgz... assuming input volume is MGH (Van der Kouwe) MP-RAGE mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.21 minutes reading wm segmentation from wm.seg.mgz... 97 voxels added to wm to prevent paths from MTL structures to cortex 4638 additional wm voxels added 0 additional wm voxels added SEG EDIT: 56475 voxels turned on, 58267 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 0 new 0 115,126,128 old 0 new 0 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 24 found - 24 modified | TOTAL: 24 pass 2 (xy+): 0 found - 24 modified | TOTAL: 24 pass 1 (xy-): 27 found - 27 modified | TOTAL: 51 pass 2 (xy-): 0 found - 27 modified | TOTAL: 51 pass 1 (yz+): 27 found - 27 modified | TOTAL: 78 pass 2 (yz+): 0 found - 27 modified | TOTAL: 78 pass 1 (yz-): 31 found - 31 modified | TOTAL: 109 pass 2 (yz-): 0 found - 31 modified | TOTAL: 109 pass 1 (xz+): 31 found - 31 modified | TOTAL: 140 pass 2 (xz+): 0 found - 31 modified | TOTAL: 140 pass 1 (xz-): 21 found - 21 modified | TOTAL: 161 pass 2 (xz-): 0 found - 21 modified | TOTAL: 161 Iteration Number : 1 pass 1 (+++): 24 found - 24 modified | TOTAL: 24 pass 2 (+++): 0 found - 24 modified | TOTAL: 24 pass 1 (+++): 51 found - 51 modified | TOTAL: 75 pass 2 (+++): 0 found - 51 modified | TOTAL: 75 pass 1 (+++): 51 found - 51 modified | TOTAL: 126 pass 2 (+++): 0 found - 51 modified | TOTAL: 126 pass 1 (+++): 27 found - 27 modified | TOTAL: 153 pass 2 (+++): 0 found - 27 modified | TOTAL: 153 Iteration Number : 1 pass 1 (++): 121 found - 121 modified | TOTAL: 121 pass 2 (++): 0 found - 121 modified | TOTAL: 121 pass 1 (+-): 139 found - 139 modified | TOTAL: 260 pass 2 (+-): 0 found - 139 modified | TOTAL: 260 pass 1 (--): 94 found - 94 modified | TOTAL: 354 pass 2 (--): 0 found - 94 modified | TOTAL: 354 pass 1 (-+): 97 found - 97 modified | TOTAL: 451 pass 2 (-+): 0 found - 97 modified | TOTAL: 451 Iteration Number : 2 pass 1 (xy+): 12 found - 12 modified | TOTAL: 12 pass 2 (xy+): 0 found - 12 modified | TOTAL: 12 pass 1 (xy-): 9 found - 9 modified | TOTAL: 21 pass 2 (xy-): 0 found - 9 modified | TOTAL: 21 pass 1 (yz+): 11 found - 11 modified | TOTAL: 32 pass 2 (yz+): 0 found - 11 modified | TOTAL: 32 pass 1 (yz-): 9 found - 9 modified | TOTAL: 41 pass 2 (yz-): 0 found - 9 modified | TOTAL: 41 pass 1 (xz+): 8 found - 8 modified | TOTAL: 49 pass 2 (xz+): 0 found - 8 modified | TOTAL: 49 pass 1 (xz-): 6 found - 6 modified | TOTAL: 55 pass 2 (xz-): 0 found - 6 modified | TOTAL: 55 Iteration Number : 2 pass 1 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 4 pass 1 (+++): 4 found - 4 modified | TOTAL: 8 pass 2 (+++): 0 found - 4 modified | TOTAL: 8 pass 1 (+++): 6 found - 6 modified | TOTAL: 14 pass 2 (+++): 0 found - 6 modified | TOTAL: 14 Iteration Number : 2 pass 1 (++): 6 found - 6 modified | TOTAL: 6 pass 2 (++): 0 found - 6 modified | TOTAL: 6 pass 1 (+-): 5 found - 5 modified | TOTAL: 11 pass 2 (+-): 0 found - 5 modified | TOTAL: 11 pass 1 (--): 5 found - 5 modified | TOTAL: 16 pass 2 (--): 0 found - 5 modified | TOTAL: 16 pass 1 (-+): 3 found - 3 modified | TOTAL: 19 pass 2 (-+): 0 found - 3 modified | TOTAL: 19 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 2 found - 2 modified | TOTAL: 3 pass 2 (yz-): 0 found - 2 modified | TOTAL: 3 pass 1 (xz+): 1 found - 1 modified | TOTAL: 4 pass 2 (xz+): 0 found - 1 modified | TOTAL: 4 pass 1 (xz-): 0 found - 0 modified | TOTAL: 4 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 (+-): 2 found - 2 modified | TOTAL: 2 pass 2 (+-): 0 found - 2 modified | TOTAL: 2 pass 1 (--): 0 found - 0 modified | TOTAL: 2 pass 1 (-+): 1 found - 1 modified | TOTAL: 3 pass 2 (-+): 0 found - 1 modified | TOTAL: 3 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 = 860 (out of 635792: 0.135264) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Fri Oct 11 01:51:54 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/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 0.98242 -0.01675 0.04059 -0.52148; 0.00726 1.11136 0.24034 -15.51851; -0.05142 -0.18939 0.95621 28.45443; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 0.98242 -0.01675 0.04059 -0.52148; 0.00726 1.11136 0.24034 -15.51851; -0.05142 -0.18939 0.95621 28.45443; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1107 (min = 350, max = 1400), aspect = 0.44 (min = 0.10, max = 0.75) no need to search using seed (125, 120, 151), TAL = (3.0, 23.0, 8.0) talairach voxel to voxel transform 1.01548 0.00763 -0.04502 1.92899; -0.01768 0.86271 -0.21609 19.52753; 0.05111 0.17128 1.00058 -25.78625; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (125, 120, 151) --> (3.0, 23.0, 8.0) done. writing output to filled.mgz... filling took 0.3 minutes talairach cc position changed to (3.00, 23.00, 8.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(21.00, 23.00, 8.00) SRC: (104.70, 88.53, 151.32) search lh wm seed point around talairach space (-15.00, 23.00, 8.00), SRC: (141.26, 87.89, 153.16) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Fri Oct 11 01:52:12 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 0 found - 0 modified | TOTAL: 2 pass 1 (yz+): 1 found - 1 modified | TOTAL: 3 pass 2 (yz+): 0 found - 1 modified | TOTAL: 3 pass 1 (yz-): 0 found - 0 modified | TOTAL: 3 pass 1 (xz+): 1 found - 1 modified | TOTAL: 4 pass 2 (xz+): 0 found - 1 modified | TOTAL: 4 pass 1 (xz-): 2 found - 2 modified | TOTAL: 6 pass 2 (xz-): 0 found - 2 modified | TOTAL: 6 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 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+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 8 (out of 301371: 0.002655) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 30: 121 vertices, 159 faces slice 40: 3986 vertices, 4181 faces slice 50: 12733 vertices, 13109 faces slice 60: 23563 vertices, 23891 faces slice 70: 34437 vertices, 34823 faces slice 80: 45840 vertices, 46179 faces slice 90: 56979 vertices, 57388 faces slice 100: 68668 vertices, 69127 faces slice 110: 80397 vertices, 80843 faces slice 120: 91462 vertices, 91890 faces slice 130: 102783 vertices, 103235 faces slice 140: 113423 vertices, 113848 faces slice 150: 122157 vertices, 122532 faces slice 160: 130660 vertices, 130986 faces slice 170: 137620 vertices, 137921 faces slice 180: 143581 vertices, 143827 faces slice 190: 147309 vertices, 147447 faces slice 200: 147808 vertices, 147876 faces slice 210: 147808 vertices, 147876 faces slice 220: 147808 vertices, 147876 faces slice 230: 147808 vertices, 147876 faces slice 240: 147808 vertices, 147876 faces slice 250: 147808 vertices, 147876 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 147808 voxel in cpt #1: X=-68 [v=147808,e=443628,f=295752] located at (-26.290377, -23.009012, 38.447777) For the whole surface: X=-68 [v=147808,e=443628,f=295752] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Fri Oct 11 01:52:15 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 3 found - 3 modified | TOTAL: 3 pass 2 (yz+): 0 found - 3 modified | TOTAL: 3 pass 1 (yz-): 0 found - 0 modified | TOTAL: 3 pass 1 (xz+): 1 found - 1 modified | TOTAL: 4 pass 2 (xz+): 0 found - 1 modified | TOTAL: 4 pass 1 (xz-): 0 found - 0 modified | TOTAL: 4 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 4 (out of 310861: 0.001287) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 30: 122 vertices, 158 faces slice 40: 4519 vertices, 4720 faces slice 50: 12692 vertices, 13015 faces slice 60: 23369 vertices, 23762 faces slice 70: 35817 vertices, 36246 faces slice 80: 47772 vertices, 48193 faces slice 90: 59770 vertices, 60226 faces slice 100: 71577 vertices, 72006 faces slice 110: 83204 vertices, 83659 faces slice 120: 95418 vertices, 95895 faces slice 130: 107126 vertices, 107586 faces slice 140: 117137 vertices, 117504 faces slice 150: 126015 vertices, 126370 faces slice 160: 133611 vertices, 133908 faces slice 170: 140249 vertices, 140509 faces slice 180: 146384 vertices, 146618 faces slice 190: 150526 vertices, 150684 faces slice 200: 151230 vertices, 151290 faces slice 210: 151230 vertices, 151290 faces slice 220: 151230 vertices, 151290 faces slice 230: 151230 vertices, 151290 faces slice 240: 151230 vertices, 151290 faces slice 250: 151230 vertices, 151290 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 151230 voxel in cpt #1: X=-60 [v=151230,e=453870,f=302580] located at (31.174456, -23.618284, 38.577953) For the whole surface: X=-60 [v=151230,e=453870,f=302580] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Fri Oct 11 01:52:17 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix #-------------------------------------------- #@# Smooth1 rh Fri Oct 11 01:52:17 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix Waiting for PID 785 of (785 788) to complete... Waiting for PID 788 of (785 788) to complete... mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... PIDs (785 788) completed and logs appended. #-------------------------------------------- #@# Inflation1 lh Fri Oct 11 01:52:20 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix #-------------------------------------------- #@# Inflation1 rh Fri Oct 11 01:52:20 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Waiting for PID 833 of (833 836) to complete... Waiting for PID 836 of (833 836) to complete... mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 48.2 mm, total surface area = 77259 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.2 minutes step 000: RMS=0.157 (target=0.015) step 005: RMS=0.116 (target=0.015) step 010: RMS=0.088 (target=0.015) step 015: RMS=0.075 (target=0.015) step 020: RMS=0.066 (target=0.015) step 025: RMS=0.057 (target=0.015) step 030: RMS=0.051 (target=0.015) step 035: RMS=0.047 (target=0.015) step 040: RMS=0.045 (target=0.015) step 045: RMS=0.043 (target=0.015) step 050: RMS=0.042 (target=0.015) step 055: RMS=0.041 (target=0.015) step 060: RMS=0.041 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 44.018239 mris_inflate stimesec 0.152201 mris_inflate ru_maxrss 232692 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 56591 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 10400 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 31670 mris_inflate ru_nivcsw 74 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 49.0 mm, total surface area = 79080 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.2 minutes step 000: RMS=0.156 (target=0.015) step 005: RMS=0.115 (target=0.015) step 010: RMS=0.087 (target=0.015) step 015: RMS=0.074 (target=0.015) step 020: RMS=0.065 (target=0.015) step 025: RMS=0.057 (target=0.015) step 030: RMS=0.052 (target=0.015) step 035: RMS=0.049 (target=0.015) step 040: RMS=0.046 (target=0.015) step 045: RMS=0.044 (target=0.015) step 050: RMS=0.043 (target=0.015) step 055: RMS=0.043 (target=0.015) step 060: RMS=0.043 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 44.830563 mris_inflate stimesec 0.148392 mris_inflate ru_maxrss 237808 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 57994 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 10640 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 34165 mris_inflate ru_nivcsw 53 PIDs (833 836) completed and logs appended. #-------------------------------------------- #@# QSphere lh Fri Oct 11 01:52:34 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix #-------------------------------------------- #@# QSphere rh Fri Oct 11 01:52:34 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix Waiting for PID 888 of (888 891) to complete... Waiting for PID 891 of (888 891) to complete... mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.95 +- 0.56 (0.00-->6.86) (max @ vno 57811 --> 58873) face area 0.02 +- 0.03 (-0.09-->0.55) == Number of threads available to mris_sphere for OpenMP = 4 == scaling brain by 0.307... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.415, avgs=0 005/300: dt: 0.9000, rms radial error=176.156, avgs=0 010/300: dt: 0.9000, rms radial error=175.601, avgs=0 015/300: dt: 0.9000, rms radial error=174.870, avgs=0 020/300: dt: 0.9000, rms radial error=174.039, avgs=0 025/300: dt: 0.9000, rms radial error=173.150, avgs=0 030/300: dt: 0.9000, rms radial error=172.228, avgs=0 035/300: dt: 0.9000, rms radial error=171.290, avgs=0 040/300: dt: 0.9000, rms radial error=170.343, avgs=0 045/300: dt: 0.9000, rms radial error=169.395, avgs=0 050/300: dt: 0.9000, rms radial error=168.448, avgs=0 055/300: dt: 0.9000, rms radial error=167.504, avgs=0 060/300: dt: 0.9000, rms radial error=166.563, avgs=0 065/300: dt: 0.9000, rms radial error=165.628, avgs=0 070/300: dt: 0.9000, rms radial error=164.697, avgs=0 075/300: dt: 0.9000, rms radial error=163.770, avgs=0 080/300: dt: 0.9000, rms radial error=162.848, avgs=0 085/300: dt: 0.9000, rms radial error=161.932, avgs=0 090/300: dt: 0.9000, rms radial error=161.019, avgs=0 095/300: dt: 0.9000, rms radial error=160.112, avgs=0 100/300: dt: 0.9000, rms radial error=159.210, avgs=0 105/300: dt: 0.9000, rms radial error=158.313, avgs=0 110/300: dt: 0.9000, rms radial error=157.420, avgs=0 115/300: dt: 0.9000, rms radial error=156.533, avgs=0 120/300: dt: 0.9000, rms radial error=155.650, avgs=0 125/300: dt: 0.9000, rms radial error=154.772, avgs=0 130/300: dt: 0.9000, rms radial error=153.898, avgs=0 135/300: dt: 0.9000, rms radial error=153.030, avgs=0 140/300: dt: 0.9000, rms radial error=152.166, avgs=0 145/300: dt: 0.9000, rms radial error=151.307, avgs=0 150/300: dt: 0.9000, rms radial error=150.452, avgs=0 155/300: dt: 0.9000, rms radial error=149.603, avgs=0 160/300: dt: 0.9000, rms radial error=148.758, avgs=0 165/300: dt: 0.9000, rms radial error=147.917, avgs=0 170/300: dt: 0.9000, rms radial error=147.081, avgs=0 175/300: dt: 0.9000, rms radial error=146.250, avgs=0 180/300: dt: 0.9000, rms radial error=145.424, avgs=0 185/300: dt: 0.9000, rms radial error=144.602, avgs=0 190/300: dt: 0.9000, rms radial error=143.784, avgs=0 195/300: dt: 0.9000, rms radial error=142.971, avgs=0 200/300: dt: 0.9000, rms radial error=142.163, avgs=0 205/300: dt: 0.9000, rms radial error=141.360, avgs=0 210/300: dt: 0.9000, rms radial error=140.561, avgs=0 215/300: dt: 0.9000, rms radial error=139.767, avgs=0 220/300: dt: 0.9000, rms radial error=138.977, avgs=0 225/300: dt: 0.9000, rms radial error=138.192, avgs=0 230/300: dt: 0.9000, rms radial error=137.412, avgs=0 235/300: dt: 0.9000, rms radial error=136.636, avgs=0 240/300: dt: 0.9000, rms radial error=135.866, avgs=0 245/300: dt: 0.9000, rms radial error=135.100, avgs=0 250/300: dt: 0.9000, rms radial error=134.338, avgs=0 255/300: dt: 0.9000, rms radial error=133.580, avgs=0 260/300: dt: 0.9000, rms radial error=132.827, avgs=0 265/300: dt: 0.9000, rms radial error=132.078, avgs=0 270/300: dt: 0.9000, rms radial error=131.333, avgs=0 275/300: dt: 0.9000, rms radial error=130.592, avgs=0 280/300: dt: 0.9000, rms radial error=129.855, avgs=0 285/300: dt: 0.9000, rms radial error=129.123, avgs=0 290/300: dt: 0.9000, rms radial error=128.395, avgs=0 295/300: dt: 0.9000, rms radial error=127.670, avgs=0 300/300: dt: 0.9000, rms radial error=126.950, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 17386.75 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00016 epoch 2 (K=40.0), pass 1, starting sse = 2946.84 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00007 epoch 3 (K=160.0), pass 1, starting sse = 317.74 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.10/12 = 0.00851 epoch 4 (K=640.0), pass 1, starting sse = 20.27 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.11/14 = 0.00772 final distance error %27.05 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.02 hours mris_sphere utimesec 243.287308 mris_sphere stimesec 0.236205 mris_sphere ru_maxrss 232960 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 56607 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 10424 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 37496 mris_sphere ru_nivcsw 369 FSRUNTIME@ mris_sphere 0.0245 hours 1 threads mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.94 +- 0.55 (0.00-->6.10) (max @ vno 65257 --> 66479) face area 0.02 +- 0.03 (-0.13-->0.50) == Number of threads available to mris_sphere for OpenMP = 4 == scaling brain by 0.302... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.277, avgs=0 005/300: dt: 0.9000, rms radial error=176.016, avgs=0 010/300: dt: 0.9000, rms radial error=175.457, avgs=0 015/300: dt: 0.9000, rms radial error=174.724, avgs=0 020/300: dt: 0.9000, rms radial error=173.890, avgs=0 025/300: dt: 0.9000, rms radial error=172.998, avgs=0 030/300: dt: 0.9000, rms radial error=172.076, avgs=0 035/300: dt: 0.9000, rms radial error=171.140, avgs=0 040/300: dt: 0.9000, rms radial error=170.197, avgs=0 045/300: dt: 0.9000, rms radial error=169.251, avgs=0 050/300: dt: 0.9000, rms radial error=168.307, avgs=0 055/300: dt: 0.9000, rms radial error=167.365, avgs=0 060/300: dt: 0.9000, rms radial error=166.427, avgs=0 065/300: dt: 0.9000, rms radial error=165.493, avgs=0 070/300: dt: 0.9000, rms radial error=164.563, avgs=0 075/300: dt: 0.9000, rms radial error=163.639, avgs=0 080/300: dt: 0.9000, rms radial error=162.719, avgs=0 085/300: dt: 0.9000, rms radial error=161.805, avgs=0 090/300: dt: 0.9000, rms radial error=160.895, avgs=0 095/300: dt: 0.9000, rms radial error=159.991, avgs=0 100/300: dt: 0.9000, rms radial error=159.091, avgs=0 105/300: dt: 0.9000, rms radial error=158.196, avgs=0 110/300: dt: 0.9000, rms radial error=157.306, avgs=0 115/300: dt: 0.9000, rms radial error=156.421, avgs=0 120/300: dt: 0.9000, rms radial error=155.541, avgs=0 125/300: dt: 0.9000, rms radial error=154.666, avgs=0 130/300: dt: 0.9000, rms radial error=153.796, avgs=0 135/300: dt: 0.9000, rms radial error=152.931, avgs=0 140/300: dt: 0.9000, rms radial error=152.070, avgs=0 145/300: dt: 0.9000, rms radial error=151.214, avgs=0 150/300: dt: 0.9000, rms radial error=150.359, avgs=0 155/300: dt: 0.9000, rms radial error=149.515, avgs=0 160/300: dt: 0.9000, rms radial error=148.674, avgs=0 165/300: dt: 0.9000, rms radial error=147.837, avgs=0 170/300: dt: 0.9000, rms radial error=147.003, avgs=0 175/300: dt: 0.9000, rms radial error=146.174, avgs=0 180/300: dt: 0.9000, rms radial error=145.353, avgs=0 185/300: dt: 0.9000, rms radial error=144.534, avgs=0 190/300: dt: 0.9000, rms radial error=143.719, avgs=0 195/300: dt: 0.9000, rms radial error=142.909, avgs=0 200/300: dt: 0.9000, rms radial error=142.104, avgs=0 205/300: dt: 0.9000, rms radial error=141.303, avgs=0 210/300: dt: 0.9000, rms radial error=140.507, avgs=0 215/300: dt: 0.9000, rms radial error=139.715, avgs=0 220/300: dt: 0.9000, rms radial error=138.928, avgs=0 225/300: dt: 0.9000, rms radial error=138.144, avgs=0 230/300: dt: 0.9000, rms radial error=137.366, avgs=0 235/300: dt: 0.9000, rms radial error=136.591, avgs=0 240/300: dt: 0.9000, rms radial error=135.821, avgs=0 245/300: dt: 0.9000, rms radial error=135.055, avgs=0 250/300: dt: 0.9000, rms radial error=134.294, avgs=0 255/300: dt: 0.9000, rms radial error=133.536, avgs=0 260/300: dt: 0.9000, rms radial error=132.783, avgs=0 265/300: dt: 0.9000, rms radial error=132.034, avgs=0 270/300: dt: 0.9000, rms radial error=131.289, avgs=0 275/300: dt: 0.9000, rms radial error=130.549, avgs=0 280/300: dt: 0.9000, rms radial error=129.812, avgs=0 285/300: dt: 0.9000, rms radial error=129.080, avgs=0 290/300: dt: 0.9000, rms radial error=128.352, avgs=0 295/300: dt: 0.9000, rms radial error=127.628, avgs=0 300/300: dt: 0.9000, rms radial error=126.908, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 17869.78 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00014 epoch 2 (K=40.0), pass 1, starting sse = 3054.37 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00004 epoch 3 (K=160.0), pass 1, starting sse = 340.35 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.08/11 = 0.00749 epoch 4 (K=640.0), pass 1, starting sse = 26.72 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.12/14 = 0.00838 final distance error %27.98 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.02 hours mris_sphere utimesec 243.444705 mris_sphere stimesec 0.176159 mris_sphere ru_maxrss 238020 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 58014 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 10664 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 34151 mris_sphere ru_nivcsw 327 FSRUNTIME@ mris_sphere 0.0246 hours 1 threads PIDs (888 891) completed and logs appended. #-------------------------------------------- #@# Fix Topology Copy lh Fri Oct 11 01:54:03 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Fri Oct 11 01:54:03 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Fri Oct 11 01:54:03 -03 2019 mris_fix_topology -rusage /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 sub-A00039639_ses-DS2_T1w.nii.gz lh #@# Fix Topology rh Fri Oct 11 01:54:03 -03 2019 mris_fix_topology -rusage /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 sub-A00039639_ses-DS2_T1w.nii.gz rh Waiting for PID 993 of (993 996) to complete... Waiting for PID 996 of (993 996) to complete... mris_fix_topology -rusage /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 sub-A00039639_ses-DS2_T1w.nii.gz lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ before topology correction, eno=-68 (nv=147808, nf=295752, ne=443628, g=35) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 14 iterations marking ambiguous vertices... 5077 ambiguous faces found in tessellation segmenting defects... 43 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 29 into 21 42 defects to be corrected 0 vertices coincident reading input surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.2051 (-4.6025) -vertex loglikelihood: -5.7701 (-2.8851) -normal dot loglikelihood: -3.5513 (-3.5513) -quad curv loglikelihood: -6.5151 (-3.2575) Total Loglikelihood : -25.0415 CORRECTING DEFECT 0 (vertices=6, convex hull=24, v0=6603) After retessellation of defect 0 (v0=6603), euler #=-39 (144779,433268,288450) : difference with theory (-39) = 0 CORRECTING DEFECT 1 (vertices=28, convex hull=73, v0=8661) After retessellation of defect 1 (v0=8661), euler #=-38 (144795,433344,288511) : difference with theory (-38) = 0 CORRECTING DEFECT 2 (vertices=32, convex hull=73, v0=35161) After retessellation of defect 2 (v0=35161), euler #=-37 (144814,433429,288578) : difference with theory (-37) = 0 CORRECTING DEFECT 3 (vertices=41, convex hull=69, v0=40353) After retessellation of defect 3 (v0=40353), euler #=-36 (144839,433531,288656) : difference with theory (-36) = 0 CORRECTING DEFECT 4 (vertices=39, convex hull=63, v0=46165) After retessellation of defect 4 (v0=46165), euler #=-35 (144849,433584,288700) : difference with theory (-35) = 0 CORRECTING DEFECT 5 (vertices=51, convex hull=83, v0=48107) After retessellation of defect 5 (v0=48107), euler #=-34 (144871,433683,288778) : difference with theory (-34) = 0 CORRECTING DEFECT 6 (vertices=122, convex hull=108, v0=49901) After retessellation of defect 6 (v0=49901), euler #=-33 (144915,433865,288917) : difference with theory (-33) = 0 CORRECTING DEFECT 7 (vertices=12, convex hull=39, v0=53071) After retessellation of defect 7 (v0=53071), euler #=-32 (144917,433885,288936) : difference with theory (-32) = 0 CORRECTING DEFECT 8 (vertices=17, convex hull=46, v0=58463) After retessellation of defect 8 (v0=58463), euler #=-31 (144926,433926,288969) : difference with theory (-31) = 0 CORRECTING DEFECT 9 (vertices=23, convex hull=58, v0=62389) After retessellation of defect 9 (v0=62389), euler #=-30 (144937,433983,289016) : difference with theory (-30) = 0 CORRECTING DEFECT 10 (vertices=246, convex hull=146, v0=63640) After retessellation of defect 10 (v0=63640), euler #=-29 (145016,434291,289246) : difference with theory (-29) = 0 CORRECTING DEFECT 11 (vertices=7, convex hull=16, v0=67557) After retessellation of defect 11 (v0=67557), euler #=-28 (145017,434298,289253) : difference with theory (-28) = 0 CORRECTING DEFECT 12 (vertices=119, convex hull=105, v0=69565) After retessellation of defect 12 (v0=69565), euler #=-27 (145028,434379,289324) : difference with theory (-27) = 0 CORRECTING DEFECT 13 (vertices=111, convex hull=32, v0=71110) After retessellation of defect 13 (v0=71110), euler #=-26 (145037,434418,289355) : difference with theory (-26) = 0 CORRECTING DEFECT 14 (vertices=22, convex hull=57, v0=72844) After retessellation of defect 14 (v0=72844), euler #=-25 (145050,434481,289406) : difference with theory (-25) = 0 CORRECTING DEFECT 15 (vertices=29, convex hull=23, v0=73654) After retessellation of defect 15 (v0=73654), euler #=-24 (145052,434495,289419) : difference with theory (-24) = 0 CORRECTING DEFECT 16 (vertices=368, convex hull=68, v0=74854) After retessellation of defect 16 (v0=74854), euler #=-23 (145074,434595,289498) : difference with theory (-23) = 0 CORRECTING DEFECT 17 (vertices=22, convex hull=19, v0=79416) After retessellation of defect 17 (v0=79416), euler #=-22 (145074,434602,289506) : difference with theory (-22) = 0 CORRECTING DEFECT 18 (vertices=61, convex hull=44, v0=82515) After retessellation of defect 18 (v0=82515), euler #=-21 (145087,434660,289552) : difference with theory (-21) = 0 CORRECTING DEFECT 19 (vertices=34, convex hull=45, v0=85613) After retessellation of defect 19 (v0=85613), euler #=-20 (145098,434710,289592) : difference with theory (-20) = 0 CORRECTING DEFECT 20 (vertices=30, convex hull=56, v0=86138) After retessellation of defect 20 (v0=86138), euler #=-19 (145107,434758,289632) : difference with theory (-19) = 0 CORRECTING DEFECT 21 (vertices=723, convex hull=330, v0=86867) After retessellation of defect 21 (v0=86867), euler #=-17 (145301,435504,290186) : difference with theory (-18) = -1 CORRECTING DEFECT 22 (vertices=6, convex hull=10, v0=88340) After retessellation of defect 22 (v0=88340), euler #=-16 (145301,435506,290189) : difference with theory (-17) = -1 CORRECTING DEFECT 23 (vertices=59, convex hull=28, v0=91449) After retessellation of defect 23 (v0=91449), euler #=-15 (145306,435530,290209) : difference with theory (-16) = -1 CORRECTING DEFECT 24 (vertices=30, convex hull=64, v0=93340) After retessellation of defect 24 (v0=93340), euler #=-14 (145315,435581,290252) : difference with theory (-15) = -1 CORRECTING DEFECT 25 (vertices=57, convex hull=32, v0=99516) After retessellation of defect 25 (v0=99516), euler #=-13 (145318,435603,290272) : difference with theory (-14) = -1 CORRECTING DEFECT 26 (vertices=11, convex hull=28, v0=102368) After retessellation of defect 26 (v0=102368), euler #=-12 (145320,435618,290286) : difference with theory (-13) = -1 CORRECTING DEFECT 27 (vertices=12, convex hull=16, v0=102425) After retessellation of defect 27 (v0=102425), euler #=-11 (145322,435629,290296) : difference with theory (-12) = -1 CORRECTING DEFECT 28 (vertices=31, convex hull=28, v0=103557) After retessellation of defect 28 (v0=103557), euler #=-10 (145325,435648,290313) : difference with theory (-11) = -1 CORRECTING DEFECT 29 (vertices=24, convex hull=66, v0=104677) After retessellation of defect 29 (v0=104677), euler #=-9 (145335,435700,290356) : difference with theory (-10) = -1 CORRECTING DEFECT 30 (vertices=19, convex hull=34, v0=106754) After retessellation of defect 30 (v0=106754), euler #=-8 (145341,435731,290382) : difference with theory (-9) = -1 CORRECTING DEFECT 31 (vertices=294, convex hull=87, v0=106921) After retessellation of defect 31 (v0=106921), euler #=-7 (145362,435831,290462) : difference with theory (-8) = -1 CORRECTING DEFECT 32 (vertices=22, convex hull=26, v0=107018) After retessellation of defect 32 (v0=107018), euler #=-6 (145366,435849,290477) : difference with theory (-7) = -1 CORRECTING DEFECT 33 (vertices=54, convex hull=101, v0=107040) After retessellation of defect 33 (v0=107040), euler #=-5 (145404,436011,290602) : difference with theory (-6) = -1 CORRECTING DEFECT 34 (vertices=36, convex hull=60, v0=115226) After retessellation of defect 34 (v0=115226), euler #=-4 (145416,436071,290651) : difference with theory (-5) = -1 CORRECTING DEFECT 35 (vertices=44, convex hull=69, v0=115934) After retessellation of defect 35 (v0=115934), euler #=-3 (145428,436135,290704) : difference with theory (-4) = -1 CORRECTING DEFECT 36 (vertices=19, convex hull=34, v0=117585) After retessellation of defect 36 (v0=117585), euler #=-2 (145433,436162,290727) : difference with theory (-3) = -1 CORRECTING DEFECT 37 (vertices=26, convex hull=66, v0=117836) After retessellation of defect 37 (v0=117836), euler #=-2 (145448,436240,290790) : difference with theory (-2) = 0 CORRECTING DEFECT 38 (vertices=60, convex hull=82, v0=119587) After retessellation of defect 38 (v0=119587), euler #=-1 (145472,436348,290875) : difference with theory (-1) = 0 CORRECTING DEFECT 39 (vertices=18, convex hull=46, v0=127471) After retessellation of defect 39 (v0=127471), euler #=0 (145481,436394,290913) : difference with theory (0) = 0 CORRECTING DEFECT 40 (vertices=26, convex hull=34, v0=128098) After retessellation of defect 40 (v0=128098), euler #=1 (145483,436413,290931) : difference with theory (1) = 0 CORRECTING DEFECT 41 (vertices=35, convex hull=74, v0=147056) After retessellation of defect 41 (v0=147056), euler #=2 (145499,436491,290994) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.22 (0.06-->7.00) (max @ vno 64546 --> 72880) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.22 (0.06-->7.00) (max @ vno 64546 --> 72880) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 146 mutations (36.2%), 257 crossovers (63.8%), 134 vertices were eliminated building final representation... 2309 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=145499, nf=290994, ne=436491, g=0) writing corrected surface to /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 12.6 minutes 0 defective edges removing intersecting faces 000: 241 intersecting mris_fix_topology utimesec 760.172533 mris_fix_topology stimesec 0.131996 mris_fix_topology ru_maxrss 467488 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 115969 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 0 mris_fix_topology ru_oublock 13856 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 1066 mris_fix_topology ru_nivcsw 3011 FSRUNTIME@ mris_fix_topology lh 0.2097 hours 1 threads mris_fix_topology -rusage /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 sub-A00039639_ses-DS2_T1w.nii.gz rh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ before topology correction, eno=-60 (nv=151230, nf=302580, ne=453870, g=31) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 9 iterations marking ambiguous vertices... 7609 ambiguous faces found in tessellation segmenting defects... 35 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 3 into 1 -merging segment 11 into 8 -merging segment 10 into 9 32 defects to be corrected 0 vertices coincident reading input surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.1687 (-4.5844) -vertex loglikelihood: -5.7999 (-2.8999) -normal dot loglikelihood: -3.5830 (-3.5830) -quad curv loglikelihood: -5.9346 (-2.9673) Total Loglikelihood : -24.4863 CORRECTING DEFECT 0 (vertices=26, convex hull=54, v0=7609) After retessellation of defect 0 (v0=7609), euler #=-31 (146928,439715,292756) : difference with theory (-29) = 2 CORRECTING DEFECT 1 (vertices=427, convex hull=92, v0=17854) After retessellation of defect 1 (v0=17854), euler #=-29 (146937,439782,292816) : difference with theory (-28) = 1 CORRECTING DEFECT 2 (vertices=22, convex hull=65, v0=27225) After retessellation of defect 2 (v0=27225), euler #=-28 (146946,439830,292856) : difference with theory (-27) = 1 CORRECTING DEFECT 3 (vertices=41, convex hull=85, v0=40467) After retessellation of defect 3 (v0=40467), euler #=-27 (146976,439955,292952) : difference with theory (-26) = 1 CORRECTING DEFECT 4 (vertices=142, convex hull=52, v0=47772) After retessellation of defect 4 (v0=47772), euler #=-26 (146991,440028,293011) : difference with theory (-25) = 1 CORRECTING DEFECT 5 (vertices=35, convex hull=61, v0=51627) After retessellation of defect 5 (v0=51627), euler #=-25 (147002,440086,293059) : difference with theory (-24) = 1 CORRECTING DEFECT 6 (vertices=49, convex hull=37, v0=53601) After retessellation of defect 6 (v0=53601), euler #=-24 (147008,440118,293086) : difference with theory (-23) = 1 CORRECTING DEFECT 7 (vertices=38, convex hull=83, v0=56839) After retessellation of defect 7 (v0=56839), euler #=-22 (147017,440182,293143) : difference with theory (-22) = 0 CORRECTING DEFECT 8 (vertices=228, convex hull=204, v0=56911) After retessellation of defect 8 (v0=56911), euler #=-20 (147047,440374,293307) : difference with theory (-21) = -1 CORRECTING DEFECT 9 (vertices=22, convex hull=29, v0=60322) After retessellation of defect 9 (v0=60322), euler #=-19 (147050,440390,293321) : difference with theory (-20) = -1 CORRECTING DEFECT 10 (vertices=46, convex hull=71, v0=62232) After retessellation of defect 10 (v0=62232), euler #=-18 (147061,440454,293375) : difference with theory (-19) = -1 CORRECTING DEFECT 11 (vertices=2369, convex hull=613, v0=63385) XL defect detected... After retessellation of defect 11 (v0=63385), euler #=-18 (147353,441646,294275) : difference with theory (-18) = 0 CORRECTING DEFECT 12 (vertices=25, convex hull=48, v0=66203) After retessellation of defect 12 (v0=66203), euler #=-17 (147364,441696,294315) : difference with theory (-17) = 0 CORRECTING DEFECT 13 (vertices=8, convex hull=24, v0=66730) After retessellation of defect 13 (v0=66730), euler #=-16 (147364,441704,294324) : difference with theory (-16) = 0 CORRECTING DEFECT 14 (vertices=107, convex hull=117, v0=71304) After retessellation of defect 14 (v0=71304), euler #=-15 (147400,441867,294452) : difference with theory (-15) = 0 CORRECTING DEFECT 15 (vertices=14, convex hull=29, v0=77854) After retessellation of defect 15 (v0=77854), euler #=-14 (147402,441885,294469) : difference with theory (-14) = 0 CORRECTING DEFECT 16 (vertices=24, convex hull=29, v0=94353) After retessellation of defect 16 (v0=94353), euler #=-13 (147403,441899,294483) : difference with theory (-13) = 0 CORRECTING DEFECT 17 (vertices=65, convex hull=40, v0=101120) After retessellation of defect 17 (v0=101120), euler #=-12 (147412,441938,294514) : difference with theory (-12) = 0 CORRECTING DEFECT 18 (vertices=45, convex hull=36, v0=104537) After retessellation of defect 18 (v0=104537), euler #=-11 (147414,441959,294534) : difference with theory (-11) = 0 CORRECTING DEFECT 19 (vertices=32, convex hull=61, v0=105711) After retessellation of defect 19 (v0=105711), euler #=-10 (147425,442014,294579) : difference with theory (-10) = 0 CORRECTING DEFECT 20 (vertices=76, convex hull=36, v0=108429) After retessellation of defect 20 (v0=108429), euler #=-9 (147430,442044,294605) : difference with theory (-9) = 0 CORRECTING DEFECT 21 (vertices=46, convex hull=46, v0=109097) After retessellation of defect 21 (v0=109097), euler #=-8 (147442,442097,294647) : difference with theory (-8) = 0 CORRECTING DEFECT 22 (vertices=7, convex hull=16, v0=110887) After retessellation of defect 22 (v0=110887), euler #=-7 (147445,442109,294657) : difference with theory (-7) = 0 CORRECTING DEFECT 23 (vertices=88, convex hull=76, v0=112125) After retessellation of defect 23 (v0=112125), euler #=-6 (147476,442232,294750) : difference with theory (-6) = 0 CORRECTING DEFECT 24 (vertices=10, convex hull=25, v0=114707) After retessellation of defect 24 (v0=114707), euler #=-5 (147477,442244,294762) : difference with theory (-5) = 0 CORRECTING DEFECT 25 (vertices=76, convex hull=45, v0=116862) After retessellation of defect 25 (v0=116862), euler #=-4 (147480,442273,294789) : difference with theory (-4) = 0 CORRECTING DEFECT 26 (vertices=10, convex hull=27, v0=128162) After retessellation of defect 26 (v0=128162), euler #=-3 (147481,442283,294799) : difference with theory (-3) = 0 CORRECTING DEFECT 27 (vertices=44, convex hull=52, v0=129767) After retessellation of defect 27 (v0=129767), euler #=-2 (147497,442352,294853) : difference with theory (-2) = 0 CORRECTING DEFECT 28 (vertices=50, convex hull=91, v0=138397) After retessellation of defect 28 (v0=138397), euler #=-1 (147515,442447,294931) : difference with theory (-1) = 0 CORRECTING DEFECT 29 (vertices=57, convex hull=66, v0=140223) After retessellation of defect 29 (v0=140223), euler #=0 (147528,442514,294986) : difference with theory (0) = 0 CORRECTING DEFECT 30 (vertices=29, convex hull=77, v0=142710) After retessellation of defect 30 (v0=142710), euler #=1 (147544,442593,295050) : difference with theory (1) = 0 CORRECTING DEFECT 31 (vertices=54, convex hull=70, v0=149341) After retessellation of defect 31 (v0=149341), euler #=2 (147557,442665,295110) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.22 (0.11-->8.57) (max @ vno 79315 --> 79430) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.22 (0.11-->8.57) (max @ vno 79315 --> 79430) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 144 mutations (38.6%), 229 crossovers (61.4%), 305 vertices were eliminated building final representation... 3673 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=147557, nf=295110, ne=442665, g=0) writing corrected surface to /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 13.6 minutes 0 defective edges removing intersecting faces 000: 246 intersecting 001: 15 intersecting mris_fix_topology utimesec 820.384379 mris_fix_topology stimesec 0.119995 mris_fix_topology ru_maxrss 495408 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 123132 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 0 mris_fix_topology ru_oublock 14064 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 778 mris_fix_topology ru_nivcsw 575 FSRUNTIME@ mris_fix_topology rh 0.2263 hours 1 threads PIDs (993 996) completed and logs appended. mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 145499 - 436491 + 290994 = 2 --> 0 holes F =2V-4: 290994 = 290998-4 (0) 2E=3F: 872982 = 872982 (0) total defect index = 0 mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 147557 - 442665 + 295110 = 2 --> 0 holes F =2V-4: 295110 = 295114-4 (0) 2E=3F: 885330 = 885330 (0) total defect index = 0 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 74 intersecting 001: 2 intersecting expanding nbhd size to 2 002: 4 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 19 intersecting 001: 2 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf lh Fri Oct 11 02:07:48 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub-A00039639_ses-DS2_T1w.nii.gz lh #-------------------------------------------- #@# Make White Surf rh Fri Oct 11 02:07:48 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub-A00039639_ses-DS2_T1w.nii.gz rh Waiting for PID 1746 of (1746 1749) to complete... Waiting for PID 1749 of (1746 1749) to complete... mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub-A00039639_ses-DS2_T1w.nii.gz lh using white.preaparc as white matter name... only generating white matter surface using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/filled.mgz... reading volume /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/brain.finalsurfs.mgz... reading volume /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/../mri/aseg.presurf.mgz... reading volume /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/wm.mgz... 28564 bright wm thresholded. 4096 bright non-wm voxels segmented. reading original surface position from /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.orig... computing class statistics... border white: 298562 voxels (1.78%) border gray 326411 voxels (1.95%) WM (102.0): 101.7 +- 6.3 [70.0 --> 110.0] GM (82.0) : 80.2 +- 11.9 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 66.1 (was 70) setting MAX_BORDER_WHITE to 111.3 (was 105) setting MIN_BORDER_WHITE to 78.0 (was 85) setting MAX_CSF to 54.2 (was 40) setting MAX_GRAY to 98.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 66.1 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 42.2 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.02-->3.50) (max @ vno 48676 --> 53044) face area 0.28 +- 0.12 (0.00-->2.79) mean absolute distance = 0.91 +- 1.13 4145 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105+-5.2, GM=78+-7.8 mean inside = 98.3, mean outside = 84.3 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group mean border=87.2, 114 (114) missing vertices, mean dist 0.3 [0.9 (%32.2)->0.9 (%67.8))] %57 local maxima, %39 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=fisic, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.26 (0.08-->4.57) (max @ vno 74900 --> 72631) face area 0.28 +- 0.13 (0.00-->2.89) mean absolute distance = 0.46 +- 0.80 4144 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2697771.5, rms=8.662 001: dt: 0.5000, sse=1657300.8, rms=6.240 (27.964%) 002: dt: 0.5000, sse=1149411.9, rms=4.564 (26.864%) 003: dt: 0.5000, sse=902025.0, rms=3.460 (24.191%) 004: dt: 0.5000, sse=786532.8, rms=2.787 (19.451%) 005: dt: 0.5000, sse=736093.3, rms=2.437 (12.551%) 006: dt: 0.5000, sse=714101.3, rms=2.265 (7.046%) 007: dt: 0.5000, sse=706688.7, rms=2.189 (3.374%) rms = 2.15, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=701825.2, rms=2.149 (1.801%) 009: dt: 0.2500, sse=643158.0, rms=1.450 (32.561%) 010: dt: 0.2500, sse=635431.1, rms=1.344 (7.252%) rms = 1.32, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=638059.4, rms=1.324 (1.552%) rms = 1.31, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=633346.3, rms=1.310 (1.054%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=89.0, 92 (46) missing vertices, mean dist -0.2 [0.6 (%61.6)->0.3 (%38.4))] %65 local maxima, %30 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=fisic, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.25 (0.10-->4.89) (max @ vno 74900 --> 72631) face area 0.35 +- 0.16 (0.00-->3.97) mean absolute distance = 0.39 +- 0.52 4979 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1097317.2, rms=3.578 013: dt: 0.5000, sse=882535.2, rms=2.250 (37.098%) 014: dt: 0.5000, sse=828539.1, rms=1.838 (18.344%) 015: dt: 0.5000, sse=813894.9, rms=1.709 (6.998%) rms = 1.71, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=789973.0, rms=1.393 (18.519%) 017: dt: 0.2500, sse=779347.2, rms=1.215 (12.748%) rms = 1.17, time step reduction 2 of 3 to 0.125... 018: dt: 0.2500, sse=776574.4, rms=1.172 (3.578%) rms = 1.15, time step reduction 3 of 3 to 0.062... 019: dt: 0.1250, sse=774241.4, rms=1.149 (1.901%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 2 vertex label from ripped group mean border=91.4, 79 (28) missing vertices, mean dist -0.2 [0.4 (%71.4)->0.2 (%28.6))] %81 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=fisic, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.24 (0.09-->5.06) (max @ vno 74900 --> 72631) face area 0.34 +- 0.16 (0.00-->4.03) mean absolute distance = 0.29 +- 0.40 4145 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1039204.7, rms=3.396 020: dt: 0.5000, sse=838292.7, rms=1.875 (44.782%) 021: dt: 0.5000, sse=789293.5, rms=1.590 (15.177%) rms = 1.55, time step reduction 1 of 3 to 0.250... 022: dt: 0.5000, sse=783233.3, rms=1.546 (2.818%) 023: dt: 0.2500, sse=753672.8, rms=1.115 (27.844%) 024: dt: 0.2500, sse=750890.5, rms=1.063 (4.729%) rms = 1.07, time step reduction 2 of 3 to 0.125... rms = 1.06, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=750164.4, rms=1.055 (0.688%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group mean border=92.4, 98 (23) missing vertices, mean dist -0.1 [0.3 (%60.9)->0.2 (%39.1))] %86 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=fisic, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.white.preaparc... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=783414.9, rms=1.730 026: dt: 0.5000, sse=737632.9, rms=1.135 (34.367%) rms = 1.38, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=724210.9, rms=0.921 (18.910%) rms = 0.87, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=721879.5, rms=0.873 (5.162%) rms = 0.85, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=719666.3, rms=0.850 (2.640%) positioning took 0.3 minutes generating cortex label... 14 non-cortical segments detected only using segment with 8479 vertices erasing segment 1 (vno[0] = 60778) erasing segment 2 (vno[0] = 88238) erasing segment 3 (vno[0] = 89252) erasing segment 4 (vno[0] = 96788) erasing segment 5 (vno[0] = 103414) erasing segment 6 (vno[0] = 106522) erasing segment 7 (vno[0] = 106526) erasing segment 8 (vno[0] = 106552) erasing segment 9 (vno[0] = 107508) erasing segment 10 (vno[0] = 107580) erasing segment 11 (vno[0] = 108340) erasing segment 12 (vno[0] = 108434) erasing segment 13 (vno[0] = 111506) writing cortex label to /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/label/lh.cortex.label... writing curvature file /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.curv writing smoothed area to lh.area writing curvature file /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.area vertex spacing 0.89 +- 0.25 (0.03-->5.14) (max @ vno 72631 --> 74900) face area 0.33 +- 0.16 (0.00-->4.00) refinement took 2.9 minutes mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub-A00039639_ses-DS2_T1w.nii.gz rh using white.preaparc as white matter name... only generating white matter surface using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/filled.mgz... reading volume /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/brain.finalsurfs.mgz... reading volume /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/../mri/aseg.presurf.mgz... reading volume /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/wm.mgz... 28564 bright wm thresholded. 4096 bright non-wm voxels segmented. reading original surface position from /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.orig... computing class statistics... border white: 298562 voxels (1.78%) border gray 326411 voxels (1.95%) WM (102.0): 101.7 +- 6.3 [70.0 --> 110.0] GM (82.0) : 80.2 +- 11.9 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 68.1 (was 70) setting MAX_BORDER_WHITE to 111.3 (was 105) setting MIN_BORDER_WHITE to 80.0 (was 85) setting MAX_CSF to 56.2 (was 40) setting MAX_GRAY to 98.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 68.1 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 44.2 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.03-->5.17) (max @ vno 147139 --> 147226) face area 0.28 +- 0.12 (0.00-->4.99) mean absolute distance = 0.89 +- 1.14 4200 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105+-4.3, GM=80+-7.0 mean inside = 98.3, mean outside = 84.6 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=88.3, 55 (55) missing vertices, mean dist 0.2 [0.9 (%34.2)->0.9 (%65.8))] %53 local maxima, %43 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=fisic, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.25 (0.08-->5.26) (max @ vno 147139 --> 147226) face area 0.28 +- 0.13 (0.00-->4.79) mean absolute distance = 0.48 +- 0.85 4526 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2513796.0, rms=8.234 001: dt: 0.5000, sse=1537411.1, rms=5.817 (29.356%) 002: dt: 0.5000, sse=1082606.0, rms=4.205 (27.710%) 003: dt: 0.5000, sse=868156.3, rms=3.194 (24.045%) 004: dt: 0.5000, sse=771570.8, rms=2.600 (18.582%) 005: dt: 0.5000, sse=729229.8, rms=2.297 (11.670%) 006: dt: 0.5000, sse=713056.6, rms=2.153 (6.257%) 007: dt: 0.5000, sse=707532.6, rms=2.086 (3.113%) rms = 2.06, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=702537.7, rms=2.056 (1.449%) 009: dt: 0.2500, sse=648495.0, rms=1.398 (31.982%) 010: dt: 0.2500, sse=642232.8, rms=1.302 (6.925%) rms = 1.30, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=641252.7, rms=1.297 (0.357%) rms = 1.27, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=639716.7, rms=1.270 (2.084%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group mean border=90.1, 70 (5) missing vertices, mean dist -0.3 [0.6 (%61.6)->0.3 (%38.4))] %62 local maxima, %33 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=fisic, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.24 (0.02-->5.14) (max @ vno 147139 --> 147226) face area 0.35 +- 0.16 (0.00-->5.63) mean absolute distance = 0.39 +- 0.54 4254 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1095855.1, rms=3.531 013: dt: 0.5000, sse=881652.9, rms=2.230 (36.849%) 014: dt: 0.5000, sse=832747.8, rms=1.784 (19.998%) 015: dt: 0.5000, sse=813767.6, rms=1.651 (7.438%) rms = 1.65, time step reduction 1 of 3 to 0.250... 016: dt: 0.5000, sse=811229.3, rms=1.646 (0.345%) 017: dt: 0.2500, sse=784065.8, rms=1.190 (27.704%) 018: dt: 0.2500, sse=777846.6, rms=1.124 (5.558%) rms = 1.12, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=777173.4, rms=1.119 (0.371%) rms = 1.10, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=777330.2, rms=1.102 (1.524%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=92.5, 64 (5) missing vertices, mean dist -0.2 [0.4 (%70.9)->0.2 (%29.1))] %79 local maxima, %16 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=fisic, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.24 (0.08-->5.01) (max @ vno 147139 --> 147226) face area 0.34 +- 0.16 (0.00-->6.06) mean absolute distance = 0.29 +- 0.40 4019 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1021122.0, rms=3.249 021: dt: 0.5000, sse=829329.1, rms=1.831 (43.644%) 022: dt: 0.5000, sse=791522.8, rms=1.523 (16.810%) rms = 1.48, time step reduction 1 of 3 to 0.250... 023: dt: 0.5000, sse=782034.8, rms=1.476 (3.105%) 024: dt: 0.2500, sse=757937.1, rms=1.083 (26.594%) 025: dt: 0.2500, sse=753587.3, rms=1.031 (4.875%) rms = 1.04, time step reduction 2 of 3 to 0.125... rms = 1.02, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=754173.4, rms=1.021 (0.876%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=93.4, 71 (4) missing vertices, mean dist -0.1 [0.3 (%60.6)->0.2 (%39.4))] %85 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=fisic, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.white.preaparc... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=784592.9, rms=1.664 027: dt: 0.5000, sse=749257.9, rms=1.080 (35.080%) rms = 1.29, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=729965.9, rms=0.887 (17.880%) rms = 0.85, time step reduction 2 of 3 to 0.125... 029: dt: 0.2500, sse=727829.2, rms=0.850 (4.202%) rms = 0.82, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=724070.6, rms=0.824 (3.060%) positioning took 0.3 minutes generating cortex label... 12 non-cortical segments detected only using segment with 8350 vertices erasing segment 1 (vno[0] = 58357) erasing segment 2 (vno[0] = 67714) erasing segment 3 (vno[0] = 77404) erasing segment 4 (vno[0] = 80706) erasing segment 5 (vno[0] = 85126) erasing segment 6 (vno[0] = 89908) erasing segment 7 (vno[0] = 105524) erasing segment 8 (vno[0] = 109030) erasing segment 9 (vno[0] = 109169) erasing segment 10 (vno[0] = 110027) erasing segment 11 (vno[0] = 111901) writing cortex label to /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/label/rh.cortex.label... writing curvature file /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.curv writing smoothed area to rh.area writing curvature file /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.area vertex spacing 0.89 +- 0.25 (0.03-->4.95) (max @ vno 147139 --> 147226) face area 0.33 +- 0.16 (0.00-->6.15) refinement took 3.0 minutes PIDs (1746 1749) completed and logs appended. #-------------------------------------------- #@# Smooth2 lh Fri Oct 11 02:10:47 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm #-------------------------------------------- #@# Smooth2 rh Fri Oct 11 02:10:47 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm Waiting for PID 1798 of (1798 1801) to complete... Waiting for PID 1801 of (1798 1801) to complete... mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... PIDs (1798 1801) completed and logs appended. #-------------------------------------------- #@# Inflation2 lh Fri Oct 11 02:10:51 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/scripts mris_inflate -rusage /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated #-------------------------------------------- #@# Inflation2 rh Fri Oct 11 02:10:51 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/scripts mris_inflate -rusage /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Waiting for PID 1846 of (1846 1849) to complete... Waiting for PID 1849 of (1846 1849) to complete... mris_inflate -rusage /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 48.4 mm, total surface area = 87568 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.179 (target=0.015) step 005: RMS=0.122 (target=0.015) step 010: RMS=0.092 (target=0.015) step 015: RMS=0.075 (target=0.015) step 020: RMS=0.063 (target=0.015) step 025: RMS=0.052 (target=0.015) step 030: RMS=0.043 (target=0.015) step 035: RMS=0.038 (target=0.015) step 040: RMS=0.033 (target=0.015) step 045: RMS=0.029 (target=0.015) step 050: RMS=0.026 (target=0.015) step 055: RMS=0.024 (target=0.015) step 060: RMS=0.023 (target=0.015) inflation complete. inflation took 0.3 minutes mris_inflate utimesec 58.016674 mris_inflate stimesec 0.247934 mris_inflate ru_maxrss 229136 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 55708 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 11384 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 45924 mris_inflate ru_nivcsw 1021 mris_inflate -rusage /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 49.0 mm, total surface area = 88314 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.176 (target=0.015) step 005: RMS=0.121 (target=0.015) step 010: RMS=0.090 (target=0.015) step 015: RMS=0.074 (target=0.015) step 020: RMS=0.061 (target=0.015) step 025: RMS=0.052 (target=0.015) step 030: RMS=0.044 (target=0.015) step 035: RMS=0.038 (target=0.015) step 040: RMS=0.033 (target=0.015) step 045: RMS=0.030 (target=0.015) step 050: RMS=0.027 (target=0.015) step 055: RMS=0.025 (target=0.015) step 060: RMS=0.024 (target=0.015) inflation complete. inflation took 0.3 minutes mris_inflate utimesec 56.479346 mris_inflate stimesec 0.284057 mris_inflate ru_maxrss 232796 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 56599 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 11544 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 50371 mris_inflate ru_nivcsw 986 PIDs (1846 1849) completed and logs appended. #-------------------------------------------- #@# Curv .H and .K lh Fri Oct 11 02:11:12 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf mris_curvature -w lh.white.preaparc rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated #-------------------------------------------- #@# Curv .H and .K rh Fri Oct 11 02:11:12 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf mris_curvature -w rh.white.preaparc rm -f rh.white.H ln -s rh.white.preaparc.H rh.white.H rm -f rh.white.K ln -s rh.white.preaparc.K rh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated cd /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf reconbatchjobs /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/scripts/recon-all.log mris_curvature_white_lh.cmd rm_curvature_white_lh.H.cmd ln_curvature_white_lh.H.cmd rm_curvature_white_lh.K.cmd ln_curvature_white_lh.K.cmd mris_curvature_inflated_lh.cmd mris_curvature_white_rh.cmd rm_curvature_white_rh.H.cmd ln_curvature_white_rh.H.cmd rm_curvature_white_rh.K.cmd ln_curvature_white_rh.K.cmd mris_curvature_inflated_rh.cmd Waiting for PID 1925 of (1925 1928 1931 1934 1937 1940 1943 1946 1949 1952 1955 1958) to complete... Waiting for PID 1928 of (1925 1928 1931 1934 1937 1940 1943 1946 1949 1952 1955 1958) to complete... Waiting for PID 1931 of (1925 1928 1931 1934 1937 1940 1943 1946 1949 1952 1955 1958) to complete... Waiting for PID 1934 of (1925 1928 1931 1934 1937 1940 1943 1946 1949 1952 1955 1958) to complete... Waiting for PID 1937 of (1925 1928 1931 1934 1937 1940 1943 1946 1949 1952 1955 1958) to complete... Waiting for PID 1940 of (1925 1928 1931 1934 1937 1940 1943 1946 1949 1952 1955 1958) to complete... Waiting for PID 1943 of (1925 1928 1931 1934 1937 1940 1943 1946 1949 1952 1955 1958) to complete... Waiting for PID 1946 of (1925 1928 1931 1934 1937 1940 1943 1946 1949 1952 1955 1958) to complete... Waiting for PID 1949 of (1925 1928 1931 1934 1937 1940 1943 1946 1949 1952 1955 1958) to complete... Waiting for PID 1952 of (1925 1928 1931 1934 1937 1940 1943 1946 1949 1952 1955 1958) to complete... Waiting for PID 1955 of (1925 1928 1931 1934 1937 1940 1943 1946 1949 1952 1955 1958) to complete... Waiting for PID 1958 of (1925 1928 1931 1934 1937 1940 1943 1946 1949 1952 1955 1958) to complete... mris_curvature -w lh.white.preaparc total integrated curvature = 6.573*4pi (82.593) --> -6 handles ICI = 179.5, FI = 1867.1, variation=29366.728 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 178 vertices thresholded to be in k1 ~ [-1.09 0.48], k2 ~ [-0.14 0.07] total integrated curvature = 0.585*4pi (7.347) --> 0 handles ICI = 1.6, FI = 9.7, variation=166.370 131 vertices thresholded to be in [-0.04 0.01] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 120 vertices thresholded to be in [-0.30 0.23] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.015, std = 0.023 done. mris_curvature -w rh.white.preaparc total integrated curvature = 2.300*4pi (28.904) --> -1 handles ICI = 179.7, FI = 1894.7, variation=29814.892 writing Gaussian curvature to ./rh.white.preaparc.K...done. writing mean curvature to ./rh.white.preaparc.H...done. rm -f rh.white.H ln -s rh.white.preaparc.H rh.white.H rm -f rh.white.K ln -s rh.white.preaparc.K rh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 185 vertices thresholded to be in k1 ~ [-0.44 0.65], k2 ~ [-0.14 0.28] total integrated curvature = 0.569*4pi (7.145) --> 0 handles ICI = 1.6, FI = 10.8, variation=179.650 167 vertices thresholded to be in [-0.06 0.02] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 142 vertices thresholded to be in [-0.17 0.27] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.015, std = 0.025 done. PIDs (1925 1928 1931 1934 1937 1940 1943 1946 1949 1952 1955 1958) completed and logs appended. #----------------------------------------- #@# Curvature Stats lh Fri Oct 11 02:11:56 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub-A00039639_ses-DS2_T1w.nii.gz lh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/lh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ sub-A00039639_ses-DS2_T1w.nii.gz/lh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 272 ] Gb_filter = 0 WARN: S lookup min: -0.645914 WARN: S explicit min: 0.000000 vertex = 115 #----------------------------------------- #@# Curvature Stats rh Fri Oct 11 02:11:59 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm sub-A00039639_ses-DS2_T1w.nii.gz rh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/rh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ sub-A00039639_ses-DS2_T1w.nii.gz/rh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 252 ] Gb_filter = 0 WARN: S lookup min: -0.221156 WARN: S explicit min: 0.000000 vertex = 24 #-------------------------------------------- #@# Sphere lh Fri Oct 11 02:12:01 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/scripts mris_sphere -rusage /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere #-------------------------------------------- #@# Sphere rh Fri Oct 11 02:12:01 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/scripts mris_sphere -rusage /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere Waiting for PID 2074 of (2074 2077) to complete... Waiting for PID 2077 of (2074 2077) to complete... mris_sphere -rusage /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... == Number of threads available to mris_sphere for OpenMP = 4 == scaling brain by 0.287... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=fisic, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.72 pass 1: epoch 2 of 3 starting distance error %19.69 unfolding complete - removing small folds... starting distance error %19.65 removing remaining folds... final distance error %19.67 MRISunfold() return, current seed 1234 -01: dt=0.0000, 133 negative triangles 212: dt=0.9900, 133 negative triangles 213: dt=0.9900, 54 negative triangles 214: dt=0.9900, 39 negative triangles 215: dt=0.9900, 34 negative triangles 216: dt=0.9900, 31 negative triangles 217: dt=0.9900, 31 negative triangles 218: dt=0.9900, 18 negative triangles 219: dt=0.9900, 34 negative triangles 220: dt=0.9900, 17 negative triangles 221: dt=0.9900, 22 negative triangles 222: dt=0.9900, 13 negative triangles 223: dt=0.9900, 12 negative triangles 224: dt=0.9900, 13 negative triangles 225: dt=0.9900, 10 negative triangles 226: dt=0.9900, 8 negative triangles 227: dt=0.9900, 3 negative triangles 228: dt=0.9900, 2 negative triangles 229: dt=0.9900, 4 negative triangles 230: dt=0.9900, 2 negative triangles 231: dt=0.9900, 2 negative triangles 232: dt=0.9900, 2 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.33 hours mris_sphere utimesec 4196.197937 mris_sphere stimesec 4.457847 mris_sphere ru_maxrss 318324 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 77949 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 10248 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 51324 mris_sphere ru_nivcsw 106146 FSRUNTIME@ mris_sphere 0.3271 hours 1 threads mris_sphere -rusage /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... == Number of threads available to mris_sphere for OpenMP = 4 == scaling brain by 0.284... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=fisic, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %20.09 pass 1: epoch 2 of 3 starting distance error %20.07 unfolding complete - removing small folds... starting distance error %19.90 removing remaining folds... final distance error %19.93 MRISunfold() return, current seed 1234 -01: dt=0.0000, 137 negative triangles 213: dt=0.9900, 137 negative triangles 214: dt=0.9900, 88 negative triangles 215: dt=0.9900, 83 negative triangles 216: dt=0.9900, 69 negative triangles 217: dt=0.9900, 55 negative triangles 218: dt=0.9900, 52 negative triangles 219: dt=0.9900, 55 negative triangles 220: dt=0.9900, 54 negative triangles 221: dt=0.9900, 49 negative triangles 222: dt=0.9900, 46 negative triangles 223: dt=0.9900, 45 negative triangles 224: dt=0.9900, 48 negative triangles 225: dt=0.9900, 50 negative triangles 226: dt=0.9900, 55 negative triangles 227: dt=0.9900, 52 negative triangles 228: dt=0.9900, 44 negative triangles 229: dt=0.9900, 46 negative triangles 230: dt=0.9900, 47 negative triangles 231: dt=0.9900, 39 negative triangles 232: dt=0.9900, 56 negative triangles 233: dt=0.9900, 41 negative triangles 234: dt=0.9900, 39 negative triangles 235: dt=0.9900, 38 negative triangles 236: dt=0.9900, 44 negative triangles 237: dt=0.9900, 34 negative triangles 238: dt=0.9900, 32 negative triangles 239: dt=0.9900, 28 negative triangles 240: dt=0.9900, 21 negative triangles 241: dt=0.9900, 19 negative triangles 242: dt=0.9900, 17 negative triangles 243: dt=0.9900, 17 negative triangles 244: dt=0.9900, 13 negative triangles 245: dt=0.9900, 10 negative triangles 246: dt=0.9900, 8 negative triangles 247: dt=0.9900, 6 negative triangles 248: dt=0.9900, 6 negative triangles 249: dt=0.9900, 4 negative triangles 250: dt=0.9900, 4 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.32 hours mris_sphere utimesec 3978.921071 mris_sphere stimesec 3.798946 mris_sphere ru_maxrss 312308 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 79139 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 10400 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 54715 mris_sphere ru_nivcsw 101771 FSRUNTIME@ mris_sphere 0.3160 hours 1 threads PIDs (2074 2077) completed and logs appended. #-------------------------------------------- #@# Surf Reg lh Fri Oct 11 02:31:39 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/scripts mris_register -curv -rusage /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /usr/local/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg #-------------------------------------------- #@# Surf Reg rh Fri Oct 11 02:31:39 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/scripts mris_register -curv -rusage /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /usr/local/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg Waiting for PID 2203 of (2203 2206) to complete... Waiting for PID 2206 of (2203 2206) to complete... mris_register -curv -rusage /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /usr/local/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/scripts cmdline mris_register -curv -rusage /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /usr/local/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /usr/local/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=fisic, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 0 randomSeed 0 tol=5.0e-01, sigma=0.0, host=fisic, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading lh.sulc curvature mean = 0.000, std = 5.443 curvature mean = 0.029, std = 0.817 curvature mean = 0.017, std = 0.859 Starting MRISrigidBodyAlignGlobal() d=32.00 min @ (0.00, -8.00, 0.00) sse = 228051.2, tmin=2.0320 d=16.00 min @ (4.00, 4.00, -4.00) sse = 218674.1, tmin=2.9214 d=8.00 min @ (-2.00, -2.00, 2.00) sse = 199217.1, tmin=3.6686 d=2.00 min @ (0.50, 0.00, 0.00) sse = 198314.4, tmin=5.1044 d=1.00 min @ (0.00, 0.00, -0.25) sse = 198227.4, tmin=5.7421 d=0.50 min @ (0.00, 0.00, 0.12) sse = 198213.1, tmin=6.5945 tol=1.0e+00, sigma=0.5, host=fisic, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 6.59 min curvature mean = 0.010, std = 0.833 curvature mean = 0.007, std = 0.947 curvature mean = 0.008, std = 0.845 curvature mean = 0.003, std = 0.978 curvature mean = 0.006, std = 0.847 curvature mean = 0.001, std = 0.991 2 Reading smoothwm curvature mean = -0.021, std = 0.303 curvature mean = 0.040, std = 0.249 curvature mean = 0.045, std = 0.325 curvature mean = 0.037, std = 0.305 curvature mean = 0.021, std = 0.509 curvature mean = 0.037, std = 0.332 curvature mean = 0.010, std = 0.650 curvature mean = 0.037, std = 0.343 curvature mean = 0.003, std = 0.754 MRISregister() return, current seed 0 -01: dt=0.0000, 99 negative triangles 112: dt=0.9900, 99 negative triangles expanding nbhd size to 1 113: dt=0.9900, 116 negative triangles 114: dt=0.9900, 90 negative triangles 115: dt=0.9900, 81 negative triangles 116: dt=0.9900, 81 negative triangles 117: dt=0.9900, 83 negative triangles 118: dt=0.9900, 69 negative triangles 119: dt=0.9900, 69 negative triangles 120: dt=0.9900, 55 negative triangles 121: dt=0.9900, 58 negative triangles 122: dt=0.9900, 55 negative triangles 123: dt=0.9900, 54 negative triangles 124: dt=0.9900, 54 negative triangles 125: dt=0.9900, 44 negative triangles 126: dt=0.9900, 44 negative triangles 127: dt=0.9900, 49 negative triangles 128: dt=0.9900, 51 negative triangles 129: dt=0.9900, 46 negative triangles 130: dt=0.9900, 44 negative triangles 131: dt=0.9900, 43 negative triangles 132: dt=0.9900, 44 negative triangles 133: dt=0.9900, 40 negative triangles 134: dt=0.9900, 42 negative triangles 135: dt=0.9900, 45 negative triangles 136: dt=0.9900, 44 negative triangles 137: dt=0.9900, 44 negative triangles 138: dt=0.9900, 38 negative triangles 139: dt=0.9900, 39 negative triangles 140: dt=0.9900, 41 negative triangles 141: dt=0.9900, 39 negative triangles 142: dt=0.9900, 45 negative triangles 143: dt=0.9900, 45 negative triangles 144: dt=0.9900, 43 negative triangles 145: dt=0.9900, 42 negative triangles 146: dt=0.9900, 41 negative triangles 147: dt=0.9900, 41 negative triangles 148: dt=0.9405, 43 negative triangles 149: dt=0.9405, 43 negative triangles 150: dt=0.9405, 44 negative triangles 151: dt=0.9405, 43 negative triangles 152: dt=0.9405, 44 negative triangles 153: dt=0.9405, 43 negative triangles 154: dt=0.9405, 43 negative triangles 155: dt=0.9405, 44 negative triangles 156: dt=0.9405, 43 negative triangles 157: dt=0.9405, 44 negative triangles 158: dt=0.8935, 47 negative triangles 159: dt=0.8935, 46 negative triangles 160: dt=0.8935, 43 negative triangles 161: dt=0.8935, 43 negative triangles 162: dt=0.8935, 44 negative triangles 163: dt=0.8935, 43 negative triangles 164: dt=0.8935, 44 negative triangles 165: dt=0.8935, 47 negative triangles 166: dt=0.8935, 44 negative triangles 167: dt=0.8935, 43 negative triangles 168: dt=0.8488, 45 negative triangles 169: dt=0.8488, 45 negative triangles 170: dt=0.8488, 45 negative triangles 171: dt=0.8488, 43 negative triangles 172: dt=0.8488, 44 negative triangles 173: dt=0.8488, 43 negative triangles 174: dt=0.8488, 44 negative triangles 175: dt=0.8488, 43 negative triangles 176: dt=0.8488, 43 negative triangles 177: dt=0.8488, 45 negative triangles 178: dt=0.8064, 45 negative triangles 179: dt=0.8064, 46 negative triangles 180: dt=0.8064, 43 negative triangles 181: dt=0.8064, 43 negative triangles 182: dt=0.8064, 44 negative triangles 183: dt=0.8064, 44 negative triangles 184: dt=0.8064, 45 negative triangles 185: dt=0.8064, 44 negative triangles 186: dt=0.8064, 44 negative triangles 187: dt=0.8064, 46 negative triangles 188: dt=0.7660, 46 negative triangles 189: dt=0.7660, 44 negative triangles 190: dt=0.7660, 44 negative triangles 191: dt=0.7660, 46 negative triangles 192: dt=0.7660, 45 negative triangles 193: dt=0.7660, 45 negative triangles 194: dt=0.7660, 47 negative triangles 195: dt=0.7660, 46 negative triangles 196: dt=0.7660, 44 negative triangles 197: dt=0.7660, 43 negative triangles 198: dt=0.7277, 44 negative triangles 199: dt=0.7277, 45 negative triangles 200: dt=0.7277, 44 negative triangles 201: dt=0.7277, 43 negative triangles 202: dt=0.7277, 45 negative triangles 203: dt=0.7277, 44 negative triangles 204: dt=0.7277, 44 negative triangles 205: dt=0.7277, 43 negative triangles 206: dt=0.7277, 44 negative triangles 207: dt=0.7277, 44 negative triangles 208: dt=0.6914, 45 negative triangles 209: dt=0.6914, 44 negative triangles 210: dt=0.6914, 43 negative triangles 211: dt=0.6914, 44 negative triangles 212: dt=0.6914, 43 negative triangles 213: dt=0.6914, 44 negative triangles 214: dt=0.6914, 43 negative triangles 215: dt=0.6914, 42 negative triangles 216: dt=0.6914, 42 negative triangles 217: dt=0.6914, 40 negative triangles 218: dt=0.6568, 40 negative triangles 219: dt=0.6568, 39 negative triangles 220: dt=0.6568, 37 negative triangles 221: dt=0.6568, 38 negative triangles 222: dt=0.6568, 37 negative triangles 223: dt=0.6568, 38 negative triangles 224: dt=0.6568, 40 negative triangles 225: dt=0.6568, 38 negative triangles 226: dt=0.6568, 37 negative triangles 227: dt=0.6568, 36 negative triangles 228: dt=0.6568, 36 negative triangles 229: dt=0.6568, 38 negative triangles 230: dt=0.6568, 37 negative triangles 231: dt=0.6568, 38 negative triangles 232: dt=0.6568, 38 negative triangles 233: dt=0.6568, 40 negative triangles 234: dt=0.6568, 39 negative triangles 235: dt=0.6568, 37 negative triangles 236: dt=0.6568, 38 negative triangles 237: dt=0.6239, 36 negative triangles 238: dt=0.6239, 36 negative triangles 239: dt=0.6239, 36 negative triangles 240: dt=0.6239, 35 negative triangles 241: dt=0.6239, 36 negative triangles 242: dt=0.6239, 35 negative triangles 243: dt=0.6239, 35 negative triangles 244: dt=0.6239, 36 negative triangles 245: dt=0.6239, 36 negative triangles 246: dt=0.6239, 36 negative triangles 247: dt=0.6239, 35 negative triangles 248: dt=0.6239, 34 negative triangles 249: dt=0.6239, 35 negative triangles 250: dt=0.6239, 34 negative triangles 251: dt=0.6239, 34 negative triangles 252: dt=0.6239, 35 negative triangles 253: dt=0.6239, 33 negative triangles 254: dt=0.6239, 34 negative triangles 255: dt=0.6239, 32 negative triangles 256: dt=0.6239, 31 negative triangles 257: dt=0.6239, 30 negative triangles 258: dt=0.6239, 29 negative triangles 259: dt=0.6239, 30 negative triangles 260: dt=0.6239, 29 negative triangles 261: dt=0.6239, 30 negative triangles 262: dt=0.6239, 30 negative triangles 263: dt=0.6239, 29 negative triangles 264: dt=0.6239, 28 negative triangles 265: dt=0.6239, 29 negative triangles 266: dt=0.6239, 28 negative triangles 267: dt=0.6239, 28 negative triangles 268: dt=0.6239, 28 negative triangles 269: dt=0.6239, 27 negative triangles 270: dt=0.6239, 27 negative triangles 271: dt=0.6239, 29 negative triangles 272: dt=0.6239, 27 negative triangles 273: dt=0.6239, 27 negative triangles 274: dt=0.6239, 27 negative triangles 275: dt=0.6239, 25 negative triangles 276: dt=0.6239, 25 negative triangles 277: dt=0.6239, 25 negative triangles 278: dt=0.6239, 23 negative triangles 279: dt=0.6239, 24 negative triangles 280: dt=0.6239, 25 negative triangles 281: dt=0.6239, 23 negative triangles 282: dt=0.6239, 23 negative triangles 283: dt=0.6239, 24 negative triangles 284: dt=0.6239, 23 negative triangles 285: dt=0.6239, 23 negative triangles 286: dt=0.6239, 23 negative triangles 287: dt=0.6239, 22 negative triangles 288: dt=0.6239, 22 negative triangles 289: dt=0.6239, 23 negative triangles 290: dt=0.6239, 21 negative triangles 291: dt=0.6239, 20 negative triangles 292: dt=0.6239, 21 negative triangles 293: dt=0.6239, 19 negative triangles 294: dt=0.6239, 18 negative triangles 295: dt=0.6239, 18 negative triangles 296: dt=0.6239, 17 negative triangles 297: dt=0.6239, 16 negative triangles 298: dt=0.6239, 16 negative triangles 299: dt=0.6239, 14 negative triangles 300: dt=0.6239, 14 negative triangles 301: dt=0.6239, 15 negative triangles 302: dt=0.6239, 14 negative triangles 303: dt=0.6239, 14 negative triangles 304: dt=0.6239, 14 negative triangles 305: dt=0.6239, 15 negative triangles 306: dt=0.6239, 14 negative triangles 307: dt=0.6239, 15 negative triangles 308: dt=0.6239, 15 negative triangles 309: dt=0.5927, 14 negative triangles 310: dt=0.5927, 14 negative triangles 311: dt=0.5927, 14 negative triangles 312: dt=0.5927, 15 negative triangles 313: dt=0.5927, 14 negative triangles 314: dt=0.5927, 14 negative triangles 315: dt=0.5927, 15 negative triangles 316: dt=0.5927, 13 negative triangles 317: dt=0.5927, 13 negative triangles 318: dt=0.5927, 13 negative triangles 319: dt=0.5927, 13 negative triangles 320: dt=0.5927, 12 negative triangles 321: dt=0.5927, 13 negative triangles 322: dt=0.5927, 12 negative triangles 323: dt=0.5927, 11 negative triangles 324: dt=0.5927, 10 negative triangles 325: dt=0.5927, 10 negative triangles 326: dt=0.5927, 11 negative triangles 327: dt=0.5927, 10 negative triangles 328: dt=0.5927, 10 negative triangles 329: dt=0.5927, 11 negative triangles 330: dt=0.5927, 10 negative triangles 331: dt=0.5927, 9 negative triangles 332: dt=0.5927, 8 negative triangles 333: dt=0.5927, 7 negative triangles 334: dt=0.5927, 7 negative triangles 335: dt=0.5927, 7 negative triangles 336: dt=0.5927, 6 negative triangles 337: dt=0.5927, 8 negative triangles 338: dt=0.5927, 8 negative triangles 339: dt=0.5927, 7 negative triangles 340: dt=0.5927, 8 negative triangles 341: dt=0.5927, 6 negative triangles 342: dt=0.5927, 5 negative triangles 343: dt=0.5927, 6 negative triangles 344: dt=0.5927, 7 negative triangles 345: dt=0.5927, 6 negative triangles 346: dt=0.5927, 6 negative triangles 347: dt=0.5927, 4 negative triangles 348: dt=0.5927, 3 negative triangles 349: dt=0.5927, 4 negative triangles 350: dt=0.5927, 5 negative triangles 351: dt=0.5927, 3 negative triangles 352: dt=0.5927, 3 negative triangles 353: dt=0.5927, 2 negative triangles 354: dt=0.5927, 1 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 0.47 hours mris_register utimesec 5005.686446 mris_register stimesec 1.556249 mris_register ru_maxrss 282332 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 68917 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 0 mris_register ru_oublock 10336 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 72877 mris_register ru_nivcsw 8778 FSRUNTIME@ mris_register 0.4675 hours 1 threads mris_register -curv -rusage /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /usr/local/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment cwd /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/scripts cmdline mris_register -curv -rusage /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /usr/local/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /usr/local/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=fisic, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 1 randomSeed 0 tol=5.0e-01, sigma=0.0, host=fisic, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading rh.sulc curvature mean = -0.000, std = 5.478 curvature mean = 0.013, std = 0.809 curvature mean = 0.022, std = 0.860 Starting MRISrigidBodyAlignGlobal() d=32.00 min @ (8.00, 0.00, 0.00) sse = 284330.2, tmin=1.6209 d=16.00 min @ (-4.00, -4.00, 4.00) sse = 249011.5, tmin=2.3969 d=8.00 min @ (2.00, 2.00, 2.00) sse = 236903.9, tmin=3.1685 d=4.00 min @ (0.00, 0.00, -1.00) sse = 234082.7, tmin=3.9372 d=2.00 min @ (-0.50, 0.00, 0.00) sse = 233505.7, tmin=4.6650 tol=1.0e+00, sigma=0.5, host=fisic, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 6.02 min curvature mean = -0.004, std = 0.822 curvature mean = 0.008, std = 0.946 curvature mean = -0.006, std = 0.833 curvature mean = 0.003, std = 0.978 curvature mean = -0.008, std = 0.835 curvature mean = 0.001, std = 0.991 2 Reading smoothwm curvature mean = -0.028, std = 0.959 curvature mean = 0.032, std = 0.240 curvature mean = 0.022, std = 0.101 curvature mean = 0.028, std = 0.298 curvature mean = 0.013, std = 0.160 curvature mean = 0.027, std = 0.324 curvature mean = 0.007, std = 0.245 curvature mean = 0.028, std = 0.331 curvature mean = 0.003, std = 0.277 MRISregister() return, current seed 0 -01: dt=0.0000, 164 negative triangles 113: dt=0.9900, 164 negative triangles expanding nbhd size to 1 114: dt=0.9900, 189 negative triangles 115: dt=0.9900, 174 negative triangles 116: dt=0.9900, 170 negative triangles 117: dt=0.9900, 173 negative triangles 118: dt=0.9900, 176 negative triangles 119: dt=0.9900, 170 negative triangles 120: dt=0.9405, 168 negative triangles 121: dt=0.9405, 162 negative triangles 122: dt=0.9405, 159 negative triangles 123: dt=0.9405, 154 negative triangles 124: dt=0.9405, 155 negative triangles 125: dt=0.9405, 156 negative triangles 126: dt=0.9405, 148 negative triangles 127: dt=0.9405, 154 negative triangles 128: dt=0.9405, 145 negative triangles 129: dt=0.9405, 147 negative triangles 130: dt=0.9405, 148 negative triangles 131: dt=0.9405, 148 negative triangles 132: dt=0.9405, 148 negative triangles 133: dt=0.9405, 144 negative triangles 134: dt=0.9405, 140 negative triangles 135: dt=0.9405, 142 negative triangles 136: dt=0.9405, 136 negative triangles 137: dt=0.9405, 134 negative triangles 138: dt=0.9405, 132 negative triangles 139: dt=0.9405, 135 negative triangles 140: dt=0.9405, 129 negative triangles 141: dt=0.9405, 126 negative triangles 142: dt=0.9405, 133 negative triangles 143: dt=0.9405, 130 negative triangles 144: dt=0.9405, 130 negative triangles 145: dt=0.9405, 127 negative triangles 146: dt=0.9405, 125 negative triangles 147: dt=0.9405, 123 negative triangles 148: dt=0.9405, 125 negative triangles 149: dt=0.9405, 130 negative triangles 150: dt=0.9405, 122 negative triangles 151: dt=0.9405, 120 negative triangles 152: dt=0.9405, 123 negative triangles 153: dt=0.9405, 124 negative triangles 154: dt=0.9405, 122 negative triangles 155: dt=0.9405, 127 negative triangles 156: dt=0.9405, 127 negative triangles 157: dt=0.9405, 117 negative triangles 158: dt=0.9405, 111 negative triangles 159: dt=0.9405, 108 negative triangles 160: dt=0.9405, 113 negative triangles 161: dt=0.9405, 110 negative triangles 162: dt=0.9405, 106 negative triangles 163: dt=0.9405, 104 negative triangles 164: dt=0.9405, 101 negative triangles 165: dt=0.9405, 102 negative triangles 166: dt=0.9405, 95 negative triangles 167: dt=0.9405, 94 negative triangles 168: dt=0.9405, 95 negative triangles 169: dt=0.9405, 94 negative triangles 170: dt=0.9405, 97 negative triangles 171: dt=0.9405, 88 negative triangles 172: dt=0.9405, 87 negative triangles 173: dt=0.9405, 84 negative triangles 174: dt=0.9405, 85 negative triangles 175: dt=0.9405, 86 negative triangles 176: dt=0.9405, 83 negative triangles 177: dt=0.9405, 80 negative triangles 178: dt=0.9405, 83 negative triangles 179: dt=0.9405, 80 negative triangles 180: dt=0.9405, 77 negative triangles 181: dt=0.9405, 78 negative triangles 182: dt=0.9405, 80 negative triangles 183: dt=0.9405, 74 negative triangles 184: dt=0.9405, 71 negative triangles 185: dt=0.9405, 75 negative triangles 186: dt=0.9405, 69 negative triangles 187: dt=0.9405, 70 negative triangles 188: dt=0.9405, 71 negative triangles 189: dt=0.9405, 68 negative triangles 190: dt=0.9405, 70 negative triangles 191: dt=0.9405, 69 negative triangles 192: dt=0.9405, 73 negative triangles 193: dt=0.9405, 69 negative triangles 194: dt=0.9405, 71 negative triangles 195: dt=0.9405, 71 negative triangles 196: dt=0.9405, 68 negative triangles 197: dt=0.9405, 69 negative triangles 198: dt=0.9405, 68 negative triangles 199: dt=0.8935, 70 negative triangles 200: dt=0.8935, 68 negative triangles 201: dt=0.8935, 70 negative triangles 202: dt=0.8935, 65 negative triangles 203: dt=0.8935, 67 negative triangles 204: dt=0.8935, 69 negative triangles 205: dt=0.8935, 63 negative triangles 206: dt=0.8935, 63 negative triangles 207: dt=0.8935, 59 negative triangles 208: dt=0.8935, 57 negative triangles 209: dt=0.8935, 57 negative triangles 210: dt=0.8935, 55 negative triangles 211: dt=0.8935, 54 negative triangles 212: dt=0.8935, 51 negative triangles 213: dt=0.8935, 49 negative triangles 214: dt=0.8935, 48 negative triangles 215: dt=0.8935, 47 negative triangles 216: dt=0.8935, 46 negative triangles 217: dt=0.8935, 41 negative triangles 218: dt=0.8935, 45 negative triangles 219: dt=0.8935, 50 negative triangles 220: dt=0.8935, 45 negative triangles 221: dt=0.8935, 42 negative triangles 222: dt=0.8935, 41 negative triangles 223: dt=0.8935, 37 negative triangles 224: dt=0.8935, 41 negative triangles 225: dt=0.8935, 44 negative triangles 226: dt=0.8935, 38 negative triangles 227: dt=0.8935, 30 negative triangles 228: dt=0.8935, 32 negative triangles 229: dt=0.8935, 35 negative triangles 230: dt=0.8935, 33 negative triangles 231: dt=0.8935, 30 negative triangles 232: dt=0.8935, 29 negative triangles 233: dt=0.8935, 25 negative triangles 234: dt=0.8935, 26 negative triangles 235: dt=0.8935, 27 negative triangles 236: dt=0.8935, 24 negative triangles 237: dt=0.8935, 25 negative triangles 238: dt=0.8935, 29 negative triangles 239: dt=0.8935, 22 negative triangles 240: dt=0.8935, 20 negative triangles 241: dt=0.8935, 25 negative triangles 242: dt=0.8935, 23 negative triangles 243: dt=0.8935, 20 negative triangles 244: dt=0.8935, 20 negative triangles 245: dt=0.8935, 20 negative triangles 246: dt=0.8935, 18 negative triangles 247: dt=0.8935, 15 negative triangles 248: dt=0.8935, 18 negative triangles 249: dt=0.8935, 13 negative triangles 250: dt=0.8935, 11 negative triangles 251: dt=0.8935, 11 negative triangles 252: dt=0.8935, 12 negative triangles 253: dt=0.8935, 9 negative triangles 254: dt=0.8935, 7 negative triangles 255: dt=0.8935, 5 negative triangles 256: dt=0.8935, 7 negative triangles 257: dt=0.8935, 6 negative triangles 258: dt=0.8935, 4 negative triangles 259: dt=0.8935, 2 negative triangles 260: dt=0.8935, 2 negative triangles 261: dt=0.8935, 1 negative triangles 262: dt=0.8935, 3 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 0.47 hours mris_register utimesec 5166.996818 mris_register stimesec 7.560053 mris_register ru_maxrss 285844 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 69807 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 0 mris_register ru_oublock 10456 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 75877 mris_register ru_nivcsw 7514 FSRUNTIME@ mris_register 0.4685 hours 1 threads PIDs (2203 2206) completed and logs appended. #-------------------------------------------- #@# Jacobian white lh Fri Oct 11 02:59:45 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white #-------------------------------------------- #@# Jacobian white rh Fri Oct 11 02:59:45 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/scripts mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white Waiting for PID 2582 of (2582 2586) to complete... Waiting for PID 2586 of (2582 2586) to complete... mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white.preaparc... writing curvature file ../surf/lh.jacobian_white mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white.preaparc... writing curvature file ../surf/rh.jacobian_white PIDs (2582 2586) completed and logs appended. #-------------------------------------------- #@# AvgCurv lh Fri Oct 11 02:59:46 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/scripts mrisp_paint -a 5 /usr/local/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv #-------------------------------------------- #@# AvgCurv rh Fri Oct 11 02:59:46 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/scripts mrisp_paint -a 5 /usr/local/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv Waiting for PID 2631 of (2631 2634) to complete... Waiting for PID 2634 of (2631 2634) to complete... mrisp_paint -a 5 /usr/local/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /usr/local/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/lh.avg_curv... mrisp_paint -a 5 /usr/local/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /usr/local/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/rh.avg_curv... PIDs (2631 2634) completed and logs appended. #----------------------------------------- #@# Cortical Parc lh Fri Oct 11 02:59:47 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-A00039639_ses-DS2_T1w.nii.gz lh ../surf/lh.sphere.reg /usr/local/freesurfer/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot #----------------------------------------- #@# Cortical Parc rh Fri Oct 11 02:59:47 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-A00039639_ses-DS2_T1w.nii.gz rh ../surf/rh.sphere.reg /usr/local/freesurfer/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.annot Waiting for PID 2679 of (2679 2683) to complete... Waiting for PID 2683 of (2679 2683) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-A00039639_ses-DS2_T1w.nii.gz lh ../surf/lh.sphere.reg /usr/local/freesurfer/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /usr/local/freesurfer/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.8 using min determinant for regularization = 0.006 0 singular and 342 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1624 labels changed using aseg relabeling using gibbs priors... 000: 3282 changed, 145499 examined... 001: 779 changed, 13672 examined... 002: 177 changed, 4220 examined... 003: 65 changed, 1098 examined... 004: 26 changed, 399 examined... 005: 14 changed, 152 examined... 006: 6 changed, 75 examined... 007: 3 changed, 35 examined... 008: 3 changed, 17 examined... 009: 3 changed, 20 examined... 010: 2 changed, 13 examined... 011: 3 changed, 14 examined... 012: 0 changed, 10 examined... 314 labels changed using aseg 000: 125 total segments, 82 labels (328 vertices) changed 001: 43 total segments, 1 labels (2 vertices) changed 002: 42 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 3 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 2140 vertices marked for relabeling... 2140 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 7 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-A00039639_ses-DS2_T1w.nii.gz rh ../surf/rh.sphere.reg /usr/local/freesurfer/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /usr/local/freesurfer/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.004 0 singular and 309 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1001 labels changed using aseg relabeling using gibbs priors... 000: 2808 changed, 147557 examined... 001: 677 changed, 12110 examined... 002: 157 changed, 3817 examined... 003: 56 changed, 964 examined... 004: 24 changed, 338 examined... 005: 2 changed, 144 examined... 006: 1 changed, 15 examined... 007: 2 changed, 7 examined... 008: 0 changed, 10 examined... 186 labels changed using aseg 000: 85 total segments, 46 labels (232 vertices) changed 001: 42 total segments, 3 labels (3 vertices) changed 002: 39 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 3 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1760 vertices marked for relabeling... 1760 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 7 seconds. PIDs (2679 2683) completed and logs appended. #-------------------------------------------- #@# Make Pial Surf lh Fri Oct 11 02:59:54 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs sub-A00039639_ses-DS2_T1w.nii.gz lh #-------------------------------------------- #@# Make Pial Surf rh Fri Oct 11 02:59:54 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs sub-A00039639_ses-DS2_T1w.nii.gz rh Waiting for PID 2730 of (2730 2733) to complete... Waiting for PID 2733 of (2730 2733) to complete... mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs sub-A00039639_ses-DS2_T1w.nii.gz lh using white.preaparc starting white location... using white.preaparc starting pial locations... using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/filled.mgz... reading volume /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/brain.finalsurfs.mgz... reading volume /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/../mri/aseg.presurf.mgz... reading volume /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/wm.mgz... 28564 bright wm thresholded. 4096 bright non-wm voxels segmented. reading original surface position from /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.orig... computing class statistics... border white: 298562 voxels (1.78%) border gray 326411 voxels (1.95%) WM (102.0): 101.7 +- 6.3 [70.0 --> 110.0] GM (82.0) : 80.2 +- 11.9 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 66.1 (was 70) setting MAX_BORDER_WHITE to 111.3 (was 105) setting MIN_BORDER_WHITE to 78.0 (was 85) setting MAX_CSF to 54.2 (was 40) setting MAX_GRAY to 98.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 66.1 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 42.2 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105+-5.2, GM=78+-7.8 mean inside = 98.3, mean outside = 84.3 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.89 +- 0.25 (0.03-->5.14) (max @ vno 72631 --> 74900) face area 0.33 +- 0.15 (0.00-->3.95) mean absolute distance = 0.80 +- 1.06 3565 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 2 with 187 points - only 0.00% unknown deleting segment 3 with 7 points - only 0.00% unknown deleting segment 4 with 5 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 5 with 4 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 6 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 7 with 1 points - only 0.00% unknown mean border=87.2, 172 (172) missing vertices, mean dist 0.4 [1.3 (%16.4)->0.7 (%83.6))] %55 local maxima, %40 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=fisic, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.26 (0.08-->5.38) (max @ vno 74900 --> 72631) face area 0.33 +- 0.16 (0.00-->3.91) mean absolute distance = 0.45 +- 0.81 4013 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1956294.5, rms=6.738 001: dt: 0.5000, sse=1171927.0, rms=4.161 (38.235%) 002: dt: 0.5000, sse=900431.2, rms=2.755 (33.803%) 003: dt: 0.5000, sse=820100.3, rms=2.191 (20.470%) 004: dt: 0.5000, sse=791512.9, rms=1.951 (10.946%) rms = 1.91, time step reduction 1 of 3 to 0.250... 005: dt: 0.5000, sse=788984.5, rms=1.912 (1.975%) 006: dt: 0.2500, sse=748517.1, rms=1.387 (27.473%) 007: dt: 0.2500, sse=742325.3, rms=1.300 (6.259%) rms = 1.28, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=741443.0, rms=1.276 (1.865%) rms = 1.26, time step reduction 3 of 3 to 0.062... 009: dt: 0.1250, sse=739763.4, rms=1.256 (1.586%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 2 with 71 points - only 0.00% unknown deleting segment 3 with 15 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 4 with 4 points - only 0.00% unknown mean border=89.0, 83 (48) missing vertices, mean dist -0.2 [0.6 (%59.9)->0.3 (%40.1))] %65 local maxima, %30 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=fisic, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.25 (0.10-->5.54) (max @ vno 74900 --> 72631) face area 0.35 +- 0.17 (0.00-->4.48) mean absolute distance = 0.39 +- 0.52 4913 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1054939.8, rms=3.338 010: dt: 0.5000, sse=866270.9, rms=2.101 (37.041%) 011: dt: 0.5000, sse=821889.9, rms=1.709 (18.673%) 012: dt: 0.5000, sse=811328.3, rms=1.612 (5.688%) rms = 1.63, time step reduction 1 of 3 to 0.250... 013: dt: 0.2500, sse=789275.2, rms=1.300 (19.356%) 014: dt: 0.2500, sse=790267.1, rms=1.131 (12.962%) rms = 1.10, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=777613.8, rms=1.100 (2.775%) rms = 1.08, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=775970.2, rms=1.085 (1.366%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 1 with 97 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 3 with 4 points - only 0.00% unknown mean border=91.4, 67 (23) missing vertices, mean dist -0.2 [0.4 (%71.5)->0.2 (%28.5))] %81 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=fisic, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.06-->5.65) (max @ vno 74900 --> 72631) face area 0.34 +- 0.16 (0.00-->4.57) mean absolute distance = 0.29 +- 0.39 4112 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1041036.6, rms=3.394 017: dt: 0.5000, sse=823063.0, rms=1.857 (45.271%) 018: dt: 0.5000, sse=788491.9, rms=1.555 (16.262%) rms = 1.51, time step reduction 1 of 3 to 0.250... 019: dt: 0.5000, sse=783903.4, rms=1.508 (3.033%) 020: dt: 0.2500, sse=755001.9, rms=1.067 (29.225%) 021: dt: 0.2500, sse=751752.7, rms=1.015 (4.906%) rms = 1.02, time step reduction 2 of 3 to 0.125... rms = 1.01, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=751425.5, rms=1.008 (0.717%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 1 with 120 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 3 with 4 points - only 0.00% unknown mean border=92.4, 79 (16) missing vertices, mean dist -0.1 [0.3 (%60.8)->0.2 (%39.2))] %87 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=fisic, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=784039.8, rms=1.695 023: dt: 0.5000, sse=747067.8, rms=1.102 (34.990%) rms = 1.35, time step reduction 1 of 3 to 0.250... 024: dt: 0.2500, sse=727677.4, rms=0.881 (20.034%) rms = 0.83, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=725094.6, rms=0.834 (5.358%) rms = 0.81, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=722151.9, rms=0.809 (3.008%) positioning took 0.3 minutes generating cortex label... 10 non-cortical segments detected only using segment with 8419 vertices erasing segment 1 (vno[0] = 88228) erasing segment 2 (vno[0] = 93700) erasing segment 3 (vno[0] = 106522) erasing segment 4 (vno[0] = 106526) erasing segment 5 (vno[0] = 106552) erasing segment 6 (vno[0] = 107508) erasing segment 7 (vno[0] = 108340) erasing segment 8 (vno[0] = 108434) erasing segment 9 (vno[0] = 111506) writing cortex label to /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/label/lh.cortex.label... writing curvature file /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.curv writing smoothed area to lh.area writing curvature file /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.area vertex spacing 0.89 +- 0.26 (0.04-->5.70) (max @ vno 72631 --> 74900) face area 0.34 +- 0.16 (0.00-->4.54) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 2 with 3 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=64.4, 175 (175) missing vertices, mean dist 1.7 [2.2 (%0.0)->2.8 (%100.0))] %17 local maxima, %41 large gradients and %37 min vals, 176 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=fisic, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=23612354.0, rms=28.803 001: dt: 0.0500, sse=21566334.0, rms=27.488 (4.567%) 002: dt: 0.0500, sse=20073074.0, rms=26.486 (3.643%) 003: dt: 0.0500, sse=18912432.0, rms=25.681 (3.041%) 004: dt: 0.0500, sse=17959100.0, rms=25.000 (2.652%) 005: dt: 0.0500, sse=17145322.0, rms=24.403 (2.386%) 006: dt: 0.0500, sse=16429614.0, rms=23.866 (2.201%) 007: dt: 0.0500, sse=15786387.0, rms=23.373 (2.067%) 008: dt: 0.0500, sse=15199084.0, rms=22.913 (1.967%) 009: dt: 0.0500, sse=14655761.0, rms=22.480 (1.893%) 010: dt: 0.0500, sse=14149247.0, rms=22.068 (1.833%) positioning took 0.5 minutes mean border=64.2, 128 (97) missing vertices, mean dist 1.4 [0.1 (%0.0)->2.3 (%100.0))] %18 local maxima, %41 large gradients and %36 min vals, 162 gradients ignored tol=1.0e-04, sigma=2.0, host=fisic, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=15139474.0, rms=22.863 011: dt: 0.0500, sse=14659653.0, rms=22.480 (1.676%) 012: dt: 0.0500, sse=14205890.0, rms=22.111 (1.640%) 013: dt: 0.0500, sse=13775470.0, rms=21.756 (1.608%) 014: dt: 0.0500, sse=13365305.0, rms=21.411 (1.583%) 015: dt: 0.0500, sse=12974215.0, rms=21.078 (1.558%) 016: dt: 0.0500, sse=12600297.0, rms=20.754 (1.537%) 017: dt: 0.0500, sse=12242670.0, rms=20.439 (1.517%) 018: dt: 0.0500, sse=11900278.0, rms=20.133 (1.497%) 019: dt: 0.0500, sse=11571747.0, rms=19.835 (1.481%) 020: dt: 0.0500, sse=11256604.0, rms=19.544 (1.464%) positioning took 0.5 minutes mean border=64.0, 138 (69) missing vertices, mean dist 1.2 [0.1 (%0.4)->1.9 (%99.6))] %19 local maxima, %41 large gradients and %36 min vals, 152 gradients ignored tol=1.0e-04, sigma=2.0, host=fisic, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=11375113.0, rms=19.658 021: dt: 0.0500, sse=11065652.0, rms=19.370 (1.463%) 022: dt: 0.0500, sse=10767876.0, rms=19.089 (1.450%) 023: dt: 0.0500, sse=10480169.0, rms=18.813 (1.443%) 024: dt: 0.0500, sse=10203360.0, rms=18.544 (1.430%) 025: dt: 0.0500, sse=9936855.0, rms=18.282 (1.417%) 026: dt: 0.0500, sse=9680665.0, rms=18.025 (1.402%) 027: dt: 0.0500, sse=9432046.0, rms=17.773 (1.400%) 028: dt: 0.0500, sse=9189375.0, rms=17.523 (1.406%) 029: dt: 0.0500, sse=8952334.0, rms=17.276 (1.413%) 030: dt: 0.0500, sse=8720719.0, rms=17.030 (1.421%) positioning took 0.5 minutes mean border=63.9, 173 (52) missing vertices, mean dist 1.0 [0.1 (%5.8)->1.7 (%94.2))] %19 local maxima, %41 large gradients and %35 min vals, 168 gradients ignored tol=1.0e-04, sigma=2.0, host=fisic, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=8841178.0, rms=17.158 031: dt: 0.5000, sse=7155457.0, rms=15.269 (11.009%) 032: dt: 0.5000, sse=5798458.0, rms=13.554 (11.232%) 033: dt: 0.5000, sse=4680686.0, rms=11.961 (11.750%) 034: dt: 0.5000, sse=3758597.0, rms=10.462 (12.536%) 035: dt: 0.5000, sse=3043512.5, rms=9.133 (12.705%) 036: dt: 0.5000, sse=2501958.8, rms=7.977 (12.652%) 037: dt: 0.5000, sse=2127714.2, rms=7.072 (11.345%) 038: dt: 0.5000, sse=1879193.4, rms=6.397 (9.547%) 039: dt: 0.5000, sse=1726515.6, rms=5.947 (7.029%) 040: dt: 0.5000, sse=1631986.8, rms=5.646 (5.064%) 041: dt: 0.5000, sse=1577487.5, rms=5.470 (3.126%) 042: dt: 0.5000, sse=1536962.4, rms=5.328 (2.595%) 043: dt: 0.5000, sse=1515981.8, rms=5.258 (1.309%) 044: dt: 0.5000, sse=1494315.8, rms=5.178 (1.532%) rms = 5.16, time step reduction 1 of 3 to 0.250... 045: dt: 0.5000, sse=1488684.4, rms=5.158 (0.374%) 046: dt: 0.2500, sse=1327001.2, rms=4.497 (12.812%) 047: dt: 0.2500, sse=1286673.2, rms=4.329 (3.731%) rms = 4.33, time step reduction 2 of 3 to 0.125... 048: dt: 0.2500, sse=1287520.6, rms=4.328 (0.032%) 049: dt: 0.1250, sse=1256446.5, rms=4.188 (3.230%) rms = 4.17, time step reduction 3 of 3 to 0.062... 050: dt: 0.1250, sse=1253271.9, rms=4.174 (0.338%) positioning took 1.3 minutes mean border=62.7, 2528 (19) missing vertices, mean dist 0.1 [0.2 (%43.4)->0.5 (%56.6))] %33 local maxima, %29 large gradients and %32 min vals, 185 gradients ignored tol=1.0e-04, sigma=1.0, host=fisic, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=1496980.4, rms=4.539 051: dt: 0.5000, sse=1445525.1, rms=4.338 (4.415%) rms = 4.33, time step reduction 1 of 3 to 0.250... 052: dt: 0.5000, sse=1434432.1, rms=4.325 (0.298%) 053: dt: 0.2500, sse=1270599.9, rms=3.501 (19.052%) 054: dt: 0.2500, sse=1237037.6, rms=3.317 (5.256%) rms = 3.30, time step reduction 2 of 3 to 0.125... 055: dt: 0.2500, sse=1233347.5, rms=3.296 (0.638%) 056: dt: 0.1250, sse=1196060.5, rms=3.070 (6.848%) rms = 3.04, time step reduction 3 of 3 to 0.062... 057: dt: 0.1250, sse=1190111.4, rms=3.036 (1.139%) positioning took 0.5 minutes mean border=61.9, 2760 (12) missing vertices, mean dist 0.1 [0.1 (%45.4)->0.3 (%54.6))] %44 local maxima, %18 large gradients and %30 min vals, 179 gradients ignored tol=1.0e-04, sigma=0.5, host=fisic, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=1241925.0, rms=3.375 rms = 3.93, time step reduction 1 of 3 to 0.250... 058: dt: 0.2500, sse=1197799.1, rms=3.122 (7.498%) rms = 3.10, time step reduction 2 of 3 to 0.125... 059: dt: 0.2500, sse=1192800.4, rms=3.096 (0.821%) 060: dt: 0.1250, sse=1183378.0, rms=3.037 (1.927%) rms = 3.02, time step reduction 3 of 3 to 0.062... 061: dt: 0.1250, sse=1180920.9, rms=3.025 (0.396%) positioning took 0.3 minutes mean border=61.2, 5021 (10) missing vertices, mean dist 0.1 [0.1 (%48.1)->0.3 (%51.9))] %48 local maxima, %15 large gradients and %29 min vals, 192 gradients ignored tol=1.0e-04, sigma=0.2, host=fisic, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=1205057.2, rms=3.162 rms = 3.53, time step reduction 1 of 3 to 0.250... 062: dt: 0.2500, sse=1183723.6, rms=3.035 (4.044%) 063: dt: 0.2500, sse=1171266.4, rms=2.974 (1.987%) rms = 2.96, time step reduction 2 of 3 to 0.125... 064: dt: 0.2500, sse=1168171.0, rms=2.963 (0.377%) 065: dt: 0.1250, sse=1152099.5, rms=2.859 (3.521%) rms = 2.83, time step reduction 3 of 3 to 0.062... 066: dt: 0.1250, sse=1147173.2, rms=2.831 (0.965%) positioning took 0.4 minutes writing curvature file /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.area.pial vertex spacing 0.99 +- 0.42 (0.05-->6.80) (max @ vno 100198 --> 99128) face area 0.39 +- 0.30 (0.00-->6.09) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 145499 vertices processed 25000 of 145499 vertices processed 50000 of 145499 vertices processed 75000 of 145499 vertices processed 100000 of 145499 vertices processed 125000 of 145499 vertices processed 0 of 145499 vertices processed 25000 of 145499 vertices processed 50000 of 145499 vertices processed 75000 of 145499 vertices processed 100000 of 145499 vertices processed 125000 of 145499 vertices processed thickness calculation complete, 275:820 truncations. 37001 vertices at 0 distance 109022 vertices at 1 distance 82490 vertices at 2 distance 32037 vertices at 3 distance 10605 vertices at 4 distance 3596 vertices at 5 distance 1127 vertices at 6 distance 330 vertices at 7 distance 117 vertices at 8 distance 63 vertices at 9 distance 50 vertices at 10 distance 34 vertices at 11 distance 35 vertices at 12 distance 24 vertices at 13 distance 16 vertices at 14 distance 17 vertices at 15 distance 18 vertices at 16 distance 11 vertices at 17 distance 8 vertices at 18 distance 11 vertices at 19 distance 16 vertices at 20 distance writing curvature file /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.thickness positioning took 7.3 minutes mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs sub-A00039639_ses-DS2_T1w.nii.gz rh using white.preaparc starting white location... using white.preaparc starting pial locations... using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/filled.mgz... reading volume /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/brain.finalsurfs.mgz... reading volume /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/../mri/aseg.presurf.mgz... reading volume /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/wm.mgz... 28564 bright wm thresholded. 4096 bright non-wm voxels segmented. reading original surface position from /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.orig... computing class statistics... border white: 298562 voxels (1.78%) border gray 326411 voxels (1.95%) WM (102.0): 101.7 +- 6.3 [70.0 --> 110.0] GM (82.0) : 80.2 +- 11.9 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 68.1 (was 70) setting MAX_BORDER_WHITE to 111.3 (was 105) setting MIN_BORDER_WHITE to 80.0 (was 85) setting MAX_CSF to 56.2 (was 40) setting MAX_GRAY to 98.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 68.1 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 44.2 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105+-4.3, GM=80+-7.0 mean inside = 98.3, mean outside = 84.6 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.89 +- 0.25 (0.03-->4.95) (max @ vno 147139 --> 147226) face area 0.33 +- 0.16 (0.00-->6.08) mean absolute distance = 0.82 +- 1.08 3775 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 3 with 163 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 4 with 2 points - only 0.00% unknown deleting segment 5 with 15 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 6 with 2 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 7 with 1 points - only 0.00% unknown deleting segment 8 with 8 points - only 0.00% unknown mean border=88.3, 155 (155) missing vertices, mean dist 0.4 [1.5 (%14.9)->0.7 (%85.1))] %52 local maxima, %44 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=fisic, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.26 (0.05-->5.05) (max @ vno 147139 --> 147226) face area 0.33 +- 0.16 (0.00-->5.06) mean absolute distance = 0.47 +- 0.84 4352 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1885378.2, rms=6.491 001: dt: 0.5000, sse=1150001.6, rms=4.012 (38.194%) 002: dt: 0.5000, sse=897391.2, rms=2.668 (33.490%) 003: dt: 0.5000, sse=817024.4, rms=2.117 (20.656%) 004: dt: 0.5000, sse=789359.2, rms=1.879 (11.222%) 005: dt: 0.5000, sse=787658.1, rms=1.829 (2.661%) rms = 1.80, time step reduction 1 of 3 to 0.250... 006: dt: 0.5000, sse=780321.6, rms=1.798 (1.743%) 007: dt: 0.2500, sse=746459.2, rms=1.298 (27.795%) 008: dt: 0.2500, sse=742126.9, rms=1.241 (4.371%) rms = 1.24, time step reduction 2 of 3 to 0.125... 009: dt: 0.2500, sse=742368.6, rms=1.239 (0.216%) rms = 1.21, time step reduction 3 of 3 to 0.062... 010: dt: 0.1250, sse=745152.4, rms=1.213 (2.047%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 5 points - only 0.00% unknown deleting segment 1 with 34 points - only 0.00% unknown deleting segment 2 with 29 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 4 with 1 points - only 0.00% unknown deleting segment 5 with 5 points - only 0.00% unknown deleting segment 6 with 15 points - only 0.00% unknown deleting segment 7 with 5 points - only 0.00% unknown mean border=90.1, 69 (28) missing vertices, mean dist -0.3 [0.6 (%59.8)->0.3 (%40.2))] %62 local maxima, %33 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=fisic, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.04-->5.06) (max @ vno 81159 --> 80002) face area 0.35 +- 0.17 (0.00-->5.65) mean absolute distance = 0.39 +- 0.54 4498 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1060172.9, rms=3.300 011: dt: 0.5000, sse=865917.8, rms=2.042 (38.125%) 012: dt: 0.5000, sse=819609.6, rms=1.620 (20.689%) 013: dt: 0.5000, sse=807897.8, rms=1.518 (6.294%) rms = 1.54, time step reduction 1 of 3 to 0.250... 014: dt: 0.2500, sse=789395.2, rms=1.236 (18.553%) 015: dt: 0.2500, sse=781675.4, rms=1.101 (10.934%) rms = 1.08, time step reduction 2 of 3 to 0.125... 016: dt: 0.2500, sse=780482.6, rms=1.077 (2.200%) rms = 1.06, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=781635.6, rms=1.061 (1.495%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 6 points - only 0.00% unknown deleting segment 1 with 51 points - only 0.00% unknown deleting segment 2 with 35 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown deleting segment 4 with 15 points - only 0.00% unknown deleting segment 5 with 5 points - only 0.00% unknown mean border=92.4, 65 (17) missing vertices, mean dist -0.3 [0.5 (%71.0)->0.2 (%29.0))] %79 local maxima, %16 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=fisic, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.03-->5.26) (max @ vno 81159 --> 80002) face area 0.34 +- 0.17 (0.00-->5.96) mean absolute distance = 0.29 +- 0.40 4095 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1028483.1, rms=3.259 018: dt: 0.5000, sse=826937.5, rms=1.840 (43.546%) 019: dt: 0.5000, sse=793615.2, rms=1.510 (17.944%) 020: dt: 0.5000, sse=787268.7, rms=1.441 (4.538%) rms = 1.54, time step reduction 1 of 3 to 0.250... 021: dt: 0.2500, sse=765390.9, rms=1.133 (21.401%) 022: dt: 0.2500, sse=759779.2, rms=1.016 (10.325%) rms = 1.01, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=758872.6, rms=1.009 (0.698%) rms = 0.99, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=758012.2, rms=0.994 (1.467%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 70 points - only 0.00% unknown deleting segment 1 with 37 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 2 points - only 0.00% unknown deleting segment 3 with 9 points - only 0.00% unknown deleting segment 4 with 6 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 5 with 3 points - only 0.00% unknown mean border=93.4, 60 (14) missing vertices, mean dist -0.1 [0.3 (%60.9)->0.2 (%39.1))] %86 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=fisic, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=786690.4, rms=1.651 025: dt: 0.5000, sse=742628.0, rms=1.029 (37.658%) rms = 1.23, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=730989.5, rms=0.851 (17.319%) rms = 0.83, time step reduction 2 of 3 to 0.125... 027: dt: 0.2500, sse=730789.8, rms=0.828 (2.732%) rms = 0.80, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=727487.4, rms=0.797 (3.658%) positioning took 0.3 minutes generating cortex label... 15 non-cortical segments detected only using segment with 8313 vertices erasing segment 1 (vno[0] = 58357) erasing segment 2 (vno[0] = 77404) erasing segment 3 (vno[0] = 80706) erasing segment 4 (vno[0] = 85126) erasing segment 5 (vno[0] = 89908) erasing segment 6 (vno[0] = 100704) erasing segment 7 (vno[0] = 105524) erasing segment 8 (vno[0] = 106244) erasing segment 9 (vno[0] = 107135) erasing segment 10 (vno[0] = 109030) erasing segment 11 (vno[0] = 109169) erasing segment 12 (vno[0] = 110027) erasing segment 13 (vno[0] = 111901) erasing segment 14 (vno[0] = 119846) writing cortex label to /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/label/rh.cortex.label... writing curvature file /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.curv writing smoothed area to rh.area writing curvature file /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.area vertex spacing 0.89 +- 0.26 (0.03-->5.33) (max @ vno 80002 --> 81159) face area 0.33 +- 0.16 (0.00-->5.97) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 10 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 2 with 3 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=65.7, 166 (166) missing vertices, mean dist 1.8 [0.2 (%0.0)->2.8 (%100.0))] %20 local maxima, %41 large gradients and %34 min vals, 187 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=fisic, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=23561012.0, rms=28.552 001: dt: 0.0500, sse=21544750.0, rms=27.265 (4.509%) 002: dt: 0.0500, sse=20086722.0, rms=26.294 (3.559%) 003: dt: 0.0500, sse=18955066.0, rms=25.516 (2.962%) 004: dt: 0.0500, sse=18027622.0, rms=24.859 (2.573%) 005: dt: 0.0500, sse=17235720.0, rms=24.284 (2.312%) 006: dt: 0.0500, sse=16540092.0, rms=23.768 (2.126%) 007: dt: 0.0500, sse=15914789.0, rms=23.294 (1.994%) 008: dt: 0.0500, sse=15343044.0, rms=22.852 (1.898%) 009: dt: 0.0500, sse=14814351.0, rms=22.435 (1.823%) 010: dt: 0.0500, sse=14321439.0, rms=22.040 (1.763%) positioning took 0.5 minutes mean border=65.5, 93 (75) missing vertices, mean dist 1.5 [0.1 (%0.0)->2.2 (%100.0))] %21 local maxima, %42 large gradients and %33 min vals, 171 gradients ignored tol=1.0e-04, sigma=2.0, host=fisic, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=15318870.0, rms=22.828 011: dt: 0.0500, sse=14852606.0, rms=22.461 (1.609%) 012: dt: 0.0500, sse=14412064.0, rms=22.108 (1.570%) 013: dt: 0.0500, sse=13993753.0, rms=21.768 (1.539%) 014: dt: 0.0500, sse=13595560.0, rms=21.439 (1.511%) 015: dt: 0.0500, sse=13216453.0, rms=21.121 (1.483%) 016: dt: 0.0500, sse=12853501.0, rms=20.812 (1.463%) 017: dt: 0.0500, sse=12506774.0, rms=20.513 (1.439%) 018: dt: 0.0500, sse=12174440.0, rms=20.221 (1.420%) 019: dt: 0.0500, sse=11856469.0, rms=19.939 (1.399%) 020: dt: 0.0500, sse=11551123.0, rms=19.663 (1.382%) positioning took 0.5 minutes mean border=65.3, 96 (56) missing vertices, mean dist 1.2 [0.1 (%0.5)->1.9 (%99.5))] %21 local maxima, %42 large gradients and %32 min vals, 172 gradients ignored tol=1.0e-04, sigma=2.0, host=fisic, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=11712119.0, rms=19.812 021: dt: 0.0500, sse=11410929.0, rms=19.539 (1.380%) 022: dt: 0.0500, sse=11121758.0, rms=19.273 (1.363%) 023: dt: 0.0500, sse=10841833.0, rms=19.011 (1.356%) 024: dt: 0.0500, sse=10573450.0, rms=18.757 (1.336%) 025: dt: 0.0500, sse=10315724.0, rms=18.510 (1.318%) 026: dt: 0.0500, sse=10067627.0, rms=18.269 (1.304%) 027: dt: 0.0500, sse=9826474.0, rms=18.031 (1.301%) 028: dt: 0.0500, sse=9590664.0, rms=17.796 (1.306%) 029: dt: 0.0500, sse=9360286.0, rms=17.562 (1.311%) 030: dt: 0.0500, sse=9134691.0, rms=17.331 (1.318%) positioning took 0.5 minutes mean border=65.2, 101 (46) missing vertices, mean dist 1.0 [0.1 (%6.7)->1.7 (%93.3))] %21 local maxima, %42 large gradients and %32 min vals, 161 gradients ignored tol=1.0e-04, sigma=2.0, host=fisic, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=9244863.0, rms=17.444 031: dt: 0.5000, sse=7575393.5, rms=15.638 (10.350%) 032: dt: 0.5000, sse=6185063.0, rms=13.953 (10.775%) 033: dt: 0.5000, sse=4998576.0, rms=12.338 (11.576%) 034: dt: 0.5000, sse=4023315.0, rms=10.826 (12.255%) 035: dt: 0.5000, sse=3270249.0, rms=9.498 (12.265%) 036: dt: 0.5000, sse=2716575.5, rms=8.384 (11.735%) 037: dt: 0.5000, sse=2319155.5, rms=7.488 (10.688%) 038: dt: 0.5000, sse=2047352.4, rms=6.801 (9.170%) 039: dt: 0.5000, sse=1859330.8, rms=6.288 (7.551%) 040: dt: 0.5000, sse=1733928.4, rms=5.916 (5.915%) 041: dt: 0.5000, sse=1653337.1, rms=5.667 (4.203%) 042: dt: 0.5000, sse=1603829.9, rms=5.503 (2.890%) 043: dt: 0.5000, sse=1571629.8, rms=5.399 (1.896%) 044: dt: 0.5000, sse=1548125.1, rms=5.317 (1.525%) 045: dt: 0.5000, sse=1532610.4, rms=5.264 (0.982%) rms = 5.23, time step reduction 1 of 3 to 0.250... 046: dt: 0.5000, sse=1522137.9, rms=5.225 (0.739%) 047: dt: 0.2500, sse=1351822.2, rms=4.552 (12.886%) 048: dt: 0.2500, sse=1311578.0, rms=4.388 (3.596%) rms = 4.38, time step reduction 2 of 3 to 0.125... 049: dt: 0.2500, sse=1309878.9, rms=4.378 (0.249%) 050: dt: 0.1250, sse=1276500.4, rms=4.231 (3.352%) rms = 4.21, time step reduction 3 of 3 to 0.062... 051: dt: 0.1250, sse=1271350.1, rms=4.208 (0.541%) positioning took 1.3 minutes mean border=63.8, 2150 (15) missing vertices, mean dist 0.1 [0.2 (%42.1)->0.5 (%57.9))] %37 local maxima, %29 large gradients and %28 min vals, 133 gradients ignored tol=1.0e-04, sigma=1.0, host=fisic, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=1565720.8, rms=4.734 052: dt: 0.5000, sse=1503416.1, rms=4.503 (4.892%) 053: dt: 0.5000, sse=1472522.6, rms=4.412 (2.001%) rms = 4.56, time step reduction 1 of 3 to 0.250... 054: dt: 0.2500, sse=1298953.0, rms=3.588 (18.680%) 055: dt: 0.2500, sse=1256172.1, rms=3.348 (6.685%) rms = 3.33, time step reduction 2 of 3 to 0.125... 056: dt: 0.2500, sse=1252770.6, rms=3.327 (0.626%) 057: dt: 0.1250, sse=1212681.5, rms=3.093 (7.050%) rms = 3.06, time step reduction 3 of 3 to 0.062... 058: dt: 0.1250, sse=1206710.5, rms=3.058 (1.135%) positioning took 0.5 minutes mean border=62.9, 2445 (12) missing vertices, mean dist 0.1 [0.1 (%43.4)->0.3 (%56.6))] %48 local maxima, %18 large gradients and %27 min vals, 141 gradients ignored tol=1.0e-04, sigma=0.5, host=fisic, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=1275200.1, rms=3.460 rms = 4.05, time step reduction 1 of 3 to 0.250... 059: dt: 0.2500, sse=1219667.6, rms=3.153 (8.865%) rms = 3.11, time step reduction 2 of 3 to 0.125... 060: dt: 0.2500, sse=1212206.8, rms=3.112 (1.304%) 061: dt: 0.1250, sse=1199857.6, rms=3.036 (2.443%) rms = 3.00, time step reduction 3 of 3 to 0.062... 062: dt: 0.1250, sse=1194295.2, rms=3.005 (1.033%) positioning took 0.3 minutes mean border=62.3, 4722 (10) missing vertices, mean dist 0.1 [0.1 (%46.9)->0.3 (%53.1))] %51 local maxima, %15 large gradients and %26 min vals, 149 gradients ignored tol=1.0e-04, sigma=0.2, host=fisic, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=1218062.2, rms=3.141 rms = 3.56, time step reduction 1 of 3 to 0.250... 063: dt: 0.2500, sse=1194156.0, rms=2.998 (4.534%) 064: dt: 0.2500, sse=1183188.8, rms=2.946 (1.738%) rms = 2.94, time step reduction 2 of 3 to 0.125... 065: dt: 0.2500, sse=1180286.6, rms=2.939 (0.256%) 066: dt: 0.1250, sse=1160556.5, rms=2.811 (4.337%) rms = 2.77, time step reduction 3 of 3 to 0.062... 067: dt: 0.1250, sse=1154242.6, rms=2.774 (1.337%) positioning took 0.4 minutes writing curvature file /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.area.pial vertex spacing 0.99 +- 0.42 (0.08-->8.92) (max @ vno 103271 --> 104250) face area 0.39 +- 0.30 (0.00-->11.08) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 147557 vertices processed 25000 of 147557 vertices processed 50000 of 147557 vertices processed 75000 of 147557 vertices processed 100000 of 147557 vertices processed 125000 of 147557 vertices processed 0 of 147557 vertices processed 25000 of 147557 vertices processed 50000 of 147557 vertices processed 75000 of 147557 vertices processed 100000 of 147557 vertices processed 125000 of 147557 vertices processed thickness calculation complete, 649:1157 truncations. 37644 vertices at 0 distance 109461 vertices at 1 distance 84560 vertices at 2 distance 32828 vertices at 3 distance 10821 vertices at 4 distance 3479 vertices at 5 distance 1190 vertices at 6 distance 371 vertices at 7 distance 162 vertices at 8 distance 79 vertices at 9 distance 41 vertices at 10 distance 36 vertices at 11 distance 44 vertices at 12 distance 19 vertices at 13 distance 10 vertices at 14 distance 12 vertices at 15 distance 8 vertices at 16 distance 11 vertices at 17 distance 3 vertices at 18 distance 4 vertices at 19 distance 7 vertices at 20 distance writing curvature file /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.thickness positioning took 7.6 minutes PIDs (2730 2733) completed and logs appended. #-------------------------------------------- #@# Surf Volume lh Fri Oct 11 03:07:28 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume sub-A00039639_ses-DS2_T1w.nii.gz lh /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.volume masking with /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/label/lh.cortex.label Total face volume 246740 Total vertex volume 243855 (mask=0) #@# sub-A00039639_ses-DS2_T1w.nii.gz lh 243855 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Fri Oct 11 03:07:30 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume sub-A00039639_ses-DS2_T1w.nii.gz rh /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.volume masking with /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/label/rh.cortex.label Total face volume 254180 Total vertex volume 250902 (mask=0) #@# sub-A00039639_ses-DS2_T1w.nii.gz rh 250902 vertexvol Done #-------------------------------------------- #@# Cortical ribbon mask Fri Oct 11 03:07:32 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri mris_volmask --aseg_name aseg.presurf --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon sub-A00039639_ses-DS2_T1w.nii.gz SUBJECTS_DIR is /mnt/disco1/subjects loading input data... computing distance to left white surface computing distance to left pial surface computing distance to right white surface computing distance to right pial surface hemi masks overlap voxels = 241 writing volume /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/ribbon.mgz mris_volmask took 5.91 minutes writing ribbon files #----------------------------------------- #@# Parcellation Stats lh Fri Oct 11 03:13:26 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab sub-A00039639_ses-DS2_T1w.nii.gz lh white mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab sub-A00039639_ses-DS2_T1w.nii.gz lh pial #----------------------------------------- #@# Parcellation Stats rh Fri Oct 11 03:13:26 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab sub-A00039639_ses-DS2_T1w.nii.gz rh white mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab sub-A00039639_ses-DS2_T1w.nii.gz rh pial Waiting for PID 4452 of (4452 4455 4458 4461) to complete... Waiting for PID 4455 of (4452 4455 4458 4461) to complete... Waiting for PID 4458 of (4452 4455 4458 4461) to complete... Waiting for PID 4461 of (4452 4455 4458 4461) to complete... mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab sub-A00039639_ses-DS2_T1w.nii.gz lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/wm.mgz... reading input surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.white... reading input pial surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.pial... reading input white surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 246740 Total vertex volume 243855 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1642165 mm^3 (det: 1.186303 ) lhCtxGM: 241987.950 242104.000 diff= -116.0 pctdiff=-0.048 rhCtxGM: 249523.742 249044.000 diff= 479.7 pctdiff= 0.192 lhCtxWM: 262629.594 262867.500 diff= -237.9 pctdiff=-0.091 rhCtxWM: 262886.151 263474.500 diff= -588.3 pctdiff=-0.224 SubCortGMVol 63223.000 SupraTentVol 1105646.438 (1101665.000) diff=3981.438 pctdiff=0.360 SupraTentVolNotVent 1084707.438 (1080726.000) diff=3981.438 pctdiff=0.367 BrainSegVol 1270335.000 (1266267.000) diff=4068.000 pctdiff=0.320 BrainSegVolNotVent 1244144.000 (1243497.438) diff=646.562 pctdiff=0.052 BrainSegVolNotVent 1244144.000 CerebellumVol 163234.000 VentChorVol 20939.000 3rd4th5thCSF 5252.000 CSFVol 1184.000, OptChiasmVol 184.000 MaskVol 1745125.000 1547 1135 2568 2.469 0.457 0.113 0.021 11 1.4 bankssts 1318 865 2295 2.519 0.583 0.138 0.019 21 0.9 caudalanteriorcingulate 4333 2720 6883 2.414 0.447 0.119 0.026 47 4.5 caudalmiddlefrontal 2271 1484 2589 1.707 0.443 0.158 0.035 36 3.3 cuneus 702 519 2429 3.838 0.586 0.129 0.032 6 0.9 entorhinal 4479 3165 10569 2.890 0.671 0.136 0.031 62 5.7 fusiform 7297 4837 12627 2.443 0.540 0.126 0.024 93 6.9 inferiorparietal 4946 3437 11268 2.810 0.688 0.141 0.032 78 6.8 inferiortemporal 1727 1141 3061 2.372 1.084 0.133 0.039 29 2.5 isthmuscingulate 7919 5238 12394 2.195 0.614 0.145 0.032 116 10.5 lateraloccipital 3975 2681 7746 2.774 0.652 0.135 0.033 49 5.3 lateralorbitofrontal 4706 3304 6218 1.827 0.621 0.155 0.038 67 7.5 lingual 3168 2108 5315 2.317 0.616 0.128 0.032 45 4.3 medialorbitofrontal 4698 3287 11923 2.939 0.666 0.125 0.025 57 4.5 middletemporal 962 658 2091 2.819 0.805 0.083 0.013 4 0.5 parahippocampal 2354 1326 3291 2.326 0.499 0.108 0.029 19 2.8 paracentral 2973 1978 5284 2.481 0.484 0.120 0.024 30 3.0 parsopercularis 1112 739 2571 2.761 0.578 0.153 0.036 19 1.7 parsorbitalis 1798 1237 3032 2.313 0.413 0.129 0.027 20 2.0 parstriangularis 2107 1444 1602 1.271 0.244 0.139 0.028 25 2.4 pericalcarine 7446 4742 11254 2.128 0.623 0.123 0.027 80 8.2 postcentral 2089 1416 3808 2.491 0.792 0.158 0.036 38 2.8 posteriorcingulate 9488 5941 15043 2.403 0.554 0.121 0.033 112 13.8 precentral 5376 3665 9245 2.495 0.554 0.139 0.031 72 6.5 precuneus 1754 1145 3557 2.694 0.714 0.150 0.039 35 2.8 rostralanteriorcingulate 8865 5872 14761 2.321 0.469 0.139 0.031 128 11.5 rostralmiddlefrontal 11476 7602 22320 2.657 0.506 0.128 0.032 140 14.5 superiorfrontal 7847 5065 12308 2.177 0.548 0.125 0.026 96 8.4 superiorparietal 6314 4192 13469 2.785 0.717 0.100 0.017 48 4.6 superiortemporal 5595 3764 10022 2.514 0.477 0.132 0.028 75 6.6 supramarginal 350 257 937 2.943 0.419 0.210 0.056 10 0.8 frontalpole 696 506 2874 3.952 0.551 0.142 0.043 9 1.3 temporalpole 823 476 1064 2.147 0.286 0.113 0.020 8 0.6 transversetemporal 3967 2608 7390 2.861 0.746 0.126 0.049 71 9.1 insula mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab sub-A00039639_ses-DS2_T1w.nii.gz lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/wm.mgz... reading input surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.pial... reading input pial surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.pial... reading input white surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 246740 Total vertex volume 243855 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1642165 mm^3 (det: 1.186303 ) lhCtxGM: 241987.950 242104.000 diff= -116.0 pctdiff=-0.048 rhCtxGM: 249523.742 249044.000 diff= 479.7 pctdiff= 0.192 lhCtxWM: 262629.594 262867.500 diff= -237.9 pctdiff=-0.091 rhCtxWM: 262886.151 263474.500 diff= -588.3 pctdiff=-0.224 SubCortGMVol 63223.000 SupraTentVol 1105646.438 (1101665.000) diff=3981.438 pctdiff=0.360 SupraTentVolNotVent 1084707.438 (1080726.000) diff=3981.438 pctdiff=0.367 BrainSegVol 1270335.000 (1266267.000) diff=4068.000 pctdiff=0.320 BrainSegVolNotVent 1244144.000 (1243497.438) diff=646.562 pctdiff=0.052 BrainSegVolNotVent 1244144.000 CerebellumVol 163234.000 VentChorVol 20939.000 3rd4th5thCSF 5252.000 CSFVol 1184.000, OptChiasmVol 184.000 MaskVol 1745125.000 1547 984 2568 2.469 0.457 0.119 0.031 26 2.2 bankssts 1318 987 2295 2.519 0.583 0.159 0.039 46 2.3 caudalanteriorcingulate 4333 3030 6883 2.414 0.447 0.112 0.023 51 4.4 caudalmiddlefrontal 2271 1705 2589 1.707 0.443 0.131 0.031 25 3.0 cuneus 702 803 2429 3.838 0.586 0.195 0.059 54 1.9 entorhinal 4479 4112 10569 2.890 0.671 0.147 0.039 163 8.4 fusiform 7297 5555 12627 2.443 0.540 0.123 0.025 78 7.7 inferiorparietal 4946 4209 11268 2.810 0.688 0.144 0.033 80 7.1 inferiortemporal 1727 1453 3061 2.372 1.084 0.157 0.046 44 3.3 isthmuscingulate 7919 6219 12394 2.195 0.614 0.125 0.028 107 9.7 lateraloccipital 3975 2914 7746 2.774 0.652 0.130 0.032 52 5.9 lateralorbitofrontal 4706 3802 6218 1.827 0.621 0.142 0.038 66 8.5 lingual 3168 2476 5315 2.317 0.616 0.137 0.031 42 4.4 medialorbitofrontal 4698 4662 11923 2.939 0.666 0.141 0.026 43 5.7 middletemporal 962 854 2091 2.819 0.805 0.131 0.028 9 1.5 parahippocampal 2354 1539 3291 2.326 0.499 0.111 0.026 25 2.6 paracentral 2973 2296 5284 2.481 0.484 0.128 0.023 30 3.2 parsopercularis 1112 1093 2571 2.761 0.578 0.171 0.032 18 1.8 parsorbitalis 1798 1381 3032 2.313 0.413 0.138 0.027 24 2.2 parstriangularis 2107 1217 1602 1.271 0.244 0.108 0.024 28 2.3 pericalcarine 7446 5848 11254 2.128 0.623 0.124 0.025 67 7.8 postcentral 2089 1596 3808 2.491 0.792 0.139 0.040 56 2.7 posteriorcingulate 9488 6565 15043 2.403 0.554 0.105 0.023 98 9.0 precentral 5376 3810 9245 2.495 0.554 0.126 0.030 84 6.7 precuneus 1754 1538 3557 2.694 0.714 0.170 0.046 39 3.5 rostralanteriorcingulate 8865 6866 14761 2.321 0.469 0.146 0.031 117 12.5 rostralmiddlefrontal 11476 9032 22320 2.657 0.506 0.132 0.034 153 17.0 superiorfrontal 7847 6104 12308 2.177 0.548 0.130 0.026 100 8.8 superiorparietal 6314 5217 13469 2.785 0.717 0.114 0.022 54 6.1 superiortemporal 5595 4148 10022 2.514 0.477 0.133 0.029 71 7.0 supramarginal 350 384 937 2.943 0.419 0.192 0.038 4 0.5 frontalpole 696 976 2874 3.952 0.551 0.189 0.035 7 1.1 temporalpole 823 555 1064 2.147 0.286 0.089 0.019 5 0.6 transversetemporal 3967 2318 7390 2.861 0.746 0.115 0.038 71 6.1 insula mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab sub-A00039639_ses-DS2_T1w.nii.gz rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/wm.mgz... reading input surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.white... reading input pial surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.pial... reading input white surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 254180 Total vertex volume 250902 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1642165 mm^3 (det: 1.186303 ) lhCtxGM: 241987.950 242104.000 diff= -116.0 pctdiff=-0.048 rhCtxGM: 249523.742 249044.000 diff= 479.7 pctdiff= 0.192 lhCtxWM: 262629.594 262867.500 diff= -237.9 pctdiff=-0.091 rhCtxWM: 262886.151 263474.500 diff= -588.3 pctdiff=-0.224 SubCortGMVol 63223.000 SupraTentVol 1105646.438 (1101665.000) diff=3981.438 pctdiff=0.360 SupraTentVolNotVent 1084707.438 (1080726.000) diff=3981.438 pctdiff=0.367 BrainSegVol 1270335.000 (1266267.000) diff=4068.000 pctdiff=0.320 BrainSegVolNotVent 1244144.000 (1243497.438) diff=646.562 pctdiff=0.052 BrainSegVolNotVent 1244144.000 CerebellumVol 163234.000 VentChorVol 20939.000 3rd4th5thCSF 5252.000 CSFVol 1184.000, OptChiasmVol 184.000 MaskVol 1745125.000 1227 874 2204 2.607 0.404 0.096 0.015 5 0.8 bankssts 1035 686 1860 2.578 0.634 0.141 0.026 19 1.0 caudalanteriorcingulate 4397 2810 7581 2.500 0.529 0.116 0.024 44 4.6 caudalmiddlefrontal 2476 1612 2685 1.603 0.369 0.152 0.033 39 3.3 cuneus 765 524 3164 4.221 0.555 0.108 0.031 5 0.9 entorhinal 4777 3241 10625 2.908 0.698 0.134 0.031 71 6.0 fusiform 7638 5089 13550 2.435 0.557 0.124 0.024 89 7.8 inferiorparietal 5733 3827 12768 2.834 0.694 0.127 0.034 98 8.4 inferiortemporal 1652 1066 3121 2.428 0.847 0.138 0.037 30 2.0 isthmuscingulate 7342 4722 11744 2.257 0.599 0.139 0.032 99 9.5 lateraloccipital 3829 2621 7764 2.749 0.687 0.151 0.043 66 7.2 lateralorbitofrontal 5246 3592 7329 1.957 0.678 0.156 0.041 84 9.2 lingual 3256 2123 5367 2.378 0.657 0.127 0.036 52 4.8 medialorbitofrontal 5251 3575 12158 2.873 0.656 0.119 0.025 62 4.8 middletemporal 930 625 1988 2.900 0.928 0.099 0.016 7 0.5 parahippocampal 2542 1564 4087 2.440 0.563 0.117 0.027 23 2.8 paracentral 2426 1599 4519 2.668 0.433 0.130 0.031 31 3.3 parsopercularis 1109 778 2723 2.815 0.620 0.161 0.041 22 1.9 parsorbitalis 2368 1593 4062 2.375 0.483 0.128 0.031 29 2.6 parstriangularis 2372 1601 2153 1.558 0.476 0.122 0.025 25 2.5 pericalcarine 7565 4632 11227 2.155 0.601 0.114 0.024 81 7.6 postcentral 1667 1121 3147 2.622 0.815 0.149 0.032 27 2.0 posteriorcingulate 9260 5609 14657 2.451 0.616 0.109 0.030 95 13.0 precentral 7068 4722 11301 2.321 0.568 0.134 0.029 91 8.2 precuneus 944 634 1943 2.727 0.464 0.141 0.036 22 1.3 rostralanteriorcingulate 9658 6506 16161 2.266 0.485 0.135 0.030 145 11.9 rostralmiddlefrontal 11813 7926 23356 2.613 0.511 0.132 0.032 145 15.7 superiorfrontal 8109 5167 13364 2.251 0.539 0.119 0.024 90 7.7 superiorparietal 5378 3579 11277 2.789 0.722 0.103 0.018 47 4.1 superiortemporal 5555 3670 10554 2.637 0.478 0.131 0.030 70 6.6 supramarginal 416 299 1092 2.703 0.660 0.203 0.065 13 1.2 frontalpole 803 538 2989 3.921 0.488 0.117 0.028 9 1.0 temporalpole 620 334 854 2.203 0.299 0.097 0.018 5 0.4 transversetemporal 3585 2411 7421 3.079 0.796 0.119 0.028 34 4.0 insula mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab sub-A00039639_ses-DS2_T1w.nii.gz rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/wm.mgz... reading input surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.pial... reading input pial surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.pial... reading input white surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 254180 Total vertex volume 250902 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1642165 mm^3 (det: 1.186303 ) lhCtxGM: 241987.950 242104.000 diff= -116.0 pctdiff=-0.048 rhCtxGM: 249523.742 249044.000 diff= 479.7 pctdiff= 0.192 lhCtxWM: 262629.594 262867.500 diff= -237.9 pctdiff=-0.091 rhCtxWM: 262886.151 263474.500 diff= -588.3 pctdiff=-0.224 SubCortGMVol 63223.000 SupraTentVol 1105646.438 (1101665.000) diff=3981.438 pctdiff=0.360 SupraTentVolNotVent 1084707.438 (1080726.000) diff=3981.438 pctdiff=0.367 BrainSegVol 1270335.000 (1266267.000) diff=4068.000 pctdiff=0.320 BrainSegVolNotVent 1244144.000 (1243497.438) diff=646.562 pctdiff=0.052 BrainSegVolNotVent 1244144.000 CerebellumVol 163234.000 VentChorVol 20939.000 3rd4th5thCSF 5252.000 CSFVol 1184.000, OptChiasmVol 184.000 MaskVol 1745125.000 1227 814 2204 2.607 0.404 0.108 0.025 14 1.2 bankssts 1035 785 1860 2.578 0.634 0.165 0.038 38 1.7 caudalanteriorcingulate 4397 3219 7581 2.500 0.529 0.115 0.024 51 4.5 caudalmiddlefrontal 2476 1859 2685 1.603 0.369 0.139 0.030 36 3.5 cuneus 765 931 3164 4.221 0.555 0.185 0.041 9 1.4 entorhinal 4777 4005 10625 2.908 0.698 0.133 0.031 76 6.8 fusiform 7638 5923 13550 2.435 0.557 0.128 0.026 80 8.7 inferiorparietal 5733 4969 12768 2.834 0.694 0.139 0.030 85 7.9 inferiortemporal 1652 1378 3121 2.428 0.847 0.154 0.043 22 3.1 isthmuscingulate 7342 5567 11744 2.257 0.599 0.125 0.032 94 10.6 lateraloccipital 3829 3001 7764 2.749 0.687 0.154 0.041 82 7.3 lateralorbitofrontal 5246 4111 7329 1.957 0.678 0.141 0.039 97 9.6 lingual 3256 2500 5367 2.378 0.657 0.144 0.034 45 5.2 medialorbitofrontal 5251 4762 12158 2.873 0.656 0.138 0.027 57 6.4 middletemporal 930 741 1988 2.900 0.928 0.139 0.037 38 1.3 parahippocampal 2542 1774 4087 2.440 0.563 0.116 0.028 32 3.1 paracentral 2426 1781 4519 2.668 0.433 0.125 0.026 35 2.7 parsopercularis 1109 1124 2723 2.815 0.620 0.170 0.032 18 1.6 parsorbitalis 2368 1837 4062 2.375 0.483 0.133 0.027 25 2.8 parstriangularis 2372 1331 2153 1.558 0.476 0.094 0.022 35 2.1 pericalcarine 7565 5720 11227 2.155 0.601 0.117 0.023 62 7.1 postcentral 1667 1226 3147 2.622 0.815 0.141 0.036 76 2.7 posteriorcingulate 9260 6450 14657 2.451 0.616 0.106 0.022 98 9.0 precentral 7068 4943 11301 2.321 0.568 0.127 0.030 97 9.1 precuneus 944 861 1943 2.727 0.464 0.175 0.041 16 1.6 rostralanteriorcingulate 9658 7696 16161 2.266 0.485 0.147 0.030 133 13.3 rostralmiddlefrontal 11813 9694 23356 2.613 0.511 0.141 0.033 157 16.8 superiorfrontal 8109 6606 13364 2.251 0.539 0.128 0.025 82 8.4 superiorparietal 5378 4425 11277 2.789 0.722 0.118 0.022 42 5.2 superiortemporal 5555 4195 10554 2.637 0.478 0.131 0.030 65 7.2 supramarginal 416 521 1092 2.703 0.660 0.234 0.051 5 1.1 frontalpole 803 955 2989 3.921 0.488 0.160 0.028 8 1.1 temporalpole 620 439 854 2.203 0.299 0.088 0.015 2 0.4 transversetemporal 3585 2207 7421 3.079 0.796 0.116 0.029 53 4.6 insula PIDs (4452 4455 4458 4461) completed and logs appended. #----------------------------------------- #@# Cortical Parc 2 lh Fri Oct 11 03:13:51 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-A00039639_ses-DS2_T1w.nii.gz lh ../surf/lh.sphere.reg /usr/local/freesurfer/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot #----------------------------------------- #@# Cortical Parc 2 rh Fri Oct 11 03:13:51 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-A00039639_ses-DS2_T1w.nii.gz rh ../surf/rh.sphere.reg /usr/local/freesurfer/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.a2009s.annot Waiting for PID 4516 of (4516 4519) to complete... Waiting for PID 4519 of (4516 4519) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-A00039639_ses-DS2_T1w.nii.gz lh ../surf/lh.sphere.reg /usr/local/freesurfer/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /usr/local/freesurfer/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 2.9 using min determinant for regularization = 0.086 0 singular and 762 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 5 labels changed using aseg relabeling using gibbs priors... 000: 9499 changed, 145499 examined... 001: 2305 changed, 37079 examined... 002: 671 changed, 12022 examined... 003: 302 changed, 3833 examined... 004: 149 changed, 1637 examined... 005: 75 changed, 762 examined... 006: 40 changed, 424 examined... 007: 20 changed, 227 examined... 008: 9 changed, 117 examined... 009: 5 changed, 62 examined... 010: 2 changed, 25 examined... 011: 0 changed, 14 examined... 1 labels changed using aseg 000: 264 total segments, 180 labels (2272 vertices) changed 001: 97 total segments, 13 labels (52 vertices) changed 002: 84 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 35 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1373 vertices marked for relabeling... 1373 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 8 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-A00039639_ses-DS2_T1w.nii.gz rh ../surf/rh.sphere.reg /usr/local/freesurfer/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /usr/local/freesurfer/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 1.4 using min determinant for regularization = 0.020 0 singular and 719 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 9 labels changed using aseg relabeling using gibbs priors... 000: 9450 changed, 147557 examined... 001: 2170 changed, 37228 examined... 002: 638 changed, 11350 examined... 003: 246 changed, 3651 examined... 004: 99 changed, 1382 examined... 005: 54 changed, 618 examined... 006: 33 changed, 295 examined... 007: 13 changed, 173 examined... 008: 2 changed, 70 examined... 009: 0 changed, 14 examined... 10 labels changed using aseg 000: 267 total segments, 185 labels (2547 vertices) changed 001: 93 total segments, 12 labels (42 vertices) changed 002: 81 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 34 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1255 vertices marked for relabeling... 1255 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 8 seconds. PIDs (4516 4519) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 2 lh Fri Oct 11 03:14:00 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab sub-A00039639_ses-DS2_T1w.nii.gz lh white #----------------------------------------- #@# Parcellation Stats 2 rh Fri Oct 11 03:14:00 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab sub-A00039639_ses-DS2_T1w.nii.gz rh white Waiting for PID 4564 of (4564 4567) to complete... Waiting for PID 4567 of (4564 4567) to complete... mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab sub-A00039639_ses-DS2_T1w.nii.gz lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/wm.mgz... reading input surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.white... reading input pial surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.pial... reading input white surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 246740 Total vertex volume 243855 (mask=0) reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1642165 mm^3 (det: 1.186303 ) lhCtxGM: 241987.950 242104.000 diff= -116.0 pctdiff=-0.048 rhCtxGM: 249523.742 249044.000 diff= 479.7 pctdiff= 0.192 lhCtxWM: 262629.594 262867.500 diff= -237.9 pctdiff=-0.091 rhCtxWM: 262886.151 263474.500 diff= -588.3 pctdiff=-0.224 SubCortGMVol 63223.000 SupraTentVol 1105646.438 (1101665.000) diff=3981.438 pctdiff=0.360 SupraTentVolNotVent 1084707.438 (1080726.000) diff=3981.438 pctdiff=0.367 BrainSegVol 1270335.000 (1266267.000) diff=4068.000 pctdiff=0.320 BrainSegVolNotVent 1244144.000 (1243497.438) diff=646.562 pctdiff=0.052 BrainSegVolNotVent 1244144.000 CerebellumVol 163234.000 VentChorVol 20939.000 3rd4th5thCSF 5252.000 CSFVol 1184.000, OptChiasmVol 184.000 MaskVol 1745125.000 1084 793 2102 2.608 0.582 0.161 0.035 17 1.7 G&S_frontomargin 1643 1127 2948 2.383 0.589 0.148 0.032 27 2.1 G&S_occipital_inf 1710 936 2456 2.246 0.459 0.111 0.030 15 2.2 G&S_paracentral 1848 1181 3319 2.649 0.458 0.137 0.036 24 2.6 G&S_subcentral 753 531 1490 2.360 0.433 0.178 0.048 19 1.5 G&S_transv_frontopol 2721 1868 5286 2.594 0.572 0.127 0.029 35 3.3 G&S_cingul-Ant 1620 1125 3021 2.656 0.440 0.132 0.021 20 1.4 G&S_cingul-Mid-Ant 1412 1000 2507 2.466 0.605 0.146 0.033 19 1.8 G&S_cingul-Mid-Post 792 523 2092 3.221 0.721 0.176 0.051 19 1.5 G_cingul-Post-dorsal 269 196 798 2.943 1.035 0.176 0.061 6 0.7 G_cingul-Post-ventral 2104 1399 2551 1.689 0.515 0.163 0.036 37 3.1 G_cuneus 1645 1085 3469 2.656 0.452 0.124 0.028 21 1.8 G_front_inf-Opercular 453 263 934 2.630 0.462 0.146 0.035 7 0.5 G_front_inf-Orbital 1107 737 2181 2.338 0.397 0.145 0.034 19 1.5 G_front_inf-Triangul 5365 3269 10148 2.468 0.458 0.136 0.034 91 7.1 G_front_middle 8140 5081 17027 2.742 0.548 0.137 0.039 121 12.4 G_front_sup 790 523 1524 2.937 0.632 0.132 0.037 10 1.1 G_Ins_lg&S_cent_ins 883 549 2523 3.339 0.789 0.141 0.101 34 4.7 G_insular_short 2628 1692 5137 2.584 0.615 0.150 0.032 44 3.2 G_occipital_middle 1258 810 2137 2.165 0.619 0.125 0.031 17 1.6 G_occipital_sup 2044 1417 5387 3.046 0.648 0.145 0.037 35 3.1 G_oc-temp_lat-fusifor 3415 2394 4740 1.803 0.671 0.170 0.045 56 6.6 G_oc-temp_med-Lingual 1391 951 4524 3.565 0.720 0.115 0.029 13 1.6 G_oc-temp_med-Parahip 2532 1684 5908 2.790 0.686 0.151 0.042 43 4.4 G_orbital 2847 1866 5677 2.450 0.573 0.135 0.028 47 3.3 G_pariet_inf-Angular 2725 1771 5856 2.668 0.476 0.137 0.031 46 3.4 G_pariet_inf-Supramar 3311 2110 6013 2.271 0.584 0.134 0.032 48 4.6 G_parietal_sup 2836 1718 4992 2.251 0.643 0.127 0.028 37 3.2 G_postcentral 3731 2151 6840 2.572 0.606 0.123 0.042 62 7.1 G_precentral 2572 1734 5297 2.540 0.537 0.151 0.037 45 3.6 G_precuneus 1268 826 2638 2.458 0.680 0.160 0.049 28 2.7 G_rectus 729 485 1194 2.486 0.826 0.100 0.036 11 0.8 G_subcallosal 541 290 769 2.176 0.287 0.100 0.019 4 0.4 G_temp_sup-G_T_transv 2012 1308 6278 3.265 0.629 0.126 0.025 25 2.0 G_temp_sup-Lateral 794 555 2171 3.432 0.654 0.080 0.014 3 0.4 G_temp_sup-Plan_polar 1144 756 2088 2.434 0.559 0.090 0.016 7 0.8 G_temp_sup-Plan_tempo 2465 1703 7129 2.978 0.766 0.157 0.045 56 4.7 G_temporal_inf 2791 1888 8205 3.152 0.638 0.146 0.032 47 3.4 G_temporal_middle 242 182 351 2.190 0.302 0.098 0.017 1 0.1 Lat_Fis-ant-Horizont 298 211 478 2.327 0.506 0.102 0.015 1 0.2 Lat_Fis-ant-Vertical 1218 824 1462 2.239 0.543 0.121 0.027 10 1.3 Lat_Fis-post 2152 1392 2687 1.830 0.484 0.161 0.040 37 3.6 Pole_occipital 1567 1136 5307 3.442 0.712 0.148 0.039 25 2.6 Pole_temporal 2715 1859 2455 1.564 0.610 0.134 0.027 31 3.0 S_calcarine 3994 2634 4494 1.926 0.544 0.123 0.027 34 4.8 S_central 1179 797 1671 2.356 0.380 0.108 0.020 8 1.0 S_cingul-Marginalis 689 486 1099 2.701 0.604 0.135 0.034 5 1.5 S_circular_insula_ant 1623 1082 2431 2.743 0.748 0.096 0.017 13 1.2 S_circular_insula_inf 1830 1255 2599 2.545 0.419 0.107 0.022 11 1.7 S_circular_insula_sup 1003 698 1692 2.747 0.459 0.103 0.015 6 0.5 S_collat_transv_ant 560 375 733 2.174 0.530 0.150 0.038 7 0.9 S_collat_transv_post 3321 2202 4521 2.132 0.385 0.123 0.023 29 3.3 S_front_inf 1246 843 1550 2.069 0.402 0.129 0.026 13 1.3 S_front_middle 3087 2149 4724 2.422 0.316 0.104 0.018 20 2.4 S_front_sup 325 244 456 2.204 0.344 0.118 0.014 2 0.3 S_interm_prim-Jensen 2541 1721 3459 2.247 0.505 0.115 0.018 21 1.8 S_intrapariet&P_trans 1102 769 1328 2.019 0.384 0.115 0.017 9 0.8 S_oc_middle&Lunatus 1267 808 1683 2.211 0.517 0.116 0.019 13 0.9 S_oc_sup&transversal 746 506 1274 2.494 0.627 0.118 0.024 6 0.6 S_occipital_ant 850 592 1394 2.524 0.409 0.130 0.022 8 0.9 S_oc-temp_lat 1913 1403 2665 2.211 0.579 0.120 0.019 16 1.4 S_oc-temp_med&Lingual 358 253 493 2.241 0.427 0.129 0.029 3 0.4 S_orbital_lateral 699 520 988 2.326 0.609 0.128 0.018 6 0.5 S_orbital_med-olfact 1394 945 2597 2.821 0.641 0.129 0.028 15 1.6 S_orbital-H_Shaped 2106 1385 2763 2.219 0.672 0.122 0.023 22 2.0 S_parieto_occipital 1789 1080 1540 1.797 0.711 0.129 0.026 33 1.5 S_pericallosal 3321 2199 4628 2.194 0.485 0.116 0.021 28 3.0 S_postcentral 1990 1358 3205 2.434 0.383 0.111 0.020 16 1.8 S_precentral-inf-part 1742 1176 2131 2.149 0.523 0.122 0.025 14 1.9 S_precentral-sup-part 737 499 848 2.066 0.325 0.108 0.016 5 0.5 S_suborbital 1047 728 1564 2.571 0.495 0.132 0.029 9 1.2 S_subparietal 1569 1138 2669 2.587 0.507 0.116 0.019 12 1.2 S_temporal_inf 6393 4471 9929 2.437 0.441 0.106 0.018 46 4.8 S_temporal_sup 485 338 632 2.100 0.481 0.102 0.014 3 0.3 S_temporal_transverse mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab sub-A00039639_ses-DS2_T1w.nii.gz rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/wm.mgz... reading input surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.white... reading input pial surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.pial... reading input white surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 254180 Total vertex volume 250902 (mask=0) reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1642165 mm^3 (det: 1.186303 ) lhCtxGM: 241987.950 242104.000 diff= -116.0 pctdiff=-0.048 rhCtxGM: 249523.742 249044.000 diff= 479.7 pctdiff= 0.192 lhCtxWM: 262629.594 262867.500 diff= -237.9 pctdiff=-0.091 rhCtxWM: 262886.151 263474.500 diff= -588.3 pctdiff=-0.224 SubCortGMVol 63223.000 SupraTentVol 1105646.438 (1101665.000) diff=3981.438 pctdiff=0.360 SupraTentVolNotVent 1084707.438 (1080726.000) diff=3981.438 pctdiff=0.367 BrainSegVol 1270335.000 (1266267.000) diff=4068.000 pctdiff=0.320 BrainSegVolNotVent 1244144.000 (1243497.438) diff=646.562 pctdiff=0.052 BrainSegVolNotVent 1244144.000 CerebellumVol 163234.000 VentChorVol 20939.000 3rd4th5thCSF 5252.000 CSFVol 1184.000, OptChiasmVol 184.000 MaskVol 1745125.000 941 664 1951 2.487 0.659 0.168 0.047 20 1.9 G&S_frontomargin 1122 764 1773 2.231 0.463 0.121 0.024 11 1.1 G&S_occipital_inf 1837 1095 3315 2.313 0.620 0.132 0.039 24 3.0 G&S_paracentral 1556 1021 2999 2.688 0.472 0.140 0.031 23 1.8 G&S_subcentral 1297 923 2625 2.314 0.513 0.168 0.040 32 2.4 G&S_transv_frontopol 3286 2282 6133 2.569 0.496 0.131 0.033 47 4.3 G&S_cingul-Ant 1471 1013 2870 2.665 0.593 0.138 0.030 19 1.8 G&S_cingul-Mid-Ant 1485 1048 2693 2.535 0.629 0.145 0.032 17 1.9 G&S_cingul-Mid-Post 731 464 1934 3.192 0.652 0.171 0.051 18 1.3 G_cingul-Post-dorsal 421 295 1067 2.631 0.739 0.169 0.054 10 0.9 G_cingul-Post-ventral 2272 1482 2495 1.567 0.394 0.155 0.034 38 3.1 G_cuneus 1747 1125 3688 2.730 0.394 0.141 0.037 29 2.8 G_front_inf-Opercular 448 293 1096 2.737 0.568 0.151 0.038 7 0.7 G_front_inf-Orbital 1033 663 2105 2.550 0.426 0.131 0.037 16 1.4 G_front_inf-Triangul 4483 2847 9231 2.508 0.549 0.136 0.033 77 6.1 G_front_middle 7937 5036 16824 2.674 0.525 0.134 0.037 118 12.9 G_front_sup 635 428 1536 3.371 0.739 0.118 0.024 7 0.5 G_Ins_lg&S_cent_ins 836 483 2131 3.444 0.811 0.136 0.057 14 2.2 G_insular_short 2461 1618 4862 2.487 0.498 0.141 0.029 39 3.0 G_occipital_middle 1986 1237 3476 2.335 0.605 0.136 0.030 26 2.6 G_occipital_sup 2277 1469 5880 3.017 0.651 0.141 0.039 45 3.7 G_oc-temp_lat-fusifor 3448 2346 5034 1.909 0.679 0.158 0.044 57 6.5 G_oc-temp_med-Lingual 1418 966 4967 3.834 0.731 0.118 0.031 14 1.7 G_oc-temp_med-Parahip 2701 1864 7060 2.902 0.701 0.157 0.044 59 5.1 G_orbital 2884 1767 6695 2.685 0.577 0.139 0.032 53 3.6 G_pariet_inf-Angular 2510 1641 5385 2.686 0.470 0.134 0.033 39 3.1 G_pariet_inf-Supramar 2538 1570 4451 2.253 0.484 0.118 0.024 33 2.4 G_parietal_sup 2872 1519 4327 2.216 0.599 0.109 0.025 35 3.1 G_postcentral 3922 2016 6871 2.591 0.701 0.112 0.038 55 6.8 G_precentral 2849 1875 5568 2.508 0.539 0.135 0.030 41 3.2 G_precuneus 937 595 1707 2.244 0.622 0.153 0.055 25 2.4 G_rectus 497 334 782 2.346 0.954 0.089 0.036 4 0.5 G_subcallosal 471 251 731 2.261 0.286 0.108 0.020 4 0.4 G_temp_sup-G_T_transv 1820 1195 5024 3.197 0.681 0.126 0.026 24 1.9 G_temp_sup-Lateral 913 636 2287 3.588 0.672 0.099 0.021 6 0.9 G_temp_sup-Plan_polar 1075 669 2049 2.605 0.477 0.115 0.024 12 1.0 G_temp_sup-Plan_tempo 3075 2008 8309 2.964 0.776 0.145 0.048 77 6.4 G_temporal_inf 3266 2135 8815 3.034 0.646 0.133 0.032 52 3.9 G_temporal_middle 353 248 401 1.988 0.384 0.109 0.013 2 0.1 Lat_Fis-ant-Horizont 155 115 276 2.672 0.289 0.117 0.027 1 0.1 Lat_Fis-ant-Vertical 1427 959 1910 2.392 0.584 0.111 0.022 9 1.3 Lat_Fis-post 3384 2086 4791 2.036 0.686 0.147 0.038 51 5.1 Pole_occipital 1744 1157 5946 3.580 0.664 0.130 0.030 22 2.2 Pole_temporal 2621 1822 2761 1.829 0.664 0.131 0.027 31 3.1 S_calcarine 3804 2624 4662 2.010 0.559 0.104 0.019 21 3.2 S_central 1497 1004 2122 2.212 0.372 0.117 0.021 16 1.0 S_cingul-Marginalis 520 374 885 2.733 0.523 0.102 0.016 2 0.4 S_circular_insula_ant 1409 964 2067 2.449 0.612 0.079 0.010 5 0.6 S_circular_insula_inf 1543 1087 2418 2.620 0.402 0.102 0.017 6 1.1 S_circular_insula_sup 1247 858 2024 2.614 0.416 0.091 0.014 6 0.6 S_collat_transv_ant 388 250 426 2.106 0.525 0.155 0.039 4 0.8 S_collat_transv_post 3506 2325 4822 2.197 0.431 0.125 0.025 35 3.5 S_front_inf 2228 1492 3103 2.186 0.375 0.120 0.026 24 2.2 S_front_middle 3129 2191 4860 2.404 0.372 0.109 0.019 25 2.5 S_front_sup 484 371 768 2.453 0.430 0.131 0.023 4 0.5 S_interm_prim-Jensen 2952 1994 4260 2.161 0.435 0.124 0.023 32 2.8 S_intrapariet&P_trans 593 421 901 2.272 0.638 0.143 0.034 8 0.7 S_oc_middle&Lunatus 1498 964 2450 2.539 0.790 0.137 0.032 20 1.8 S_oc_sup&transversal 449 332 691 2.332 0.615 0.134 0.030 4 0.4 S_occipital_ant 1201 832 1874 2.653 0.524 0.122 0.026 12 1.2 S_oc-temp_lat 2092 1499 3104 2.366 0.739 0.118 0.019 19 1.6 S_oc-temp_med&Lingual 428 314 556 2.107 0.600 0.139 0.030 5 0.6 S_orbital_lateral 661 454 979 2.400 0.749 0.109 0.017 5 0.4 S_orbital_med-olfact 1360 931 2427 2.722 0.631 0.155 0.041 21 2.4 S_orbital-H_Shaped 2978 1943 3644 2.026 0.599 0.123 0.025 31 2.9 S_parieto_occipital 1501 914 1283 1.999 0.718 0.132 0.022 27 0.9 S_pericallosal 2940 1933 3714 2.128 0.485 0.108 0.019 23 2.2 S_postcentral 1971 1347 2848 2.412 0.416 0.109 0.020 12 1.6 S_precentral-inf-part 1543 1043 2172 2.306 0.509 0.097 0.018 9 1.3 S_precentral-sup-part 297 199 481 2.881 0.642 0.109 0.019 2 0.2 S_suborbital 1330 930 2076 2.363 0.447 0.139 0.030 15 1.6 S_subparietal 1788 1274 2603 2.518 0.426 0.110 0.017 12 1.2 S_temporal_inf 6044 4206 9468 2.481 0.452 0.093 0.014 27 3.5 S_temporal_sup 326 222 383 2.238 0.458 0.118 0.015 3 0.2 S_temporal_transverse PIDs (4564 4567) completed and logs appended. #----------------------------------------- #@# Cortical Parc 3 lh Fri Oct 11 03:14:19 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-A00039639_ses-DS2_T1w.nii.gz lh ../surf/lh.sphere.reg /usr/local/freesurfer/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot #----------------------------------------- #@# Cortical Parc 3 rh Fri Oct 11 03:14:19 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-A00039639_ses-DS2_T1w.nii.gz rh ../surf/rh.sphere.reg /usr/local/freesurfer/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.DKTatlas.annot Waiting for PID 4612 of (4612 4615) to complete... Waiting for PID 4615 of (4612 4615) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-A00039639_ses-DS2_T1w.nii.gz lh ../surf/lh.sphere.reg /usr/local/freesurfer/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /usr/local/freesurfer/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 1.4 using min determinant for regularization = 0.020 0 singular and 383 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1437 labels changed using aseg relabeling using gibbs priors... 000: 1950 changed, 145499 examined... 001: 462 changed, 9315 examined... 002: 132 changed, 2619 examined... 003: 59 changed, 839 examined... 004: 43 changed, 335 examined... 005: 19 changed, 212 examined... 006: 10 changed, 108 examined... 007: 7 changed, 58 examined... 008: 4 changed, 39 examined... 009: 2 changed, 31 examined... 010: 2 changed, 14 examined... 011: 1 changed, 12 examined... 012: 2 changed, 9 examined... 013: 2 changed, 11 examined... 014: 4 changed, 12 examined... 015: 3 changed, 21 examined... 016: 3 changed, 19 examined... 017: 2 changed, 16 examined... 018: 5 changed, 14 examined... 019: 5 changed, 19 examined... 020: 2 changed, 23 examined... 021: 1 changed, 15 examined... 022: 2 changed, 9 examined... 023: 0 changed, 8 examined... 258 labels changed using aseg 000: 50 total segments, 17 labels (307 vertices) changed 001: 34 total segments, 1 labels (9 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 9 filter iterations complete (10 requested, 0 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 830 vertices marked for relabeling... 830 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 7 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-A00039639_ses-DS2_T1w.nii.gz rh ../surf/rh.sphere.reg /usr/local/freesurfer/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.DKTatlas.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /usr/local/freesurfer/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.009 0 singular and 325 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1356 labels changed using aseg relabeling using gibbs priors... 000: 2063 changed, 147557 examined... 001: 456 changed, 9482 examined... 002: 145 changed, 2582 examined... 003: 55 changed, 835 examined... 004: 27 changed, 344 examined... 005: 19 changed, 141 examined... 006: 7 changed, 89 examined... 007: 3 changed, 42 examined... 008: 5 changed, 21 examined... 009: 5 changed, 31 examined... 010: 5 changed, 25 examined... 011: 1 changed, 23 examined... 012: 2 changed, 6 examined... 013: 1 changed, 11 examined... 014: 2 changed, 7 examined... 015: 3 changed, 11 examined... 016: 4 changed, 15 examined... 017: 5 changed, 18 examined... 018: 1 changed, 21 examined... 019: 3 changed, 7 examined... 020: 3 changed, 13 examined... 021: 1 changed, 17 examined... 022: 1 changed, 7 examined... 023: 1 changed, 7 examined... 024: 1 changed, 7 examined... 025: 1 changed, 7 examined... 026: 1 changed, 7 examined... 027: 1 changed, 7 examined... 028: 1 changed, 7 examined... 029: 2 changed, 7 examined... 030: 3 changed, 9 examined... 031: 2 changed, 15 examined... 032: 3 changed, 14 examined... 033: 4 changed, 17 examined... 034: 2 changed, 20 examined... 035: 1 changed, 14 examined... 036: 1 changed, 7 examined... 037: 1 changed, 7 examined... 038: 1 changed, 7 examined... 039: 1 changed, 8 examined... 040: 0 changed, 7 examined... 276 labels changed using aseg 000: 55 total segments, 22 labels (223 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 4 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 846 vertices marked for relabeling... 846 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 7 seconds. PIDs (4612 4615) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 3 lh Fri Oct 11 03:14:25 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas.stats -b -a ../label/lh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab sub-A00039639_ses-DS2_T1w.nii.gz lh white #----------------------------------------- #@# Parcellation Stats 3 rh Fri Oct 11 03:14:25 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab sub-A00039639_ses-DS2_T1w.nii.gz rh white Waiting for PID 4660 of (4660 4663) to complete... Waiting for PID 4663 of (4660 4663) to complete... mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas.stats -b -a ../label/lh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab sub-A00039639_ses-DS2_T1w.nii.gz lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/wm.mgz... reading input surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.white... reading input pial surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.pial... reading input white surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 246740 Total vertex volume 243855 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1642165 mm^3 (det: 1.186303 ) lhCtxGM: 241987.950 242104.000 diff= -116.0 pctdiff=-0.048 rhCtxGM: 249523.742 249044.000 diff= 479.7 pctdiff= 0.192 lhCtxWM: 262629.594 262867.500 diff= -237.9 pctdiff=-0.091 rhCtxWM: 262886.151 263474.500 diff= -588.3 pctdiff=-0.224 SubCortGMVol 63223.000 SupraTentVol 1105646.438 (1101665.000) diff=3981.438 pctdiff=0.360 SupraTentVolNotVent 1084707.438 (1080726.000) diff=3981.438 pctdiff=0.367 BrainSegVol 1270335.000 (1266267.000) diff=4068.000 pctdiff=0.320 BrainSegVolNotVent 1244144.000 (1243497.438) diff=646.562 pctdiff=0.052 BrainSegVolNotVent 1244144.000 CerebellumVol 163234.000 VentChorVol 20939.000 3rd4th5thCSF 5252.000 CSFVol 1184.000, OptChiasmVol 184.000 MaskVol 1745125.000 2023 1336 3564 2.573 0.529 0.134 0.021 30 1.5 caudalanteriorcingulate 4659 2917 7362 2.411 0.449 0.118 0.027 52 5.0 caudalmiddlefrontal 2962 1959 3527 1.761 0.483 0.149 0.031 44 3.8 cuneus 670 491 2383 3.876 0.561 0.128 0.034 6 0.9 entorhinal 4059 2877 9237 2.842 0.646 0.134 0.029 54 4.9 fusiform 7427 4899 12950 2.442 0.537 0.126 0.024 98 7.0 inferiorparietal 4957 3432 11914 2.864 0.723 0.141 0.035 81 7.2 inferiortemporal 1665 1098 2981 2.394 1.081 0.134 0.039 28 2.5 isthmuscingulate 7806 5179 12133 2.190 0.621 0.147 0.032 115 10.2 lateraloccipital 4340 2964 8794 2.779 0.670 0.140 0.035 62 6.1 lateralorbitofrontal 4840 3392 6377 1.826 0.618 0.156 0.038 69 7.8 lingual 2520 1685 4493 2.339 0.643 0.130 0.034 39 3.7 medialorbitofrontal 6377 4465 14771 2.836 0.647 0.127 0.025 75 6.5 middletemporal 1021 704 2198 2.800 0.800 0.084 0.013 4 0.5 parahippocampal 2783 1555 4016 2.383 0.537 0.110 0.032 25 3.7 paracentral 2700 1812 4806 2.501 0.477 0.119 0.023 26 2.6 parsopercularis 1066 695 2127 2.678 0.579 0.136 0.027 12 1.2 parsorbitalis 2440 1654 3958 2.314 0.398 0.131 0.030 29 2.8 parstriangularis 2075 1425 1585 1.273 0.251 0.140 0.029 25 2.5 pericalcarine 8320 5320 12612 2.147 0.618 0.123 0.027 88 9.3 postcentral 2241 1523 3934 2.472 0.790 0.156 0.035 40 3.0 posteriorcingulate 9347 5859 14865 2.405 0.554 0.121 0.033 110 13.5 precentral 5282 3599 9311 2.512 0.547 0.139 0.031 72 6.5 precuneus 2397 1578 4504 2.639 0.663 0.144 0.037 40 3.4 rostralanteriorcingulate 6611 4353 11214 2.326 0.460 0.138 0.031 96 8.6 rostralmiddlefrontal 12227 8172 23645 2.593 0.523 0.132 0.032 161 15.9 superiorfrontal 6421 4121 10051 2.190 0.539 0.123 0.026 77 7.1 superiorparietal 8008 5406 17952 2.866 0.773 0.104 0.020 62 6.6 superiortemporal 5091 3434 9064 2.523 0.479 0.134 0.029 67 6.1 supramarginal 823 477 1063 2.149 0.285 0.113 0.019 8 0.6 transversetemporal 3313 2169 6463 2.900 0.739 0.124 0.049 60 8.0 insula mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab sub-A00039639_ses-DS2_T1w.nii.gz rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/wm.mgz... reading input surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.white... reading input pial surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.pial... reading input white surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 254180 Total vertex volume 250902 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1642165 mm^3 (det: 1.186303 ) lhCtxGM: 241987.950 242104.000 diff= -116.0 pctdiff=-0.048 rhCtxGM: 249523.742 249044.000 diff= 479.7 pctdiff= 0.192 lhCtxWM: 262629.594 262867.500 diff= -237.9 pctdiff=-0.091 rhCtxWM: 262886.151 263474.500 diff= -588.3 pctdiff=-0.224 SubCortGMVol 63223.000 SupraTentVol 1105646.438 (1101665.000) diff=3981.438 pctdiff=0.360 SupraTentVolNotVent 1084707.438 (1080726.000) diff=3981.438 pctdiff=0.367 BrainSegVol 1270335.000 (1266267.000) diff=4068.000 pctdiff=0.320 BrainSegVolNotVent 1244144.000 (1243497.438) diff=646.562 pctdiff=0.052 BrainSegVolNotVent 1244144.000 CerebellumVol 163234.000 VentChorVol 20939.000 3rd4th5thCSF 5252.000 CSFVol 1184.000, OptChiasmVol 184.000 MaskVol 1745125.000 1176 778 2153 2.608 0.627 0.144 0.027 21 1.2 caudalanteriorcingulate 4576 2937 7820 2.488 0.528 0.117 0.025 47 4.9 caudalmiddlefrontal 3033 1991 3454 1.638 0.415 0.147 0.031 45 3.8 cuneus 655 467 2769 4.251 0.524 0.106 0.028 4 0.7 entorhinal 4364 2950 9597 2.883 0.678 0.133 0.031 67 5.5 fusiform 7629 5047 13699 2.452 0.573 0.125 0.025 92 7.9 inferiorparietal 6111 4102 13952 2.864 0.714 0.130 0.035 102 8.9 inferiortemporal 1628 1059 3104 2.439 0.837 0.137 0.037 27 1.9 isthmuscingulate 7421 4763 11876 2.244 0.599 0.138 0.032 101 9.4 lateraloccipital 4379 2985 9467 2.797 0.711 0.156 0.047 85 8.8 lateralorbitofrontal 5169 3531 7209 1.962 0.680 0.156 0.041 82 9.1 lingual 2289 1506 3972 2.358 0.731 0.131 0.040 41 3.7 medialorbitofrontal 6358 4331 14108 2.832 0.625 0.116 0.024 69 5.7 middletemporal 1040 701 2224 2.909 0.965 0.101 0.017 8 0.6 parahippocampal 2758 1687 4629 2.456 0.598 0.118 0.029 27 3.2 paracentral 2787 1829 5037 2.644 0.434 0.127 0.030 34 3.4 parsopercularis 984 681 2238 2.738 0.668 0.133 0.028 11 1.2 parsorbitalis 2397 1624 4003 2.327 0.505 0.137 0.033 32 3.1 parstriangularis 2333 1581 2127 1.563 0.479 0.122 0.025 24 2.4 pericalcarine 8280 5078 12175 2.163 0.584 0.113 0.023 88 8.0 postcentral 1775 1197 3380 2.602 0.834 0.149 0.032 29 2.2 posteriorcingulate 8954 5417 14255 2.458 0.614 0.109 0.029 87 11.4 precentral 7186 4790 11504 2.323 0.554 0.134 0.029 94 8.2 precuneus 1257 843 2362 2.693 0.532 0.132 0.032 25 1.6 rostralanteriorcingulate 6990 4668 11669 2.271 0.456 0.135 0.030 102 8.6 rostralmiddlefrontal 14729 9918 28060 2.532 0.512 0.132 0.032 199 20.5 superiorfrontal 6532 4180 10802 2.266 0.533 0.118 0.024 72 6.3 superiorparietal 7152 4786 16048 2.924 0.787 0.106 0.021 64 6.2 superiortemporal 5145 3435 9724 2.625 0.480 0.131 0.030 63 6.2 supramarginal 605 327 854 2.227 0.310 0.097 0.018 5 0.4 transversetemporal 3157 2128 6631 3.072 0.753 0.116 0.025 28 3.1 insula PIDs (4660 4663) completed and logs appended. #----------------------------------------- #@# WM/GM Contrast lh Fri Oct 11 03:14:42 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/scripts pctsurfcon --s sub-A00039639_ses-DS2_T1w.nii.gz --lh-only #----------------------------------------- #@# WM/GM Contrast rh Fri Oct 11 03:14:42 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/scripts pctsurfcon --s sub-A00039639_ses-DS2_T1w.nii.gz --rh-only Waiting for PID 4708 of (4708 4711) to complete... Waiting for PID 4711 of (4708 4711) to complete... pctsurfcon --s sub-A00039639_ses-DS2_T1w.nii.gz --lh-only Log file is /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/scripts/pctsurfcon.log Fri Oct 11 03:14:42 -03 2019 setenv SUBJECTS_DIR /mnt/disco1/subjects cd /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/scripts /usr/local/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux fisicos-ub2 5.0.0-29-generic #31~18.04.1-Ubuntu SMP Thu Sep 12 18:29:21 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_vol2surf --mov /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/tmp.pctsurfcon.4708/lh.wm.mgh --regheader sub-A00039639_ses-DS2_T1w.nii.gz --cortex srcvol = /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00002; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/label/lh.cortex.label Reading surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 82301 Masking with /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/label/lh.cortex.label Writing to /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/tmp.pctsurfcon.4708/lh.wm.mgh Dim: 145499 1 1 mri_vol2surf --mov /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/tmp.pctsurfcon.4708/lh.gm.mgh --projfrac 0.3 --regheader sub-A00039639_ses-DS2_T1w.nii.gz --cortex srcvol = /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00002; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/label/lh.cortex.label Reading surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.white Done reading source surface Reading thickness /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 96370 Masking with /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/label/lh.cortex.label Writing to /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/tmp.pctsurfcon.4708/lh.gm.mgh Dim: 145499 1 1 mri_concat /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/tmp.pctsurfcon.4708/lh.wm.mgh /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/tmp.pctsurfcon.4708/lh.gm.mgh --paired-diff-norm --mul 100 --o /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.w-g.pct.mgh mri_segstats --in /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.w-g.pct.mgh --annot sub-A00039639_ses-DS2_T1w.nii.gz lh aparc --sum /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/stats/lh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --in /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.w-g.pct.mgh --annot sub-A00039639_ses-DS2_T1w.nii.gz lh aparc --sum /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/stats/lh.w-g.pct.stats --snr sysname Linux hostname fisicos-ub2 machine x86_64 user fisicos UseRobust 0 Constructing seg from annotation Reading annotation /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Seg base 1000 Loading /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.w-g.pct.mgh Vertex Area is 0.663473 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up pctsurfcon --s sub-A00039639_ses-DS2_T1w.nii.gz --rh-only Log file is /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/scripts/pctsurfcon.log Fri Oct 11 03:14:42 -03 2019 setenv SUBJECTS_DIR /mnt/disco1/subjects cd /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/scripts /usr/local/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux fisicos-ub2 5.0.0-29-generic #31~18.04.1-Ubuntu SMP Thu Sep 12 18:29:21 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_vol2surf --mov /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/tmp.pctsurfcon.4711/rh.wm.mgh --regheader sub-A00039639_ses-DS2_T1w.nii.gz --cortex srcvol = /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00002; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/label/rh.cortex.label Reading surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 82702 Masking with /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/label/rh.cortex.label Writing to /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/tmp.pctsurfcon.4711/rh.wm.mgh Dim: 147557 1 1 mri_vol2surf --mov /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/tmp.pctsurfcon.4711/rh.gm.mgh --projfrac 0.3 --regheader sub-A00039639_ses-DS2_T1w.nii.gz --cortex srcvol = /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00002; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/label/rh.cortex.label Reading surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.white Done reading source surface Reading thickness /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 97763 Masking with /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/label/rh.cortex.label Writing to /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/tmp.pctsurfcon.4711/rh.gm.mgh Dim: 147557 1 1 mri_concat /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/tmp.pctsurfcon.4711/rh.wm.mgh /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/tmp.pctsurfcon.4711/rh.gm.mgh --paired-diff-norm --mul 100 --o /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.w-g.pct.mgh mri_segstats --in /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.w-g.pct.mgh --annot sub-A00039639_ses-DS2_T1w.nii.gz rh aparc --sum /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/stats/rh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --in /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.w-g.pct.mgh --annot sub-A00039639_ses-DS2_T1w.nii.gz rh aparc --sum /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/stats/rh.w-g.pct.stats --snr sysname Linux hostname fisicos-ub2 machine x86_64 user fisicos UseRobust 0 Constructing seg from annotation Reading annotation /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Seg base 2000 Loading /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.w-g.pct.mgh Vertex Area is 0.658076 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up PIDs (4708 4711) completed and logs appended. #----------------------------------------- #@# Relabel Hypointensities Fri Oct 11 03:14:45 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 4563 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 3731 voxels changed to hypointensity... 8107 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg aparc Fri Oct 11 03:14:55 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz mri_aparc2aseg --s sub-A00039639_ses-DS2_T1w.nii.gz --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt #----------------------------------------- #@# AParc-to-ASeg a2009s Fri Oct 11 03:14:55 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz mri_aparc2aseg --s sub-A00039639_ses-DS2_T1w.nii.gz --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --a2009s #----------------------------------------- #@# AParc-to-ASeg DKTatlas Fri Oct 11 03:14:55 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz mri_aparc2aseg --s sub-A00039639_ses-DS2_T1w.nii.gz --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --annot aparc.DKTatlas --o mri/aparc.DKTatlas+aseg.mgz Waiting for PID 4881 of (4881 4885 4888) to complete... Waiting for PID 4885 of (4881 4885 4888) to complete... Waiting for PID 4888 of (4881 4885 4888) to complete... mri_aparc2aseg --s sub-A00039639_ses-DS2_T1w.nii.gz --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /mnt/disco1/subjects subject sub-A00039639_ses-DS2_T1w.nii.gz outvol /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.white Reading lh pial surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.pial Loading lh annotations from /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading rh white surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.white Reading rh pial surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.pial Loading rh annotations from /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 7.33 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 106 rescaling Left_Cerebral_Cortex from 61 --> 76 rescaling Left_Lateral_Ventricle from 13 --> 27 rescaling Left_Inf_Lat_Vent from 34 --> 34 rescaling Left_Cerebellum_White_Matter from 86 --> 95 rescaling Left_Cerebellum_Cortex from 60 --> 72 rescaling Left_Thalamus from 94 --> 104 rescaling Left_Thalamus_Proper from 84 --> 98 rescaling Left_Caudate from 75 --> 89 rescaling Left_Putamen from 80 --> 93 rescaling Left_Pallidum from 98 --> 101 rescaling Third_Ventricle from 25 --> 32 rescaling Fourth_Ventricle from 22 --> 27 rescaling Brain_Stem from 81 --> 82 rescaling Left_Hippocampus from 57 --> 72 rescaling Left_Amygdala from 56 --> 76 rescaling CSF from 32 --> 60 rescaling Left_Accumbens_area from 62 --> 71 rescaling Left_VentralDC from 87 --> 98 rescaling Right_Cerebral_White_Matter from 105 --> 103 rescaling Right_Cerebral_Cortex from 58 --> 75 rescaling Right_Lateral_Ventricle from 13 --> 27 rescaling Right_Inf_Lat_Vent from 25 --> 31 rescaling Right_Cerebellum_White_Matter from 87 --> 90 rescaling Right_Cerebellum_Cortex from 59 --> 72 rescaling Right_Thalamus_Proper from 85 --> 96 rescaling Right_Caudate from 62 --> 85 rescaling Right_Putamen from 80 --> 86 rescaling Right_Pallidum from 97 --> 101 rescaling Right_Hippocampus from 53 --> 74 rescaling Right_Amygdala from 55 --> 75 rescaling Right_Accumbens_area from 65 --> 83 rescaling Right_VentralDC from 86 --> 99 rescaling Fifth_Ventricle from 40 --> 51 rescaling WM_hypointensities from 78 --> 77 rescaling non_WM_hypointensities from 40 --> 55 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 491903 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 168 changed. pass 2: 5 changed. pass 3: 0 changed. nchanged = 0 Writing output aseg to /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/aparc+aseg.mgz mri_aparc2aseg --s sub-A00039639_ses-DS2_T1w.nii.gz --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --a2009s relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /mnt/disco1/subjects subject sub-A00039639_ses-DS2_T1w.nii.gz outvol /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.white Reading lh pial surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.pial Loading lh annotations from /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/label/lh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Reading rh white surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.white Reading rh pial surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.pial Loading rh annotations from /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/label/rh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 7.33 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 106 rescaling Left_Cerebral_Cortex from 61 --> 76 rescaling Left_Lateral_Ventricle from 13 --> 27 rescaling Left_Inf_Lat_Vent from 34 --> 34 rescaling Left_Cerebellum_White_Matter from 86 --> 95 rescaling Left_Cerebellum_Cortex from 60 --> 72 rescaling Left_Thalamus from 94 --> 104 rescaling Left_Thalamus_Proper from 84 --> 98 rescaling Left_Caudate from 75 --> 89 rescaling Left_Putamen from 80 --> 93 rescaling Left_Pallidum from 98 --> 101 rescaling Third_Ventricle from 25 --> 32 rescaling Fourth_Ventricle from 22 --> 27 rescaling Brain_Stem from 81 --> 82 rescaling Left_Hippocampus from 57 --> 72 rescaling Left_Amygdala from 56 --> 76 rescaling CSF from 32 --> 60 rescaling Left_Accumbens_area from 62 --> 71 rescaling Left_VentralDC from 87 --> 98 rescaling Right_Cerebral_White_Matter from 105 --> 103 rescaling Right_Cerebral_Cortex from 58 --> 75 rescaling Right_Lateral_Ventricle from 13 --> 27 rescaling Right_Inf_Lat_Vent from 25 --> 31 rescaling Right_Cerebellum_White_Matter from 87 --> 90 rescaling Right_Cerebellum_Cortex from 59 --> 72 rescaling Right_Thalamus_Proper from 85 --> 96 rescaling Right_Caudate from 62 --> 85 rescaling Right_Putamen from 80 --> 86 rescaling Right_Pallidum from 97 --> 101 rescaling Right_Hippocampus from 53 --> 74 rescaling Right_Amygdala from 55 --> 75 rescaling Right_Accumbens_area from 65 --> 83 rescaling Right_VentralDC from 86 --> 99 rescaling Fifth_Ventricle from 40 --> 51 rescaling WM_hypointensities from 78 --> 77 rescaling non_WM_hypointensities from 40 --> 55 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 491941 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 168 changed. pass 2: 5 changed. pass 3: 0 changed. nchanged = 0 Writing output aseg to /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/aparc.a2009s+aseg.mgz mri_aparc2aseg --s sub-A00039639_ses-DS2_T1w.nii.gz --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --annot aparc.DKTatlas --o mri/aparc.DKTatlas+aseg.mgz relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /mnt/disco1/subjects subject sub-A00039639_ses-DS2_T1w.nii.gz outvol mri/aparc.DKTatlas+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.white Reading lh pial surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.pial Loading lh annotations from /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/label/lh.aparc.DKTatlas.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading rh white surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.white Reading rh pial surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.pial Loading rh annotations from /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/label/rh.aparc.DKTatlas.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 7.33 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 106 rescaling Left_Cerebral_Cortex from 61 --> 76 rescaling Left_Lateral_Ventricle from 13 --> 27 rescaling Left_Inf_Lat_Vent from 34 --> 34 rescaling Left_Cerebellum_White_Matter from 86 --> 95 rescaling Left_Cerebellum_Cortex from 60 --> 72 rescaling Left_Thalamus from 94 --> 104 rescaling Left_Thalamus_Proper from 84 --> 98 rescaling Left_Caudate from 75 --> 89 rescaling Left_Putamen from 80 --> 93 rescaling Left_Pallidum from 98 --> 101 rescaling Third_Ventricle from 25 --> 32 rescaling Fourth_Ventricle from 22 --> 27 rescaling Brain_Stem from 81 --> 82 rescaling Left_Hippocampus from 57 --> 72 rescaling Left_Amygdala from 56 --> 76 rescaling CSF from 32 --> 60 rescaling Left_Accumbens_area from 62 --> 71 rescaling Left_VentralDC from 87 --> 98 rescaling Right_Cerebral_White_Matter from 105 --> 103 rescaling Right_Cerebral_Cortex from 58 --> 75 rescaling Right_Lateral_Ventricle from 13 --> 27 rescaling Right_Inf_Lat_Vent from 25 --> 31 rescaling Right_Cerebellum_White_Matter from 87 --> 90 rescaling Right_Cerebellum_Cortex from 59 --> 72 rescaling Right_Thalamus_Proper from 85 --> 96 rescaling Right_Caudate from 62 --> 85 rescaling Right_Putamen from 80 --> 86 rescaling Right_Pallidum from 97 --> 101 rescaling Right_Hippocampus from 53 --> 74 rescaling Right_Amygdala from 55 --> 75 rescaling Right_Accumbens_area from 65 --> 83 rescaling Right_VentralDC from 86 --> 99 rescaling Fifth_Ventricle from 40 --> 51 rescaling WM_hypointensities from 78 --> 77 rescaling non_WM_hypointensities from 40 --> 55 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 491941 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 168 changed. pass 2: 5 changed. pass 3: 0 changed. nchanged = 0 Writing output aseg to mri/aparc.DKTatlas+aseg.mgz PIDs (4881 4885 4888) completed and logs appended. #----------------------------------------- #@# APas-to-ASeg Fri Oct 11 03:17:30 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri apas2aseg --i aparc+aseg.mgz --o aseg.mgz Fri Oct 11 03:17:30 -03 2019 setenv SUBJECTS_DIR /mnt/disco1/subjects cd /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri /usr/local/freesurfer/bin/apas2aseg --i aparc+aseg.mgz --o aseg.mgz freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c $Id: apas2aseg,v 1.2 2016/02/12 21:43:14 zkaufman Exp $ Linux fisicos-ub2 5.0.0-29-generic #31~18.04.1-Ubuntu SMP Thu Sep 12 18:29:21 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux mri_binarize --i aparc+aseg.mgz --o aseg.mgz --replace 1000 3 --replace 2000 42 --replace 1001 3 --replace 2001 42 --replace 1002 3 --replace 2002 42 --replace 1003 3 --replace 2003 42 --replace 1004 3 --replace 2004 42 --replace 1005 3 --replace 2005 42 --replace 1006 3 --replace 2006 42 --replace 1007 3 --replace 2007 42 --replace 1008 3 --replace 2008 42 --replace 1009 3 --replace 2009 42 --replace 1010 3 --replace 2010 42 --replace 1011 3 --replace 2011 42 --replace 1012 3 --replace 2012 42 --replace 1013 3 --replace 2013 42 --replace 1014 3 --replace 2014 42 --replace 1015 3 --replace 2015 42 --replace 1016 3 --replace 2016 42 --replace 1017 3 --replace 2017 42 --replace 1018 3 --replace 2018 42 --replace 1019 3 --replace 2019 42 --replace 1020 3 --replace 2020 42 --replace 1021 3 --replace 2021 42 --replace 1022 3 --replace 2022 42 --replace 1023 3 --replace 2023 42 --replace 1024 3 --replace 2024 42 --replace 1025 3 --replace 2025 42 --replace 1026 3 --replace 2026 42 --replace 1027 3 --replace 2027 42 --replace 1028 3 --replace 2028 42 --replace 1029 3 --replace 2029 42 --replace 1030 3 --replace 2030 42 --replace 1031 3 --replace 2031 42 --replace 1032 3 --replace 2032 42 --replace 1033 3 --replace 2033 42 --replace 1034 3 --replace 2034 42 --replace 1035 3 --replace 2035 42 $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri cmdline mri_binarize.bin --i aparc+aseg.mgz --o aseg.mgz --replace 1000 3 --replace 2000 42 --replace 1001 3 --replace 2001 42 --replace 1002 3 --replace 2002 42 --replace 1003 3 --replace 2003 42 --replace 1004 3 --replace 2004 42 --replace 1005 3 --replace 2005 42 --replace 1006 3 --replace 2006 42 --replace 1007 3 --replace 2007 42 --replace 1008 3 --replace 2008 42 --replace 1009 3 --replace 2009 42 --replace 1010 3 --replace 2010 42 --replace 1011 3 --replace 2011 42 --replace 1012 3 --replace 2012 42 --replace 1013 3 --replace 2013 42 --replace 1014 3 --replace 2014 42 --replace 1015 3 --replace 2015 42 --replace 1016 3 --replace 2016 42 --replace 1017 3 --replace 2017 42 --replace 1018 3 --replace 2018 42 --replace 1019 3 --replace 2019 42 --replace 1020 3 --replace 2020 42 --replace 1021 3 --replace 2021 42 --replace 1022 3 --replace 2022 42 --replace 1023 3 --replace 2023 42 --replace 1024 3 --replace 2024 42 --replace 1025 3 --replace 2025 42 --replace 1026 3 --replace 2026 42 --replace 1027 3 --replace 2027 42 --replace 1028 3 --replace 2028 42 --replace 1029 3 --replace 2029 42 --replace 1030 3 --replace 2030 42 --replace 1031 3 --replace 2031 42 --replace 1032 3 --replace 2032 42 --replace 1033 3 --replace 2033 42 --replace 1034 3 --replace 2034 42 --replace 1035 3 --replace 2035 42 sysname Linux hostname fisicos-ub2 machine x86_64 user fisicos input aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output aseg.mgz Binarizing based on threshold min -infinity max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Replacing 72 1: 1000 3 2: 2000 42 3: 1001 3 4: 2001 42 5: 1002 3 6: 2002 42 7: 1003 3 8: 2003 42 9: 1004 3 10: 2004 42 11: 1005 3 12: 2005 42 13: 1006 3 14: 2006 42 15: 1007 3 16: 2007 42 17: 1008 3 18: 2008 42 19: 1009 3 20: 2009 42 21: 1010 3 22: 2010 42 23: 1011 3 24: 2011 42 25: 1012 3 26: 2012 42 27: 1013 3 28: 2013 42 29: 1014 3 30: 2014 42 31: 1015 3 32: 2015 42 33: 1016 3 34: 2016 42 35: 1017 3 36: 2017 42 37: 1018 3 38: 2018 42 39: 1019 3 40: 2019 42 41: 1020 3 42: 2020 42 43: 1021 3 44: 2021 42 45: 1022 3 46: 2022 42 47: 1023 3 48: 2023 42 49: 1024 3 50: 2024 42 51: 1025 3 52: 2025 42 53: 1026 3 54: 2026 42 55: 1027 3 56: 2027 42 57: 1028 3 58: 2028 42 59: 1029 3 60: 2029 42 61: 1030 3 62: 2030 42 63: 1031 3 64: 2031 42 65: 1032 3 66: 2032 42 67: 1033 3 68: 2033 42 69: 1034 3 70: 2034 42 71: 1035 3 72: 2035 42 Found 0 values in range Counting number of voxels in first frame Found 0 voxels in final mask Count: 0 0.000000 16777216 0.000000 mri_binarize done Started at Fri Oct 11 03:17:30 -03 2019 Ended at Fri Oct 11 03:17:33 -03 2019 Apas2aseg-Run-Time-Sec 3 apas2aseg Done #-------------------------------------------- #@# ASeg Stats Fri Oct 11 03:17:33 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/freesurfer/ASegStatsLUT.txt --subject sub-A00039639_ses-DS2_T1w.nii.gz $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/freesurfer/ASegStatsLUT.txt --subject sub-A00039639_ses-DS2_T1w.nii.gz sysname Linux hostname fisicos-ub2 machine x86_64 user fisicos UseRobust 0 atlas_icv (eTIV) = 1642165 mm^3 (det: 1.186303 ) Computing euler number orig.nofix lheno = -68, rheno = -60 orig.nofix lhholes = 35, rhholes = 31 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 241987.950 242104.000 diff= -116.0 pctdiff=-0.048 rhCtxGM: 249523.742 249044.000 diff= 479.7 pctdiff= 0.192 lhCtxWM: 262629.594 262867.500 diff= -237.9 pctdiff=-0.091 rhCtxWM: 262886.151 263474.500 diff= -588.3 pctdiff=-0.224 SubCortGMVol 63223.000 SupraTentVol 1105646.438 (1101665.000) diff=3981.438 pctdiff=0.360 SupraTentVolNotVent 1084707.438 (1080726.000) diff=3981.438 pctdiff=0.367 BrainSegVol 1270335.000 (1266267.000) diff=4068.000 pctdiff=0.320 BrainSegVolNotVent 1244144.000 (1243497.438) diff=646.562 pctdiff=0.052 BrainSegVolNotVent 1244144.000 CerebellumVol 163234.000 VentChorVol 20939.000 3rd4th5thCSF 5252.000 CSFVol 1184.000, OptChiasmVol 184.000 MaskVol 1745125.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation Reporting on 45 segmentations Using PrintSegStat mri_segstats done #----------------------------------------- #@# WMParc Fri Oct 11 03:18:05 -03 2019 /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz mri_aparc2aseg --s sub-A00039639_ses-DS2_T1w.nii.gz --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /mnt/disco1/subjects subject sub-A00039639_ses-DS2_T1w.nii.gz outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/aparc+aseg.mgz Reading lh white surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.white Reading lh pial surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.pial Loading lh annotations from /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading rh white surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.white Reading rh pial surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.pial Loading rh annotations from /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/ribbon.mgz Loading filled from /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/ribbon.mgz Ripping vertices labeled as unkown Ripped 9021 vertices from left hemi Ripped 8745 vertices from right hemi Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/aseg.mgz Loading Ctx Seg File /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/aparc+aseg.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 1015848 Used brute-force search on 216 voxels Fixing Parahip LH WM Found 4 clusters 0 k 1.000000 1 k 2.000000 2 k 1820.000000 3 k 1.000000 Fixing Parahip RH WM Found 12 clusters 0 k 7.000000 1 k 5.000000 2 k 1.000000 3 k 1.000000 4 k 1710.000000 5 k 1.000000 6 k 1.000000 7 k 2.000000 8 k 1.000000 9 k 1.000000 10 k 1.000000 11 k 15.000000 Writing output aseg to mri/wmparc.mgz mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject sub-A00039639_ses-DS2_T1w.nii.gz --surf-wm-vol --ctab /usr/local/freesurfer/WMParcStatsLUT.txt --etiv $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject sub-A00039639_ses-DS2_T1w.nii.gz --surf-wm-vol --ctab /usr/local/freesurfer/WMParcStatsLUT.txt --etiv sysname Linux hostname fisicos-ub2 machine x86_64 user fisicos UseRobust 0 atlas_icv (eTIV) = 1642165 mm^3 (det: 1.186303 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 241987.950 242104.000 diff= -116.0 pctdiff=-0.048 rhCtxGM: 249523.742 249044.000 diff= 479.7 pctdiff= 0.192 lhCtxWM: 262629.594 262867.500 diff= -237.9 pctdiff=-0.091 rhCtxWM: 262886.151 263474.500 diff= -588.3 pctdiff=-0.224 SubCortGMVol 63223.000 SupraTentVol 1105646.438 (1101665.000) diff=3981.438 pctdiff=0.360 SupraTentVolNotVent 1084707.438 (1080726.000) diff=3981.438 pctdiff=0.367 BrainSegVol 1270335.000 (1266267.000) diff=4068.000 pctdiff=0.320 BrainSegVolNotVent 1244144.000 (1243497.438) diff=646.562 pctdiff=0.052 BrainSegVolNotVent 1244144.000 CerebellumVol 163234.000 VentChorVol 20939.000 3rd4th5thCSF 5252.000 CSFVol 1184.000, OptChiasmVol 184.000 MaskVol 1745125.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 390 segmentations Computing statistics for each segmentation Reporting on 70 segmentations Using PrintSegStat mri_segstats done /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/label #-------------------------------------------- #@# BA_exvivo Labels lh Fri Oct 11 03:21:35 -03 2019 mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.BA1_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.BA2_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.BA3a_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.BA3b_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.BA4a_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface Waiting for PID 5291 of (5291 5296 5302 5308 5314) to complete... Waiting for PID 5296 of (5291 5296 5302 5308 5314) to complete... Waiting for PID 5302 of (5291 5296 5302 5308 5314) to complete... Waiting for PID 5308 of (5291 5296 5302 5308 5314) to complete... Waiting for PID 5314 of (5291 5296 5302 5308 5314) to complete... mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.BA1_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./lh.BA1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4129 nlabel points Performing mapping from target back to the source label 145499 Number of reverse mapping hits = 470 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4599 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.BA2_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/lh.BA2_exvivo.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./lh.BA2_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 7909 nlabel points Performing mapping from target back to the source label 145499 Number of reverse mapping hits = 730 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8639 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.BA3a_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/lh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./lh.BA3a_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4077 nlabel points Performing mapping from target back to the source label 145499 Number of reverse mapping hits = 376 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4453 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.BA3b_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/lh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./lh.BA3b_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5983 nlabel points Performing mapping from target back to the source label 145499 Number of reverse mapping hits = 524 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6507 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.BA4a_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/lh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./lh.BA4a_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5784 nlabel points Performing mapping from target back to the source label 145499 Number of reverse mapping hits = 978 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 6762 mri_label2label: Done PIDs (5291 5296 5302 5308 5314) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.BA4p_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.BA6_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.BA44_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.BA45_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface Waiting for PID 5360 of (5360 5365 5371 5377) to complete... Waiting for PID 5365 of (5360 5365 5371 5377) to complete... Waiting for PID 5371 of (5360 5365 5371 5377) to complete... Waiting for PID 5377 of (5360 5365 5371 5377) to complete... mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.BA4p_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/lh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./lh.BA4p_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4070 nlabel points Performing mapping from target back to the source label 145499 Number of reverse mapping hits = 543 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4613 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.BA6_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/lh.BA6_exvivo.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./lh.BA6_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 13589 nlabel points Performing mapping from target back to the source label 145499 Number of reverse mapping hits = 2318 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 15907 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.BA44_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/lh.BA44_exvivo.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./lh.BA44_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4181 nlabel points Performing mapping from target back to the source label 145499 Number of reverse mapping hits = 810 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4991 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.BA45_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/lh.BA45_exvivo.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./lh.BA45_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3422 nlabel points Performing mapping from target back to the source label 145499 Number of reverse mapping hits = 812 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 4234 mri_label2label: Done PIDs (5360 5365 5371 5377) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.V1_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.V2_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.MT_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface Waiting for PID 5421 of (5421 5426 5432 5438 5444) to complete... Waiting for PID 5426 of (5421 5426 5432 5438 5444) to complete... Waiting for PID 5432 of (5421 5426 5432 5438 5444) to complete... Waiting for PID 5438 of (5421 5426 5432 5438 5444) to complete... Waiting for PID 5444 of (5421 5426 5432 5438 5444) to complete... mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.V1_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/lh.V1_exvivo.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./lh.V1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4641 nlabel points Performing mapping from target back to the source label 145499 Number of reverse mapping hits = 1365 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 6006 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.V2_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/lh.V2_exvivo.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./lh.V2_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8114 nlabel points Performing mapping from target back to the source label 145499 Number of reverse mapping hits = 2722 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 10836 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.MT_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/lh.MT_exvivo.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./lh.MT_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2018 nlabel points Performing mapping from target back to the source label 145499 Number of reverse mapping hits = 605 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2623 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/lh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./lh.entorhinal_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1290 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1290 nlabel points Performing mapping from target back to the source label 145499 Number of reverse mapping hits = 148 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1438 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/lh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./lh.perirhinal_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1199 nlabel points Performing mapping from target back to the source label 145499 Number of reverse mapping hits = 175 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1374 mri_label2label: Done PIDs (5421 5426 5432 5438 5444) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 5493 of (5493 5498 5504 5510 5516) to complete... Waiting for PID 5498 of (5493 5498 5504 5510 5516) to complete... Waiting for PID 5504 of (5493 5498 5504 5510 5516) to complete... Waiting for PID 5510 of (5493 5498 5504 5510 5516) to complete... Waiting for PID 5516 of (5493 5498 5504 5510 5516) to complete... mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/lh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./lh.BA1_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1014 nlabel points Performing mapping from target back to the source label 145499 Number of reverse mapping hits = 149 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1163 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/lh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./lh.BA2_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2092 nlabel points Performing mapping from target back to the source label 145499 Number of reverse mapping hits = 366 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2458 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/lh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./lh.BA3a_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1504 nlabel points Performing mapping from target back to the source label 145499 Number of reverse mapping hits = 104 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1608 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/lh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./lh.BA3b_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1996 nlabel points Performing mapping from target back to the source label 145499 Number of reverse mapping hits = 245 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2241 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/lh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./lh.BA4a_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2319 nlabel points Performing mapping from target back to the source label 145499 Number of reverse mapping hits = 362 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2681 mri_label2label: Done PIDs (5493 5498 5504 5510 5516) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 5562 of (5562 5567 5573 5579) to complete... Waiting for PID 5567 of (5562 5567 5573 5579) to complete... Waiting for PID 5573 of (5562 5567 5573 5579) to complete... Waiting for PID 5579 of (5562 5567 5573 5579) to complete... mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/lh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./lh.BA4p_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1549 nlabel points Performing mapping from target back to the source label 145499 Number of reverse mapping hits = 232 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1781 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/lh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./lh.BA6_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 7035 nlabel points Performing mapping from target back to the source label 145499 Number of reverse mapping hits = 1062 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 8097 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/lh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./lh.BA44_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1912 nlabel points Performing mapping from target back to the source label 145499 Number of reverse mapping hits = 434 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 2346 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/lh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./lh.BA45_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1151 nlabel points Performing mapping from target back to the source label 145499 Number of reverse mapping hits = 336 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1487 mri_label2label: Done PIDs (5562 5567 5573 5579) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 5623 of (5623 5628 5634 5640 5646) to complete... Waiting for PID 5628 of (5623 5628 5634 5640 5646) to complete... Waiting for PID 5634 of (5623 5628 5634 5640 5646) to complete... Waiting for PID 5640 of (5623 5628 5634 5640 5646) to complete... Waiting for PID 5646 of (5623 5628 5634 5640 5646) to complete... mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/lh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./lh.V1_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3405 nlabel points Performing mapping from target back to the source label 145499 Number of reverse mapping hits = 995 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 4400 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/lh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./lh.V2_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3334 nlabel points Performing mapping from target back to the source label 145499 Number of reverse mapping hits = 1317 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 4651 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/lh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./lh.MT_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 513 nlabel points Performing mapping from target back to the source label 145499 Number of reverse mapping hits = 165 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 678 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/lh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./lh.entorhinal_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 470 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 470 nlabel points Performing mapping from target back to the source label 145499 Number of reverse mapping hits = 50 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 520 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/lh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./lh.perirhinal_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 450 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 450 nlabel points Performing mapping from target back to the source label 145499 Number of reverse mapping hits = 96 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 546 mri_label2label: Done PIDs (5623 5628 5634 5640 5646) completed and logs appended. mris_label2annot --s sub-A00039639_ses-DS2_T1w.nii.gz --hemi lh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.entorhinal_exvivo.label --l lh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/label cmdline mris_label2annot --s sub-A00039639_ses-DS2_T1w.nii.gz --hemi lh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.entorhinal_exvivo.label --l lh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose sysname Linux hostname fisicos-ub2 machine x86_64 user fisicos subject sub-A00039639_ses-DS2_T1w.nii.gz hemi lh SUBJECTS_DIR /mnt/disco1/subjects ColorTable /usr/local/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 98451 unhit vertices Writing annot to /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/label/lh.BA_exvivo.annot mris_label2annot --s sub-A00039639_ses-DS2_T1w.nii.gz --hemi lh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/label cmdline mris_label2annot --s sub-A00039639_ses-DS2_T1w.nii.gz --hemi lh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose sysname Linux hostname fisicos-ub2 machine x86_64 user fisicos subject sub-A00039639_ses-DS2_T1w.nii.gz hemi lh SUBJECTS_DIR /mnt/disco1/subjects ColorTable /usr/local/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 116928 unhit vertices Writing annot to /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/label/lh.BA_exvivo.thresh.annot mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.stats -b -a ./lh.BA_exvivo.annot -c ./BA_exvivo.ctab sub-A00039639_ses-DS2_T1w.nii.gz lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/wm.mgz... reading input surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.white... reading input pial surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.pial... reading input white surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 246740 Total vertex volume 243855 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /usr/local/freesurfer/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1642165 mm^3 (det: 1.186303 ) lhCtxGM: 241987.950 242104.000 diff= -116.0 pctdiff=-0.048 rhCtxGM: 249523.742 249044.000 diff= 479.7 pctdiff= 0.192 lhCtxWM: 262629.594 262867.500 diff= -237.9 pctdiff=-0.091 rhCtxWM: 262886.151 263474.500 diff= -588.3 pctdiff=-0.224 SubCortGMVol 63223.000 SupraTentVol 1105646.438 (1101665.000) diff=3981.438 pctdiff=0.360 SupraTentVolNotVent 1084707.438 (1080726.000) diff=3981.438 pctdiff=0.367 BrainSegVol 1270335.000 (1266267.000) diff=4068.000 pctdiff=0.320 BrainSegVolNotVent 1244144.000 (1243497.438) diff=646.562 pctdiff=0.052 BrainSegVolNotVent 1244144.000 CerebellumVol 163234.000 VentChorVol 20939.000 3rd4th5thCSF 5252.000 CSFVol 1184.000, OptChiasmVol 184.000 MaskVol 1745125.000 1291 766 2454 2.379 0.683 0.130 0.031 17 1.5 BA1_exvivo 4439 2874 6953 2.271 0.510 0.122 0.024 45 4.5 BA2_exvivo 1273 865 1190 1.711 0.400 0.136 0.028 12 1.5 BA3a_exvivo 2696 1757 3646 1.897 0.576 0.128 0.028 30 3.3 BA3b_exvivo 2077 1116 2962 2.410 0.490 0.125 0.039 32 3.6 BA4a_exvivo 1749 1084 2588 2.479 0.475 0.111 0.028 14 2.0 BA4p_exvivo 11272 7019 20586 2.582 0.596 0.121 0.033 133 16.0 BA6_exvivo 3110 2071 5617 2.525 0.445 0.124 0.026 33 3.1 BA44_exvivo 3166 2155 5100 2.208 0.416 0.130 0.030 38 3.6 BA45_exvivo 3756 2551 3501 1.418 0.406 0.144 0.032 50 5.0 V1_exvivo 8352 5582 10903 1.901 0.595 0.162 0.039 134 13.5 V2_exvivo 2409 1576 3903 2.431 0.549 0.132 0.023 30 2.2 MT_exvivo 628 443 2030 3.622 0.674 0.106 0.028 5 0.7 perirhinal_exvivo 830 579 2445 3.503 0.693 0.125 0.031 9 0.9 entorhinal_exvivo mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab sub-A00039639_ses-DS2_T1w.nii.gz lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/wm.mgz... reading input surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.white... reading input pial surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.pial... reading input white surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 246740 Total vertex volume 243855 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /usr/local/freesurfer/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1642165 mm^3 (det: 1.186303 ) lhCtxGM: 241987.950 242104.000 diff= -116.0 pctdiff=-0.048 rhCtxGM: 249523.742 249044.000 diff= 479.7 pctdiff= 0.192 lhCtxWM: 262629.594 262867.500 diff= -237.9 pctdiff=-0.091 rhCtxWM: 262886.151 263474.500 diff= -588.3 pctdiff=-0.224 SubCortGMVol 63223.000 SupraTentVol 1105646.438 (1101665.000) diff=3981.438 pctdiff=0.360 SupraTentVolNotVent 1084707.438 (1080726.000) diff=3981.438 pctdiff=0.367 BrainSegVol 1270335.000 (1266267.000) diff=4068.000 pctdiff=0.320 BrainSegVolNotVent 1244144.000 (1243497.438) diff=646.562 pctdiff=0.052 BrainSegVolNotVent 1244144.000 CerebellumVol 163234.000 VentChorVol 20939.000 3rd4th5thCSF 5252.000 CSFVol 1184.000, OptChiasmVol 184.000 MaskVol 1745125.000 901 504 1763 2.459 0.689 0.131 0.032 12 1.1 BA1_exvivo 2083 1325 3256 2.226 0.507 0.115 0.022 21 1.9 BA2_exvivo 1094 753 979 1.662 0.353 0.148 0.029 12 1.4 BA3a_exvivo 1760 1158 1897 1.608 0.344 0.115 0.024 16 1.8 BA3b_exvivo 2054 1130 2976 2.441 0.483 0.115 0.036 26 3.1 BA4a_exvivo 1410 866 1982 2.472 0.481 0.109 0.027 10 1.5 BA4p_exvivo 6270 3799 11439 2.595 0.651 0.124 0.036 82 9.7 BA6_exvivo 1943 1292 3751 2.583 0.434 0.124 0.025 21 1.9 BA44_exvivo 1333 906 2530 2.270 0.405 0.137 0.031 20 1.7 BA45_exvivo 3978 2722 3862 1.439 0.411 0.143 0.032 51 5.3 V1_exvivo 4337 2838 5255 1.818 0.543 0.170 0.043 76 7.7 V2_exvivo 639 433 1125 2.653 0.596 0.144 0.027 9 0.6 MT_exvivo 300 225 985 3.659 0.523 0.095 0.017 1 0.2 perirhinal_exvivo 469 328 1311 3.636 0.568 0.125 0.030 4 0.6 entorhinal_exvivo #-------------------------------------------- #@# BA_exvivo Labels rh Fri Oct 11 03:22:31 -03 2019 mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.BA1_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.BA2_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.BA3a_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.BA3b_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.BA4a_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface Waiting for PID 5743 of (5743 5748 5754 5760 5766) to complete... Waiting for PID 5748 of (5743 5748 5754 5760 5766) to complete... Waiting for PID 5754 of (5743 5748 5754 5760 5766) to complete... Waiting for PID 5760 of (5743 5748 5754 5760 5766) to complete... Waiting for PID 5766 of (5743 5748 5754 5760 5766) to complete... mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.BA1_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/rh.BA1_exvivo.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./rh.BA1_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3962 nlabel points Performing mapping from target back to the source label 147557 Number of reverse mapping hits = 666 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4628 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.BA2_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/rh.BA2_exvivo.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./rh.BA2_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6687 nlabel points Performing mapping from target back to the source label 147557 Number of reverse mapping hits = 769 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 7456 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.BA3a_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/rh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./rh.BA3a_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3980 nlabel points Performing mapping from target back to the source label 147557 Number of reverse mapping hits = 293 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4273 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.BA3b_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/rh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./rh.BA3b_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4522 nlabel points Performing mapping from target back to the source label 147557 Number of reverse mapping hits = 585 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 5107 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.BA4a_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/rh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./rh.BA4a_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5747 nlabel points Performing mapping from target back to the source label 147557 Number of reverse mapping hits = 753 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 6500 mri_label2label: Done PIDs (5743 5748 5754 5760 5766) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.BA4p_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.BA6_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.BA44_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.BA45_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface Waiting for PID 5812 of (5812 5817 5823 5829) to complete... Waiting for PID 5817 of (5812 5817 5823 5829) to complete... Waiting for PID 5823 of (5812 5817 5823 5829) to complete... Waiting for PID 5829 of (5812 5817 5823 5829) to complete... mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.BA4p_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/rh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./rh.BA4p_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4473 nlabel points Performing mapping from target back to the source label 147557 Number of reverse mapping hits = 566 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 5039 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.BA6_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/rh.BA6_exvivo.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./rh.BA6_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 12256 nlabel points Performing mapping from target back to the source label 147557 Number of reverse mapping hits = 1987 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 14243 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.BA44_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/rh.BA44_exvivo.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./rh.BA44_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6912 nlabel points Performing mapping from target back to the source label 147557 Number of reverse mapping hits = 1480 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 8392 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.BA45_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/rh.BA45_exvivo.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./rh.BA45_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5355 nlabel points Performing mapping from target back to the source label 147557 Number of reverse mapping hits = 1479 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 6834 mri_label2label: Done PIDs (5812 5817 5823 5829) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.V1_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.V2_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.MT_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface Waiting for PID 5874 of (5874 5879 5885 5891 5897) to complete... Waiting for PID 5879 of (5874 5879 5885 5891 5897) to complete... Waiting for PID 5885 of (5874 5879 5885 5891 5897) to complete... Waiting for PID 5891 of (5874 5879 5885 5891 5897) to complete... Waiting for PID 5897 of (5874 5879 5885 5891 5897) to complete... mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.V1_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/rh.V1_exvivo.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./rh.V1_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4727 nlabel points Performing mapping from target back to the source label 147557 Number of reverse mapping hits = 1540 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 6267 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.V2_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/rh.V2_exvivo.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./rh.V2_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8016 nlabel points Performing mapping from target back to the source label 147557 Number of reverse mapping hits = 3179 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 11195 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.MT_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/rh.MT_exvivo.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./rh.MT_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1932 nlabel points Performing mapping from target back to the source label 147557 Number of reverse mapping hits = 349 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2281 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/rh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./rh.entorhinal_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1038 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1038 nlabel points Performing mapping from target back to the source label 147557 Number of reverse mapping hits = 243 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1281 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/rh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./rh.perirhinal_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 752 nlabel points Performing mapping from target back to the source label 147557 Number of reverse mapping hits = 195 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 947 mri_label2label: Done PIDs (5874 5879 5885 5891 5897) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 5946 of (5946 5951 5957 5962 5969) to complete... Waiting for PID 5951 of (5946 5951 5957 5962 5969) to complete... Waiting for PID 5957 of (5946 5951 5957 5962 5969) to complete... Waiting for PID 5962 of (5946 5951 5957 5962 5969) to complete... Waiting for PID 5969 of (5946 5951 5957 5962 5969) to complete... mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/rh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./rh.BA1_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 876 nlabel points Performing mapping from target back to the source label 147557 Number of reverse mapping hits = 196 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 1072 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/rh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./rh.BA2_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2688 nlabel points Performing mapping from target back to the source label 147557 Number of reverse mapping hits = 285 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2973 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/rh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./rh.BA3a_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1698 nlabel points Performing mapping from target back to the source label 147557 Number of reverse mapping hits = 88 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1786 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/rh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./rh.BA3b_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2183 nlabel points Performing mapping from target back to the source label 147557 Number of reverse mapping hits = 298 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2481 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/rh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./rh.BA4a_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1388 nlabel points Performing mapping from target back to the source label 147557 Number of reverse mapping hits = 81 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1469 mri_label2label: Done PIDs (5946 5951 5957 5962 5969) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 6015 of (6015 6020 6026 6032) to complete... Waiting for PID 6020 of (6015 6020 6026 6032) to complete... Waiting for PID 6026 of (6015 6020 6026 6032) to complete... Waiting for PID 6032 of (6015 6020 6026 6032) to complete... mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/rh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./rh.BA4p_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1489 nlabel points Performing mapping from target back to the source label 147557 Number of reverse mapping hits = 246 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1735 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/rh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./rh.BA6_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6959 nlabel points Performing mapping from target back to the source label 147557 Number of reverse mapping hits = 1036 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 7995 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/rh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./rh.BA44_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1012 nlabel points Performing mapping from target back to the source label 147557 Number of reverse mapping hits = 205 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1217 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/rh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./rh.BA45_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1178 nlabel points Performing mapping from target back to the source label 147557 Number of reverse mapping hits = 156 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1334 mri_label2label: Done PIDs (6015 6020 6026 6032) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 6076 of (6076 6081 6087 6093 6099) to complete... Waiting for PID 6081 of (6076 6081 6087 6093 6099) to complete... Waiting for PID 6087 of (6076 6081 6087 6093 6099) to complete... Waiting for PID 6093 of (6076 6081 6087 6093 6099) to complete... Waiting for PID 6099 of (6076 6081 6087 6093 6099) to complete... mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/rh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./rh.V1_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3232 nlabel points Performing mapping from target back to the source label 147557 Number of reverse mapping hits = 990 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 4222 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/rh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./rh.V2_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3437 nlabel points Performing mapping from target back to the source label 147557 Number of reverse mapping hits = 1550 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 4987 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/rh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./rh.MT_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 268 nlabel points Performing mapping from target back to the source label 147557 Number of reverse mapping hits = 28 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 296 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/rh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./rh.entorhinal_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 694 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 694 nlabel points Performing mapping from target back to the source label 147557 Number of reverse mapping hits = 157 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 851 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/disco1/subjects/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject sub-A00039639_ses-DS2_T1w.nii.gz --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /mnt/disco1/subjects/fsaverage/label/rh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-A00039639_ses-DS2_T1w.nii.gz trglabel = ./rh.perirhinal_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/disco1/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 291 points in source label. Starting surface-based mapping Reading source registration /mnt/disco1/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.white Reading target registration /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 291 nlabel points Performing mapping from target back to the source label 147557 Number of reverse mapping hits = 64 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 355 mri_label2label: Done PIDs (6076 6081 6087 6093 6099) completed and logs appended. mris_label2annot --s sub-A00039639_ses-DS2_T1w.nii.gz --hemi rh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.entorhinal_exvivo.label --l rh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/label cmdline mris_label2annot --s sub-A00039639_ses-DS2_T1w.nii.gz --hemi rh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.entorhinal_exvivo.label --l rh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose sysname Linux hostname fisicos-ub2 machine x86_64 user fisicos subject sub-A00039639_ses-DS2_T1w.nii.gz hemi rh SUBJECTS_DIR /mnt/disco1/subjects ColorTable /usr/local/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 100363 unhit vertices Writing annot to /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/label/rh.BA_exvivo.annot mris_label2annot --s sub-A00039639_ses-DS2_T1w.nii.gz --hemi rh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/label cmdline mris_label2annot --s sub-A00039639_ses-DS2_T1w.nii.gz --hemi rh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose sysname Linux hostname fisicos-ub2 machine x86_64 user fisicos subject sub-A00039639_ses-DS2_T1w.nii.gz hemi rh SUBJECTS_DIR /mnt/disco1/subjects ColorTable /usr/local/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 121040 unhit vertices Writing annot to /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/label/rh.BA_exvivo.thresh.annot mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.stats -b -a ./rh.BA_exvivo.annot -c ./BA_exvivo.ctab sub-A00039639_ses-DS2_T1w.nii.gz rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/mri/wm.mgz... reading input surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.white... reading input pial surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.pial... reading input white surface /mnt/disco1/subjects/sub-A00039639_ses-DS2_T1w.nii.gz/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 254180 Total vertex volume 250902 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /usr/local/freesurfer/average/colortable_BA.txt) Segmentation fault (core dumped) Linux fisicos-ub2 5.0.0-29-generic #31~18.04.1-Ubuntu SMP Thu Sep 12 18:29:21 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-A00039639_ses-DS2_T1w.nii.gz exited with ERRORS at Fri Oct 11 03:23:13 -03 2019 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting