Thu Oct 3 10:12:00 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine /usr/local/freesurfer/bin/recon-all -subject S131032017_Supine -i /mnt/8E74B1C874B1B377/PhD/Scans/scans_S131032017/T1_MPRAGE_0P8ISO_S7_DIS3D_0010/20170331145854_t1_mprage_0p8iso_S7_DIS3D_c32_Crop_1_restore.nii.gz -all -parallel subjid S131032017_Supine setenv SUBJECTS_DIR /mnt/8E74B1C874B1B377/FreeSurfer/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 zappst-Q170M-C 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 1024 memorylocked 16384 kbytes maxproc 128019 maxlocks unlimited maxsignal 128019 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 32820844 6746492 491008 1569924 25583344 24039772 Swap: 33554428 0 33554428 ######################################## 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: 2019/10/03-09:12:00-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: zappst Machine: zappst-Q170M-C 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: 2019/10/03-09:12:00-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: zappst Machine: zappst-Q170M-C 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: 2019/10/03-09:12:00-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: zappst Machine: zappst-Q170M-C Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/10/03-09:12:00-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: zappst Machine: zappst-Q170M-C Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/03-09:12:00-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: zappst Machine: zappst-Q170M-C Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/03-09:12:00-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: zappst Machine: zappst-Q170M-C Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/10/03-09:12:00-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: zappst Machine: zappst-Q170M-C Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/10/03-09:12:00-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: zappst Machine: zappst-Q170M-C Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/10/03-09:12:00-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: zappst Machine: zappst-Q170M-C Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/10/03-09:12:00-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: zappst Machine: zappst-Q170M-C Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/10/03-09:12:00-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: zappst Machine: zappst-Q170M-C Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/10/03-09:12:00-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: zappst Machine: zappst-Q170M-C Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/03-09:12:00-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: zappst Machine: zappst-Q170M-C Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/03-09:12:00-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: zappst Machine: zappst-Q170M-C Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/10/03-09:12:00-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: zappst Machine: zappst-Q170M-C Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/03-09:12:00-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: zappst Machine: zappst-Q170M-C Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/03-09:12:00-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: zappst Machine: zappst-Q170M-C Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/03-09:12:00-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: zappst Machine: zappst-Q170M-C Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/03-09:12:00-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: zappst Machine: zappst-Q170M-C Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/03-09:12:00-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: zappst Machine: zappst-Q170M-C Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/03-09:12:00-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: zappst Machine: zappst-Q170M-C Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/10/03-09:12:00-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: zappst Machine: zappst-Q170M-C Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/03-09:12:00-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: zappst Machine: zappst-Q170M-C Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/03-09:12:00-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: zappst Machine: zappst-Q170M-C Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/03-09:12:00-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: zappst Machine: zappst-Q170M-C Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/10/03-09:12:00-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: zappst Machine: zappst-Q170M-C Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/03-09:12:00-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: zappst Machine: zappst-Q170M-C Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2019/10/03-09:12:00-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: zappst Machine: zappst-Q170M-C Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/03-09:12:00-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: zappst Machine: zappst-Q170M-C Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/03-09:12:00-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: zappst Machine: zappst-Q170M-C Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/03-09:12:00-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: zappst Machine: zappst-Q170M-C Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/03-09:12:00-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: zappst Machine: zappst-Q170M-C 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: 2019/10/03-09:12:00-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: zappst Machine: zappst-Q170M-C 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: 2019/10/03-09:12:00-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: zappst Machine: zappst-Q170M-C Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/03-09:12:00-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: zappst Machine: zappst-Q170M-C Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/03-09:12:00-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: zappst Machine: zappst-Q170M-C Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/03-09:12:00-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: zappst Machine: zappst-Q170M-C Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/03-09:12:00-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: zappst Machine: zappst-Q170M-C Platform: Linux PlatformVersion: 5.0.0-29-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/10/03-09:12:00-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: zappst Machine: zappst-Q170M-C 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/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine mri_convert /mnt/8E74B1C874B1B377/PhD/Scans/scans_S131032017/T1_MPRAGE_0P8ISO_S7_DIS3D_0010/20170331145854_t1_mprage_0p8iso_S7_DIS3D_c32_Crop_1_restore.nii.gz /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/orig/001.mgz mri_convert.bin /mnt/8E74B1C874B1B377/PhD/Scans/scans_S131032017/T1_MPRAGE_0P8ISO_S7_DIS3D_0010/20170331145854_t1_mprage_0p8iso_S7_DIS3D_c32_Crop_1_restore.nii.gz /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /mnt/8E74B1C874B1B377/PhD/Scans/scans_S131032017/T1_MPRAGE_0P8ISO_S7_DIS3D_0010/20170331145854_t1_mprage_0p8iso_S7_DIS3D_c32_Crop_1_restore.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Thu Oct 3 10:12:06 BST 2019 Found 1 runs /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/orig/001.mgz /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/rawavg.mgz /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine mri_convert /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/rawavg.mgz /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/orig.mgz --conform mri_convert.bin /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/rawavg.mgz /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/rawavg.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/orig.mgz... mri_add_xform_to_header -c /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/transforms/talairach.xfm /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/orig.mgz /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Oct 3 10:12:16 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 zappst-Q170M-C 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 3 10:12:16 BST 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.9619 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.9619/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.9619/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.9619/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Oct 3 10:12:18 BST 2019 nu_correct -clobber ./tmp.mri_nu_correct.mni.9619/nu0.mnc ./tmp.mri_nu_correct.mni.9619/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.9619/0/ -iterations 1000 -distance 50 [zappst@zappst-Q170M-C:/mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/] [2019-10-03 10:12:18] 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.9619/0/ ./tmp.mri_nu_correct.mni.9619/nu0.mnc ./tmp.mri_nu_correct.mni.9619/nu1.imp 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./tmp.mri_nu_correct.mni.9619/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.9619/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 3 10:13:15 BST 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 3 10:13:15 BST 2019 Ended at Thu Oct 3 10:13:36 BST 2019 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Thu Oct 3 10:13:38 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.8298, pval=0.9628 >= threshold=0.0050) awk -f /usr/local/freesurfer/bin/extract_talairach_avi_QA.awk /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/transforms/talairach_avi.log tal_QC_AZS /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/transforms/talairach_avi.log TalAviQA: 0.96265 z-score: -3 #-------------------------------------------- #@# Nu Intensity Correction Thu Oct 3 10:13:38 BST 2019 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 zappst-Q170M-C 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 3 10:13:38 BST 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.11757 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.11757/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.11757/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.11757/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Oct 3 10:13:40 BST 2019 nu_correct -clobber ./tmp.mri_nu_correct.mni.11757/nu0.mnc ./tmp.mri_nu_correct.mni.11757/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.11757/0/ [zappst@zappst-Q170M-C:/mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/] [2019-10-03 10:13:40] 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.11757/0/ ./tmp.mri_nu_correct.mni.11757/nu0.mnc ./tmp.mri_nu_correct.mni.11757/nu1.imp Processing:.................................................................Done 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-------------------------------------------------------- Iteration 2 Thu Oct 3 10:14:13 BST 2019 nu_correct -clobber ./tmp.mri_nu_correct.mni.11757/nu1.mnc ./tmp.mri_nu_correct.mni.11757/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.11757/1/ [zappst@zappst-Q170M-C:/mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/] [2019-10-03 10:14:13] 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.11757/1/ ./tmp.mri_nu_correct.mni.11757/nu1.mnc ./tmp.mri_nu_correct.mni.11757/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done 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Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 19 CV of field change: 0.000970396 mri_binarize --i ./tmp.mri_nu_correct.mni.11757/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.11757/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.11757/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.11757/ones.mgz sysname Linux hostname zappst-Q170M-C machine x86_64 user zappst input ./tmp.mri_nu_correct.mni.11757/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.11757/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.11757/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.11757/sum.junk --avgwf ./tmp.mri_nu_correct.mni.11757/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.11757/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.11757/sum.junk --avgwf ./tmp.mri_nu_correct.mni.11757/input.mean.dat sysname Linux hostname zappst-Q170M-C machine x86_64 user zappst UseRobust 0 Loading ./tmp.mri_nu_correct.mni.11757/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.11757/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.11757/ones.mgz --i ./tmp.mri_nu_correct.mni.11757/nu2.mnc --sum ./tmp.mri_nu_correct.mni.11757/sum.junk --avgwf ./tmp.mri_nu_correct.mni.11757/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.11757/ones.mgz --i ./tmp.mri_nu_correct.mni.11757/nu2.mnc --sum ./tmp.mri_nu_correct.mni.11757/sum.junk --avgwf ./tmp.mri_nu_correct.mni.11757/output.mean.dat sysname Linux hostname zappst-Q170M-C machine x86_64 user zappst UseRobust 0 Loading ./tmp.mri_nu_correct.mni.11757/ones.mgz Loading ./tmp.mri_nu_correct.mni.11757/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.11757/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.11757/nu2.mnc ./tmp.mri_nu_correct.mni.11757/nu2.mnc mul 1.03983933761206946757 Saving result to './tmp.mri_nu_correct.mni.11757/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.11757/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.11757/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.11757/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 5 seconds. mapping (10, 118) to ( 3, 110) Thu Oct 3 10:15:02 BST 2019 mri_nu_correct.mni done mri_add_xform_to_header -c /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Thu Oct 3 10:15:02 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 1.07634 0.00126 -0.04671 -0.73734; 0.01290 1.11956 0.10873 -55.70473; 0.03567 -0.17844 1.26290 21.78522; 0.00000 0.00000 0.00000 1.00000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 14 Starting OpenSpline(): npoints = 14 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 109 gm peak at 76 (76), valley at 37 (37) csf peak at 38, setting threshold to 63 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 72 (72), valley at 36 (36) csf peak at 36, setting threshold to 60 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 15 seconds. #-------------------------------------------- #@# Skull Stripping Thu Oct 3 10:16:18 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri mri_em_register -rusage /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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=35.0 skull bounding box = (45, 44, 20) --> (205, 204, 231) using (98, 97, 126) as brain centroid... mean wm in atlas = 108, using box (78,77,100) --> (117, 116,152) to find MRI wm before smoothing, mri peak at 99 robust fit to distribution - 99 +- 7.7 after smoothing, mri peak at 99, scaling input intensities by 1.091 scaling channel 0 by 1.09091 initial log_p = -4.565 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.598418 @ (-9.091, -9.091, -9.091) max log p = -4.535900 @ (4.545, -4.545, -13.636) max log p = -4.428486 @ (2.273, 2.273, 6.818) max log p = -4.428486 @ (0.000, 0.000, 0.000) max log p = -4.407611 @ (0.568, 1.705, -0.568) max log p = -4.407611 @ (0.000, 0.000, 0.000) Found translation: (-1.7, -9.7, -16.5): log p = -4.408 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.324, old_max_log_p =-4.408 (thresh=-4.4) 1.23625 0.00000 0.00000 -31.60903; 0.00000 1.22545 0.04031 -33.44992; 0.00000 0.03469 0.93429 -9.78196; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.324, old_max_log_p =-4.324 (thresh=-4.3) 1.23625 0.00000 0.00000 -31.60903; 0.00000 1.22545 0.04031 -33.44992; 0.00000 0.03469 0.93429 -9.78196; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.302, old_max_log_p =-4.324 (thresh=-4.3) 1.16508 0.00214 0.05771 -30.05636; -0.00280 1.20216 0.07175 -33.75267; -0.08384 -0.00270 0.96547 2.17009; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.296, old_max_log_p =-4.302 (thresh=-4.3) 1.16508 0.00214 0.05771 -30.05636; 0.00269 1.19977 0.00845 -26.26321; -0.08542 0.07735 0.98624 -9.47872; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.291, old_max_log_p =-4.296 (thresh=-4.3) 1.16508 0.00214 0.05771 -30.05636; -0.00290 1.20226 0.07294 -33.77724; -0.08381 -0.00126 0.96514 1.96655; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.291, old_max_log_p =-4.291 (thresh=-4.3) 1.16508 0.00214 0.05771 -30.05636; -0.00290 1.20226 0.07294 -33.77724; -0.08381 -0.00126 0.96514 1.96655; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.280, old_max_log_p =-4.291 (thresh=-4.3) 1.15926 0.02204 0.07444 -33.22556; -0.02067 1.20615 0.05645 -30.02488; -0.10284 0.01808 0.96171 2.56451; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.274, old_max_log_p =-4.280 (thresh=-4.3) 1.15819 0.04170 0.06754 -34.97526; -0.04053 1.20856 0.06335 -28.24484; -0.09329 0.00838 0.96292 2.56352; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 8 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.274, old_max_log_p =-4.274 (thresh=-4.3) 1.15819 0.04170 0.06754 -34.97526; -0.04053 1.20856 0.06335 -28.24484; -0.09329 0.00838 0.96292 2.56352; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3243 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.15819 0.04170 0.06754 -34.97526; -0.04053 1.20856 0.06335 -28.24484; -0.09329 0.00838 0.96292 2.56352; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 1.15819 0.04170 0.06754 -34.97526; -0.04053 1.20856 0.06335 -28.24484; -0.09329 0.00838 0.96292 2.56352; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.15819 0.04170 0.06754 -34.97526; -0.04053 1.20856 0.06335 -28.24484; -0.09329 0.00838 0.96292 2.56352; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -4.274 (old=-4.565) transform before final EM align: 1.15819 0.04170 0.06754 -34.97526; -0.04053 1.20856 0.06335 -28.24484; -0.09329 0.00838 0.96292 2.56352; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 364799 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.15819 0.04170 0.06754 -34.97526; -0.04053 1.20856 0.06335 -28.24484; -0.09329 0.00838 0.96292 2.56352; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 1.15819 0.04170 0.06754 -34.97526; -0.04053 1.20856 0.06335 -28.24484; -0.09329 0.00838 0.96292 2.56352; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 013: -log(p) = 4.7 tol 0.000000 final transform: 1.15819 0.04170 0.06754 -34.97526; -0.04053 1.20856 0.06335 -28.24484; -0.09329 0.00838 0.96292 2.56352; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 1421.309831 mri_em_register stimesec 3.192980 mri_em_register ru_maxrss 614620 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 161778 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 148912 mri_em_register ru_oublock 0 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 735 mri_em_register ru_nivcsw 290179 registration took 6 minutes and 37 seconds. mri_watershed -rusage /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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=127 y=114 z=130 r=77 first estimation of the main basin volume: 1919202 voxels Looking for seedpoints 2 found in the cerebellum 17 found in the rest of the brain global maximum in x=108, y=107, z=94, Imax=255 CSF=17, 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=9255674988 voxels, voxel volume =1.000 = 9255674988 mmm3 = 9255674.880 cm3 done. PostAnalyze...Basin Prior 778 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=126,y=124, z=121, r=10261 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=8 , nb = 44864 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=10 , nb = -1033854605 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=12 , nb = 1102326297 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=8 , nb = -1112557835 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=8 , nb = 1044887980 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=23 , nb = 1079199808 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 8, 14, 42, 66 after analyzing : 8, 32, 42, 40 RIGHT_CER before analyzing : 10, 17, 48, 82 after analyzing : 10, 37, 48, 48 LEFT_CER before analyzing : 12, 19, 43, 73 after analyzing : 12, 35, 43, 44 RIGHT_BRAIN before analyzing : 8, 14, 41, 65 after analyzing : 8, 32, 41, 40 LEFT_BRAIN before analyzing : 8, 14, 41, 66 after analyzing : 8, 32, 41, 40 OTHER before analyzing : 23, 46, 59, 70 after analyzing : 23, 54, 59, 58 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...61 iterations *********************VALIDATION********************* curvature mean = -0.012, std = 0.011 curvature mean = 70.997, std = 9.043 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 2.43, sigma = 3.78 after rotation: sse = 2.43, sigma = 3.78 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 2.51, its var is 3.21 before Erosion-Dilatation 0.17% 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 = 1749689 voxels, voxel volume = 1.000 mm3 = 1749689 mmm3 = 1749.689 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 26.199702 mri_watershed stimesec 0.262195 mri_watershed ru_maxrss 840688 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 208503 mri_watershed ru_majflt 0 mri_watershed ru_nswap 0 mri_watershed ru_inblock 0 mri_watershed ru_oublock 0 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 3370 mri_watershed ru_nivcsw 9316 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Thu Oct 3 10:23:11 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri mri_em_register -rusage /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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=14.0 skull bounding box = (60, 63, 38) --> (193, 179, 217) using (104, 102, 128) as brain centroid... mean wm in atlas = 107, using box (88,88,106) --> (120, 116,150) to find MRI wm before smoothing, mri peak at 97 robust fit to distribution - 98 +- 6.4 after smoothing, mri peak at 98, scaling input intensities by 1.092 scaling channel 0 by 1.09184 initial log_p = -4.294 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.295785 @ (-9.091, -9.091, -9.091) max log p = -4.109490 @ (4.545, 4.545, -4.545) max log p = -4.011447 @ (2.273, 6.818, -2.273) max log p = -3.992598 @ (1.136, -5.682, 1.136) max log p = -3.992598 @ (0.000, 0.000, 0.000) max log p = -3.983679 @ (0.852, 1.989, -2.557) Found translation: (-0.3, -1.4, -17.3): log p = -3.984 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.952, old_max_log_p =-3.984 (thresh=-4.0) 1.07500 0.00000 0.00000 -9.81069; 0.00000 1.07500 0.00000 -17.97375; 0.00000 0.00000 0.92500 -8.12151; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.935, old_max_log_p =-3.952 (thresh=-3.9) 1.07500 0.00000 0.00000 -9.81069; 0.00000 1.06580 0.12074 -31.62276; 0.00000 -0.14032 0.91709 10.76658; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.935, old_max_log_p =-3.935 (thresh=-3.9) 1.07500 0.00000 0.00000 -9.81069; 0.00000 1.06580 0.12074 -31.62276; 0.00000 -0.14032 0.91709 10.76658; 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=-3.876, old_max_log_p =-3.935 (thresh=-3.9) 1.05312 -0.02717 -0.03313 2.25829; 0.03647 1.05980 0.15156 -39.14669; 0.03207 -0.18046 0.92901 12.29547; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.865, old_max_log_p =-3.876 (thresh=-3.9) 1.07287 -0.02768 -0.03375 -0.07568; 0.03578 1.03993 0.14872 -36.17601; 0.03207 -0.18046 0.92901 12.29547; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.865, old_max_log_p =-3.865 (thresh=-3.9) 1.07287 -0.02768 -0.03375 -0.07568; 0.03578 1.03993 0.14872 -36.17601; 0.03207 -0.18046 0.92901 12.29547; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.857, old_max_log_p =-3.865 (thresh=-3.9) 1.07505 -0.03624 -0.03510 0.90943; 0.04484 1.03816 0.15604 -37.49881; 0.03174 -0.18874 0.92668 13.67814; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.856, old_max_log_p =-3.857 (thresh=-3.9) 1.07379 -0.03619 -0.03506 1.05689; 0.04463 1.04088 0.14862 -37.39440; 0.03214 -0.18045 0.92901 12.28946; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2830 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.07379 -0.03619 -0.03506 1.05689; 0.04463 1.04088 0.14862 -37.39440; 0.03214 -0.18045 0.92901 12.28946; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.07379 -0.03619 -0.03506 1.05689; 0.04463 1.04088 0.14862 -37.39440; 0.03214 -0.18045 0.92901 12.28946; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.07379 -0.03619 -0.03506 1.05689; 0.04463 1.04088 0.14862 -37.39440; 0.03214 -0.18045 0.92901 12.28946; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.856 (old=-4.294) transform before final EM align: 1.07379 -0.03619 -0.03506 1.05689; 0.04463 1.04088 0.14862 -37.39440; 0.03214 -0.18045 0.92901 12.28946; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 315557 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.07379 -0.03619 -0.03506 1.05689; 0.04463 1.04088 0.14862 -37.39440; 0.03214 -0.18045 0.92901 12.28946; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 1.07379 -0.03619 -0.03506 1.05689; 0.04463 1.04088 0.14862 -37.39440; 0.03214 -0.18045 0.92901 12.28946; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 012: -log(p) = 4.2 tol 0.000000 final transform: 1.07379 -0.03619 -0.03506 1.05689; 0.04463 1.04088 0.14862 -37.39440; 0.03214 -0.18045 0.92901 12.28946; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 1054.221494 mri_em_register stimesec 2.465587 mri_em_register ru_maxrss 604276 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 166556 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 0 mri_em_register ru_oublock 0 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 499 mri_em_register ru_nivcsw 240262 registration took 4 minutes and 48 seconds. #-------------------------------------- #@# CA Normalize Thu Oct 3 10:27:58 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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=12.0 skull bounding box = (60, 62, 38) --> (193, 180, 217) using (104, 101, 128) as brain centroid... mean wm in atlas = 107, using box (88,87,106) --> (120, 115,150) to find MRI wm before smoothing, mri peak at 97 robust fit to distribution - 98 +- 6.7 after smoothing, mri peak at 98, scaling input intensities by 1.092 scaling channel 0 by 1.09184 using 246344 sample points... INFO: compute sample coordinates transform 1.07379 -0.03619 -0.03506 1.05689; 0.04463 1.04088 0.14862 -37.39440; 0.03214 -0.18045 0.92901 12.28946; 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 (122, 64, 38) --> (187, 173, 215) Left_Cerebral_White_Matter: limiting intensities to 99.0 --> 132.0 1 of 358 (0.3%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (64, 67, 38) --> (127, 176, 216) Right_Cerebral_White_Matter: limiting intensities to 106.0 --> 132.0 95 of 348 (27.3%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (126, 150, 67) --> (172, 189, 125) Left_Cerebellum_White_Matter: limiting intensities to 98.0 --> 132.0 0 of 10 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (85, 150, 66) --> (125, 190, 127) Right_Cerebellum_White_Matter: limiting intensities to 106.0 --> 132.0 0 of 15 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (110, 138, 106) --> (143, 206, 138) Brain_Stem: limiting intensities to 118.0 --> 132.0 10 of 11 (90.9%) samples deleted using 742 total control points for intensity normalization... bias field = 0.930 +- 0.063 1 of 636 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (122, 64, 38) --> (187, 173, 215) Left_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0 0 of 631 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (64, 67, 38) --> (127, 176, 216) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 118.0 2 of 699 (0.3%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (126, 150, 67) --> (172, 189, 125) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 17 of 47 (36.2%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (85, 150, 66) --> (125, 190, 127) Right_Cerebellum_White_Matter: limiting intensities to 94.0 --> 132.0 36 of 60 (60.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (110, 138, 106) --> (143, 206, 138) Brain_Stem: limiting intensities to 88.0 --> 132.0 17 of 40 (42.5%) samples deleted using 1477 total control points for intensity normalization... bias field = 1.029 +- 0.069 8 of 1396 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (122, 64, 38) --> (187, 173, 215) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 6 of 739 (0.8%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (64, 67, 38) --> (127, 176, 216) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 127.0 1 of 776 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (126, 150, 67) --> (172, 189, 125) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 53 of 64 (82.8%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (85, 150, 66) --> (125, 190, 127) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 48 of 71 (67.6%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (110, 138, 106) --> (143, 206, 138) Brain_Stem: limiting intensities to 88.0 --> 132.0 45 of 111 (40.5%) samples deleted using 1761 total control points for intensity normalization... bias field = 1.024 +- 0.075 4 of 1575 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 7 seconds. #-------------------------------------- #@# CA Reg Thu Oct 3 10:29:06 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri mri_ca_register -rusage /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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) = 1.07 (predicted orig area = 7.5) 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=0.983, neg=0, invalid=762 0001: dt=295.936000, rms=0.880 (10.510%), neg=0, invalid=762 0002: dt=272.919766, rms=0.844 (4.043%), neg=0, invalid=762 0003: dt=193.969231, rms=0.834 (1.229%), neg=0, invalid=762 0004: dt=369.920000, rms=0.826 (0.892%), neg=0, invalid=762 0005: dt=140.560748, rms=0.822 (0.572%), neg=0, invalid=762 0006: dt=517.888000, rms=0.816 (0.742%), neg=0, invalid=762 0007: dt=129.472000, rms=0.813 (0.316%), neg=0, invalid=762 0008: dt=1479.680000, rms=0.805 (0.967%), neg=0, invalid=762 0009: dt=129.472000, rms=0.802 (0.449%), neg=0, invalid=762 0010: dt=443.904000, rms=0.800 (0.136%), neg=0, invalid=762 0011: dt=443.904000, rms=0.800 (-0.279%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.801, neg=0, invalid=762 0012: dt=129.472000, rms=0.799 (0.283%), neg=0, invalid=762 0013: dt=295.936000, rms=0.798 (0.119%), neg=0, invalid=762 0014: dt=295.936000, rms=0.796 (0.228%), neg=0, invalid=762 0015: dt=295.936000, rms=0.795 (0.205%), neg=0, invalid=762 0016: dt=295.936000, rms=0.794 (0.113%), neg=0, invalid=762 0017: dt=295.936000, rms=0.792 (0.198%), neg=0, invalid=762 0018: dt=295.936000, rms=0.789 (0.357%), neg=0, invalid=762 0019: dt=295.936000, rms=0.787 (0.295%), neg=0, invalid=762 0020: dt=295.936000, rms=0.786 (0.182%), neg=0, invalid=762 0021: dt=295.936000, rms=0.784 (0.254%), neg=0, invalid=762 0022: dt=295.936000, rms=0.782 (0.211%), neg=0, invalid=762 0023: dt=295.936000, rms=0.780 (0.199%), neg=0, invalid=762 0024: dt=295.936000, rms=0.779 (0.150%), neg=0, invalid=762 0025: dt=295.936000, rms=0.777 (0.224%), neg=0, invalid=762 0026: dt=295.936000, rms=0.776 (0.159%), neg=0, invalid=762 0027: dt=295.936000, rms=0.775 (0.104%), neg=0, invalid=762 0028: dt=295.936000, rms=0.774 (0.121%), neg=0, invalid=762 0029: dt=295.936000, rms=0.773 (0.157%), neg=0, invalid=762 0030: dt=295.936000, rms=0.772 (0.164%), neg=0, invalid=762 0031: dt=295.936000, rms=0.771 (0.088%), neg=0, invalid=762 0032: dt=295.936000, rms=0.771 (0.079%), neg=0, invalid=762 0033: dt=295.936000, rms=0.770 (0.066%), neg=0, invalid=762 0034: dt=295.936000, rms=0.770 (-0.083%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.776, neg=0, invalid=762 0035: dt=74.269044, rms=0.772 (0.522%), neg=0, invalid=762 0036: dt=331.776000, rms=0.764 (1.052%), neg=0, invalid=762 0037: dt=125.407595, rms=0.758 (0.820%), neg=0, invalid=762 0038: dt=103.680000, rms=0.753 (0.646%), neg=0, invalid=762 0039: dt=103.652174, rms=0.751 (0.279%), neg=0, invalid=762 0040: dt=188.631579, rms=0.747 (0.570%), neg=0, invalid=762 0041: dt=50.716981, rms=0.745 (0.269%), neg=0, invalid=762 0042: dt=580.608000, rms=0.736 (1.197%), neg=0, invalid=762 0043: dt=36.288000, rms=0.735 (0.149%), neg=0, invalid=762 0044: dt=36.288000, rms=0.734 (0.067%), neg=0, invalid=762 0045: dt=36.288000, rms=0.733 (0.087%), neg=0, invalid=762 0046: dt=36.288000, rms=0.733 (0.123%), neg=0, invalid=762 0047: dt=36.288000, rms=0.731 (0.182%), neg=0, invalid=762 0048: dt=36.288000, rms=0.730 (0.225%), neg=0, invalid=762 0049: dt=36.288000, rms=0.728 (0.242%), neg=0, invalid=762 0050: dt=36.288000, rms=0.726 (0.250%), neg=0, invalid=762 0051: dt=36.288000, rms=0.724 (0.260%), neg=0, invalid=762 0052: dt=36.288000, rms=0.722 (0.258%), neg=0, invalid=762 0053: dt=36.288000, rms=0.721 (0.231%), neg=0, invalid=762 0054: dt=36.288000, rms=0.719 (0.225%), neg=0, invalid=762 0055: dt=36.288000, rms=0.717 (0.208%), neg=0, invalid=762 0056: dt=36.288000, rms=0.716 (0.188%), neg=0, invalid=762 0057: dt=36.288000, rms=0.715 (0.198%), neg=0, invalid=762 0058: dt=36.288000, rms=0.713 (0.222%), neg=0, invalid=762 0059: dt=36.288000, rms=0.712 (0.200%), neg=0, invalid=762 0060: dt=36.288000, rms=0.711 (0.148%), neg=0, invalid=762 0061: dt=36.288000, rms=0.710 (0.123%), neg=0, invalid=762 0062: dt=36.288000, rms=0.709 (0.107%), neg=0, invalid=762 0063: dt=145.152000, rms=0.708 (0.076%), neg=0, invalid=762 0064: dt=145.152000, rms=0.708 (-0.360%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.709, neg=0, invalid=762 0065: dt=36.288000, rms=0.707 (0.315%), neg=0, invalid=762 0066: dt=82.944000, rms=0.707 (0.076%), neg=0, invalid=762 0067: dt=82.944000, rms=0.706 (0.056%), neg=0, invalid=762 0068: dt=82.944000, rms=0.706 (-0.003%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.739, neg=0, invalid=762 0069: dt=8.000000, rms=0.738 (0.193%), neg=0, invalid=762 0070: dt=4.800000, rms=0.737 (0.027%), neg=0, invalid=762 0071: dt=4.800000, rms=0.737 (0.015%), neg=0, invalid=762 0072: dt=4.800000, rms=0.737 (-0.037%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.738, neg=0, invalid=762 0073: dt=-0.000732, rms=0.737 (0.110%), neg=0, invalid=762 0074: dt=0.000000, rms=0.737 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.817, neg=0, invalid=762 0075: dt=5.786942, rms=0.797 (2.380%), neg=0, invalid=762 0076: dt=7.334940, rms=0.792 (0.675%), neg=0, invalid=762 0077: dt=4.333333, rms=0.792 (0.059%), neg=0, invalid=762 0078: dt=4.333333, rms=0.791 (0.055%), neg=0, invalid=762 0079: dt=4.333333, rms=0.791 (-0.024%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.792, neg=0, invalid=762 0080: dt=0.000000, rms=0.791 (0.095%), neg=0, invalid=762 0081: dt=0.000000, rms=0.791 (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=0.848, neg=0, invalid=762 0082: dt=0.000000, rms=0.847 (0.083%), neg=0, invalid=762 0083: dt=0.000000, rms=0.847 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.848, neg=0, invalid=762 0084: dt=0.000000, rms=0.847 (0.083%), neg=0, invalid=762 0085: dt=0.000000, rms=0.847 (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=0.752, neg=0, invalid=762 0086: dt=0.988024, rms=0.725 (3.565%), neg=0, invalid=762 0087: dt=0.096000, rms=0.724 (0.167%), neg=0, invalid=762 0088: dt=0.096000, rms=0.724 (-0.120%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.725, neg=0, invalid=762 0089: dt=0.028000, rms=0.724 (0.137%), neg=0, invalid=762 0090: dt=0.020000, rms=0.724 (0.004%), neg=0, invalid=762 0091: dt=0.020000, rms=0.724 (-0.004%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.11660 (26) Left_Lateral_Ventricle (4): linear fit = 1.33 x + 0.0 (906 voxels, overlap=0.454) Left_Lateral_Ventricle (4): linear fit = 1.33 x + 0.0 (906 voxels, peak = 26), gca=26.5 gca peak = 0.15565 (16) mri peak = 0.13442 (25) Right_Lateral_Ventricle (43): linear fit = 1.59 x + 0.0 (663 voxels, overlap=0.311) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (663 voxels, peak = 25), gca=24.0 gca peak = 0.26829 (96) mri peak = 0.04874 (103) Right_Pallidum (52): linear fit = 1.07 x + 0.0 (700 voxels, overlap=0.090) Right_Pallidum (52): linear fit = 1.07 x + 0.0 (700 voxels, peak = 102), gca=102.2 gca peak = 0.20183 (93) mri peak = 0.06174 (106) Left_Pallidum (13): linear fit = 1.12 x + 0.0 (639 voxels, overlap=0.306) Left_Pallidum (13): linear fit = 1.12 x + 0.0 (639 voxels, peak = 104), gca=103.7 gca peak = 0.21683 (55) mri peak = 0.07576 (63) Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (528 voxels, overlap=0.782) Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (528 voxels, peak = 57), gca=57.5 gca peak = 0.30730 (58) mri peak = 0.05449 (64) Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (463 voxels, overlap=0.291) Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (463 voxels, peak = 64), gca=63.5 gca peak = 0.11430 (101) mri peak = 0.08135 (101) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (65948 voxels, overlap=0.858) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (65948 voxels, peak = 103), gca=102.5 gca peak = 0.12076 (102) mri peak = 0.07375 (100) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (61980 voxels, overlap=0.878) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (61980 voxels, peak = 104), gca=103.5 gca peak = 0.14995 (59) mri peak = 0.03790 (70) Left_Cerebral_Cortex (3): linear fit = 1.20 x + 0.0 (17138 voxels, overlap=0.072) Left_Cerebral_Cortex (3): linear fit = 1.20 x + 0.0 (17138 voxels, peak = 71), gca=70.5 gca peak = 0.15082 (58) mri peak = 0.03767 (75) Right_Cerebral_Cortex (42): linear fit = 1.35 x + 0.0 (16482 voxels, overlap=0.001) Right_Cerebral_Cortex (42): linear fit = 1.35 x + 0.0 (16482 voxels, peak = 78), gca=78.0 gca peak = 0.14161 (67) mri peak = 0.08079 (73) Right_Caudate (50): linear fit = 1.12 x + 0.0 (1085 voxels, overlap=0.289) Right_Caudate (50): linear fit = 1.12 x + 0.0 (1085 voxels, peak = 75), gca=74.7 gca peak = 0.15243 (71) mri peak = 0.08876 (83) Left_Caudate (11): linear fit = 1.12 x + 0.0 (1062 voxels, overlap=0.350) Left_Caudate (11): linear fit = 1.12 x + 0.0 (1062 voxels, peak = 80), gca=79.9 gca peak = 0.13336 (57) mri peak = 0.03482 (77) Left_Cerebellum_Cortex (8): linear fit = 1.46 x + 0.0 (12202 voxels, overlap=0.001) Left_Cerebellum_Cortex (8): linear fit = 1.46 x + 0.0 (12202 voxels, peak = 83), gca=82.9 gca peak = 0.13252 (56) mri peak = 0.04654 (84) Right_Cerebellum_Cortex (47): linear fit = 1.48 x + 0.0 (17470 voxels, overlap=0.001) Right_Cerebellum_Cortex (47): linear fit = 1.48 x + 0.0 (17470 voxels, peak = 83), gca=82.6 gca peak = 0.18181 (84) mri peak = 0.03474 (70) Left_Cerebellum_White_Matter (7): linear fit = 0.98 x + 0.0 (7448 voxels, overlap=0.946) Left_Cerebellum_White_Matter (7): linear fit = 0.98 x + 0.0 (7448 voxels, peak = 82), gca=81.9 gca peak = 0.20573 (83) mri peak = 0.04002 (77) Right_Cerebellum_White_Matter (46): linear fit = 0.92 x + 0.0 (6413 voxels, overlap=0.824) Right_Cerebellum_White_Matter (46): linear fit = 0.92 x + 0.0 (6413 voxels, peak = 76), gca=75.9 gca peak = 0.21969 (57) mri peak = 0.05833 (65) Left_Amygdala (18): linear fit = 1.12 x + 0.0 (382 voxels, overlap=0.807) Left_Amygdala (18): linear fit = 1.12 x + 0.0 (382 voxels, peak = 64), gca=63.6 gca peak = 0.39313 (56) mri peak = 0.08024 (59) Right_Amygdala (54): linear fit = 1.04 x + 0.0 (464 voxels, overlap=0.877) Right_Amygdala (54): linear fit = 1.04 x + 0.0 (464 voxels, peak = 59), gca=58.5 gca peak = 0.14181 (85) mri peak = 0.05147 (93) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (5048 voxels, overlap=0.627) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (5048 voxels, peak = 91), gca=90.5 gca peak = 0.11978 (83) mri peak = 0.05602 (100) Right_Thalamus_Proper (49): linear fit = 1.17 x + 0.0 (4720 voxels, overlap=0.252) Right_Thalamus_Proper (49): linear fit = 1.17 x + 0.0 (4720 voxels, peak = 98), gca=97.5 gca peak = 0.13399 (79) mri peak = 0.07313 (90) Left_Putamen (12): linear fit = 1.16 x + 0.0 (2064 voxels, overlap=0.009) Left_Putamen (12): linear fit = 1.16 x + 0.0 (2064 voxels, peak = 92), gca=92.0 gca peak = 0.14159 (79) mri peak = 0.06569 (89) Right_Putamen (51): linear fit = 1.14 x + 0.0 (2117 voxels, overlap=0.339) Right_Putamen (51): linear fit = 1.14 x + 0.0 (2117 voxels, peak = 90), gca=90.5 gca peak = 0.10025 (80) mri peak = 0.05992 (81) Brain_Stem (16): linear fit = 1.14 x + 0.0 (7799 voxels, overlap=0.403) Brain_Stem (16): linear fit = 1.14 x + 0.0 (7799 voxels, peak = 92), gca=91.6 gca peak = 0.13281 (86) mri peak = 0.07307 (94) Right_VentralDC (60): linear fit = 1.16 x + 0.0 (699 voxels, overlap=0.333) Right_VentralDC (60): linear fit = 1.16 x + 0.0 (699 voxels, peak = 100), gca=100.2 gca peak = 0.12801 (89) mri peak = 0.07026 (95) Left_VentralDC (28): linear fit = 1.14 x + 0.0 (839 voxels, overlap=0.395) Left_VentralDC (28): linear fit = 1.14 x + 0.0 (839 voxels, peak = 102), gca=101.9 gca peak = 0.20494 (23) mri peak = 1.00000 (26) gca peak = 0.15061 (21) mri peak = 0.10103 (15) Fourth_Ventricle (15): linear fit = 0.77 x + 0.0 (359 voxels, overlap=0.638) Fourth_Ventricle (15): linear fit = 0.77 x + 0.0 (359 voxels, peak = 16), gca=16.3 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 1.14 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 1.20 x + 0.0 Left_Pallidum too bright - rescaling by 0.964 (from 1.115) to 99.9 (was 103.7) Right_Pallidum too bright - rescaling by 0.977 (from 1.065) to 99.9 (was 102.2) 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=0.724, neg=0, invalid=762 0092: dt=73.984000, rms=0.710 (1.837%), neg=0, invalid=762 0093: dt=92.480000, rms=0.709 (0.255%), neg=0, invalid=762 0094: dt=129.472000, rms=0.707 (0.258%), neg=0, invalid=762 0095: dt=369.920000, rms=0.704 (0.341%), neg=0, invalid=762 0096: dt=517.888000, rms=0.699 (0.774%), neg=0, invalid=762 0097: dt=27.744000, rms=0.699 (-0.001%), neg=0, invalid=762 0098: dt=27.744000, rms=0.699 (0.006%), neg=0, invalid=762 0099: dt=27.744000, rms=0.699 (-0.007%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.700, neg=0, invalid=762 0100: dt=295.936000, rms=0.694 (0.759%), neg=0, invalid=762 0101: dt=73.984000, rms=0.694 (0.046%), neg=0, invalid=762 0102: dt=73.984000, rms=0.694 (0.008%), neg=0, invalid=762 0103: dt=73.984000, rms=0.694 (-0.003%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.695, neg=0, invalid=762 0104: dt=62.208000, rms=0.690 (0.674%), neg=0, invalid=762 0105: dt=309.794932, rms=0.673 (2.420%), neg=0, invalid=762 0106: dt=36.288000, rms=0.670 (0.433%), neg=0, invalid=762 0107: dt=145.152000, rms=0.667 (0.540%), neg=0, invalid=762 0108: dt=159.288889, rms=0.660 (0.951%), neg=0, invalid=762 0109: dt=31.104000, rms=0.659 (0.204%), neg=0, invalid=762 0110: dt=36.288000, rms=0.659 (0.042%), neg=0, invalid=762 0111: dt=36.288000, rms=0.658 (0.082%), neg=0, invalid=762 0112: dt=36.288000, rms=0.657 (0.153%), neg=0, invalid=762 0113: dt=36.288000, rms=0.656 (0.242%), neg=0, invalid=762 0114: dt=36.288000, rms=0.654 (0.310%), neg=0, invalid=762 0115: dt=36.288000, rms=0.651 (0.340%), neg=0, invalid=762 0116: dt=36.288000, rms=0.649 (0.325%), neg=0, invalid=762 0117: dt=36.288000, rms=0.647 (0.290%), neg=0, invalid=762 0118: dt=36.288000, rms=0.646 (0.237%), neg=0, invalid=762 0119: dt=36.288000, rms=0.644 (0.226%), neg=0, invalid=762 0120: dt=36.288000, rms=0.644 (0.046%), neg=0, invalid=762 0121: dt=36.288000, rms=0.644 (0.079%), neg=0, invalid=762 0122: dt=36.288000, rms=0.643 (0.089%), neg=0, invalid=762 0123: dt=36.288000, rms=0.642 (0.096%), neg=0, invalid=762 0124: dt=36.288000, rms=0.642 (0.108%), neg=0, invalid=762 0125: dt=36.288000, rms=0.641 (0.122%), neg=0, invalid=762 0126: dt=36.288000, rms=0.640 (0.139%), neg=0, invalid=762 0127: dt=36.288000, rms=0.639 (0.158%), neg=0, invalid=762 0128: dt=36.288000, rms=0.638 (0.163%), neg=0, invalid=762 0129: dt=36.288000, rms=0.637 (0.166%), neg=0, invalid=762 0130: dt=36.288000, rms=0.637 (0.016%), neg=0, invalid=762 0131: dt=36.288000, rms=0.637 (0.032%), neg=0, invalid=762 0132: dt=36.288000, rms=0.636 (0.028%), neg=0, invalid=762 0133: dt=9.072000, rms=0.636 (0.005%), neg=0, invalid=762 0134: dt=4.536000, rms=0.636 (0.003%), neg=0, invalid=762 0135: dt=2.268000, rms=0.636 (0.001%), neg=0, invalid=762 0136: dt=0.567000, rms=0.636 (0.000%), neg=0, invalid=762 0137: dt=0.141750, rms=0.636 (0.000%), neg=0, invalid=762 0138: dt=0.070875, rms=0.636 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.637, neg=0, invalid=762 0139: dt=124.416000, rms=0.633 (0.651%), neg=0, invalid=762 0140: dt=36.288000, rms=0.632 (0.098%), neg=0, invalid=762 0141: dt=145.152000, rms=0.631 (0.127%), neg=0, invalid=762 0142: dt=124.416000, rms=0.630 (0.153%), neg=0, invalid=762 0143: dt=36.288000, rms=0.630 (0.060%), neg=0, invalid=762 0144: dt=145.152000, rms=0.629 (0.087%), neg=0, invalid=762 0145: dt=145.152000, rms=0.629 (0.108%), neg=0, invalid=762 0146: dt=36.288000, rms=0.629 (0.044%), neg=0, invalid=762 0147: dt=36.288000, rms=0.628 (0.030%), neg=0, invalid=762 0148: dt=36.288000, rms=0.628 (0.038%), neg=0, invalid=762 0149: dt=36.288000, rms=0.628 (0.055%), neg=0, invalid=762 0150: dt=36.288000, rms=0.627 (0.069%), neg=0, invalid=762 0151: dt=36.288000, rms=0.627 (0.073%), neg=0, invalid=762 0152: dt=36.288000, rms=0.626 (0.076%), neg=0, invalid=762 0153: dt=36.288000, rms=0.626 (0.073%), neg=0, invalid=762 0154: dt=36.288000, rms=0.625 (0.074%), neg=0, invalid=762 0155: dt=36.288000, rms=0.625 (0.080%), neg=0, invalid=762 0156: dt=36.288000, rms=0.624 (0.083%), neg=0, invalid=762 0157: dt=36.288000, rms=0.624 (0.089%), neg=0, invalid=762 0158: dt=36.288000, rms=0.623 (0.087%), neg=0, invalid=762 0159: dt=36.288000, rms=0.623 (0.080%), neg=0, invalid=762 0160: dt=36.288000, rms=0.622 (0.074%), neg=0, invalid=762 0161: dt=36.288000, rms=0.622 (0.072%), neg=0, invalid=762 0162: dt=36.288000, rms=0.622 (0.012%), neg=0, invalid=762 0163: dt=36.288000, rms=0.622 (0.010%), neg=0, invalid=762 0164: dt=36.288000, rms=0.622 (0.010%), neg=0, invalid=762 0165: dt=2.268000, rms=0.622 (-0.001%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.627, neg=0, invalid=762 0166: dt=35.662651, rms=0.623 (0.588%), neg=0, invalid=762 0167: dt=44.800000, rms=0.615 (1.318%), neg=0, invalid=762 0168: dt=32.000000, rms=0.614 (0.246%), neg=0, invalid=762 0169: dt=11.200000, rms=0.612 (0.272%), neg=0, invalid=762 0170: dt=9.600000, rms=0.611 (0.158%), neg=0, invalid=762 0171: dt=0.700000, rms=0.611 (0.014%), neg=0, invalid=762 0172: dt=0.043750, rms=0.611 (0.001%), neg=0, invalid=762 0173: dt=0.021875, rms=0.611 (0.000%), neg=0, invalid=762 0174: dt=0.010937, rms=0.611 (0.000%), neg=0, invalid=762 0175: dt=0.009375, rms=0.611 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.612, neg=0, invalid=762 0176: dt=52.299169, rms=0.604 (1.213%), neg=0, invalid=762 0177: dt=23.071605, rms=0.602 (0.393%), neg=0, invalid=762 0178: dt=78.468085, rms=0.599 (0.502%), neg=0, invalid=762 0179: dt=11.200000, rms=0.597 (0.270%), neg=0, invalid=762 0180: dt=38.400000, rms=0.596 (0.195%), neg=0, invalid=762 0181: dt=25.600000, rms=0.595 (0.213%), neg=0, invalid=762 0182: dt=25.600000, rms=0.594 (0.146%), neg=0, invalid=762 0183: dt=25.600000, rms=0.593 (0.118%), neg=0, invalid=762 0184: dt=38.400000, rms=0.592 (0.168%), neg=0, invalid=762 0185: dt=11.200000, rms=0.592 (0.104%), neg=0, invalid=762 0186: dt=44.800000, rms=0.591 (0.185%), neg=0, invalid=762 0187: dt=44.800000, rms=0.590 (0.141%), neg=0, invalid=762 0188: dt=11.200000, rms=0.589 (0.100%), neg=0, invalid=762 0189: dt=32.000000, rms=0.589 (0.106%), neg=0, invalid=762 0190: dt=0.700000, rms=0.589 (0.002%), neg=0, invalid=762 0191: dt=0.700000, rms=0.588 (0.003%), neg=0, invalid=762 0192: dt=0.175000, rms=0.588 (0.005%), neg=0, invalid=762 0193: dt=0.087500, rms=0.588 (-0.003%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.602, neg=0, invalid=762 0194: dt=1.728000, rms=0.601 (0.137%), neg=0, invalid=762 0195: dt=1.008000, rms=0.601 (0.011%), neg=0, invalid=762 0196: dt=1.008000, rms=0.601 (0.002%), neg=0, invalid=762 0197: dt=1.008000, rms=0.601 (-0.012%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.602, neg=0, invalid=762 0198: dt=3.456000, rms=0.601 (0.156%), neg=0, invalid=762 0199: dt=4.032000, rms=0.601 (0.027%), neg=0, invalid=762 0200: dt=4.032000, rms=0.600 (0.031%), neg=0, invalid=762 0201: dt=4.032000, rms=0.600 (0.019%), neg=0, invalid=762 0202: dt=4.032000, rms=0.600 (0.000%), neg=0, invalid=762 0203: dt=16.128000, rms=0.597 (0.583%), neg=0, invalid=762 0204: dt=16.128000, rms=0.595 (0.214%), neg=0, invalid=762 0205: dt=16.128000, rms=0.594 (0.276%), neg=0, invalid=762 0206: dt=16.128000, rms=0.593 (0.135%), neg=0, invalid=762 0207: dt=16.128000, rms=0.592 (0.243%), neg=0, invalid=762 0208: dt=11.520000, rms=0.591 (0.077%), neg=0, invalid=762 0209: dt=16.128000, rms=0.590 (0.171%), neg=0, invalid=762 0210: dt=8.941176, rms=0.590 (0.050%), neg=0, invalid=762 0211: dt=16.128000, rms=0.589 (0.130%), neg=0, invalid=762 0212: dt=9.655172, rms=0.589 (0.054%), neg=0, invalid=762 0213: dt=18.823529, rms=0.588 (0.115%), neg=0, invalid=762 0214: dt=8.666667, rms=0.588 (0.058%), neg=0, invalid=762 0215: dt=21.818182, rms=0.587 (0.107%), neg=0, invalid=762 0216: dt=7.555556, rms=0.587 (0.069%), neg=0, invalid=762 0217: dt=24.000000, rms=0.586 (0.113%), neg=0, invalid=762 0218: dt=4.032000, rms=0.586 (0.039%), neg=0, invalid=762 0219: dt=4.032000, rms=0.586 (0.028%), neg=0, invalid=762 0220: dt=4.032000, rms=0.585 (0.025%), neg=0, invalid=762 0221: dt=4.032000, rms=0.585 (0.047%), neg=0, invalid=762 0222: dt=4.032000, rms=0.585 (0.072%), neg=0, invalid=762 0223: dt=4.032000, rms=0.584 (0.084%), neg=0, invalid=762 0224: dt=4.032000, rms=0.584 (0.086%), neg=0, invalid=762 0225: dt=4.032000, rms=0.583 (0.095%), neg=0, invalid=762 0226: dt=4.032000, rms=0.583 (0.091%), neg=0, invalid=762 0227: dt=4.032000, rms=0.582 (0.089%), neg=0, invalid=762 0228: dt=4.032000, rms=0.582 (0.095%), neg=0, invalid=762 0229: dt=4.032000, rms=0.581 (0.095%), neg=0, invalid=762 0230: dt=4.032000, rms=0.581 (0.095%), neg=0, invalid=762 0231: dt=4.032000, rms=0.580 (0.095%), neg=0, invalid=762 0232: dt=4.032000, rms=0.579 (0.086%), neg=0, invalid=762 0233: dt=4.032000, rms=0.579 (0.079%), neg=0, invalid=762 0234: dt=4.032000, rms=0.579 (0.077%), neg=0, invalid=762 0235: dt=4.032000, rms=0.578 (0.071%), neg=0, invalid=762 0236: dt=4.032000, rms=0.578 (0.077%), neg=0, invalid=762 0237: dt=4.032000, rms=0.577 (0.068%), neg=0, invalid=762 0238: dt=4.032000, rms=0.577 (0.055%), neg=0, invalid=762 0239: dt=4.032000, rms=0.577 (0.050%), neg=0, invalid=762 0240: dt=4.032000, rms=0.576 (0.053%), neg=0, invalid=762 0241: dt=4.032000, rms=0.576 (0.052%), neg=0, invalid=762 0242: dt=4.032000, rms=0.576 (0.061%), neg=0, invalid=762 0243: dt=4.032000, rms=0.575 (0.053%), neg=0, invalid=762 0244: dt=4.032000, rms=0.575 (0.045%), neg=0, invalid=762 0245: dt=4.032000, rms=0.575 (0.040%), neg=0, invalid=762 0246: dt=4.032000, rms=0.575 (0.032%), neg=0, invalid=762 0247: dt=4.032000, rms=0.575 (0.037%), neg=0, invalid=762 0248: dt=4.032000, rms=0.574 (0.034%), neg=0, invalid=762 0249: dt=4.032000, rms=0.574 (0.039%), neg=0, invalid=762 0250: dt=4.032000, rms=0.574 (0.030%), neg=0, invalid=762 0251: dt=4.032000, rms=0.574 (0.029%), neg=0, invalid=762 0252: dt=4.032000, rms=0.574 (0.024%), neg=0, invalid=762 0253: dt=4.032000, rms=0.574 (0.025%), neg=0, invalid=762 0254: dt=4.032000, rms=0.573 (0.024%), neg=0, invalid=762 0255: dt=11.520000, rms=0.573 (0.016%), neg=0, invalid=762 0256: dt=11.520000, rms=0.573 (0.003%), neg=0, invalid=762 0257: dt=11.520000, rms=0.573 (0.014%), neg=0, invalid=762 0258: dt=11.520000, rms=0.573 (0.004%), neg=0, invalid=762 0259: dt=11.520000, rms=0.573 (0.014%), neg=0, invalid=762 0260: dt=11.520000, rms=0.573 (0.017%), neg=0, invalid=762 0261: dt=11.520000, rms=0.573 (0.020%), neg=0, invalid=762 0262: dt=11.520000, rms=0.573 (0.013%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.586, neg=0, invalid=762 0263: dt=0.000000, rms=0.586 (0.107%), neg=0, invalid=762 0264: dt=0.000000, rms=0.586 (0.000%), neg=0, invalid=762 0265: dt=0.100000, rms=0.586 (-0.175%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.586, neg=0, invalid=762 0266: dt=0.000000, rms=0.586 (0.107%), neg=0, invalid=762 0267: dt=0.000000, rms=0.586 (0.000%), neg=0, invalid=762 0268: dt=0.100000, rms=0.586 (-0.148%), 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=0.565, neg=0, invalid=762 0269: dt=0.448000, rms=0.547 (3.193%), neg=0, invalid=762 0270: dt=0.448000, rms=0.543 (0.661%), neg=0, invalid=762 0271: dt=0.448000, rms=0.541 (0.375%), neg=0, invalid=762 0272: dt=0.525000, rms=0.540 (0.209%), neg=0, invalid=762 0273: dt=0.448000, rms=0.539 (0.128%), neg=0, invalid=762 0274: dt=0.448000, rms=0.539 (0.073%), neg=0, invalid=762 0275: dt=0.448000, rms=0.538 (0.072%), neg=0, invalid=762 0276: dt=0.448000, rms=0.538 (0.036%), neg=0, invalid=762 0277: dt=0.448000, rms=0.538 (0.050%), neg=0, invalid=762 0278: dt=0.448000, rms=0.538 (0.055%), neg=0, invalid=762 0279: dt=0.448000, rms=0.537 (0.063%), neg=0, invalid=762 0280: dt=0.448000, rms=0.537 (0.065%), neg=0, invalid=762 0281: dt=0.448000, rms=0.537 (0.001%), neg=0, invalid=762 0282: dt=0.448000, rms=0.537 (-0.009%), neg=0, invalid=762 0283: dt=0.112000, rms=0.537 (0.001%), neg=0, invalid=762 0284: dt=0.384000, rms=0.537 (0.003%), neg=0, invalid=762 0285: dt=0.024000, rms=0.537 (0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.538, neg=0, invalid=762 0286: dt=0.448000, rms=0.528 (1.890%), neg=0, invalid=762 0287: dt=0.448000, rms=0.526 (0.366%), neg=0, invalid=762 0288: dt=0.448000, rms=0.525 (0.175%), neg=0, invalid=762 0289: dt=0.448000, rms=0.524 (0.054%), neg=0, invalid=762 0290: dt=0.448000, rms=0.524 (0.035%), neg=0, invalid=762 0291: dt=0.448000, rms=0.524 (0.005%), neg=0, invalid=762 0292: dt=0.448000, rms=0.524 (0.019%), neg=0, invalid=762 0293: dt=0.448000, rms=0.524 (0.018%), neg=0, invalid=762 0294: dt=0.448000, rms=0.524 (-0.006%), 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=0.523, neg=0, invalid=762 0295: dt=0.000000, rms=0.522 (0.135%), neg=0, invalid=762 0296: dt=0.000000, rms=0.522 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.523, neg=0, invalid=762 0297: dt=0.000000, rms=0.522 (0.135%), neg=0, invalid=762 0298: dt=0.000000, rms=0.522 (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=0.523, neg=0, invalid=762 0299: dt=0.000000, rms=0.522 (0.135%), neg=0, invalid=762 0300: dt=0.000000, rms=0.522 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.523, neg=0, invalid=762 0301: dt=36.288000, rms=0.521 (0.205%), neg=0, invalid=762 0302: dt=103.680000, rms=0.521 (0.109%), neg=0, invalid=762 0303: dt=103.680000, rms=0.521 (-0.009%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.522, neg=0, invalid=762 0304: dt=9.600000, rms=0.520 (0.279%), neg=0, invalid=762 0305: dt=6.400000, rms=0.520 (0.031%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0306: dt=6.400000, rms=0.520 (-0.007%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.521, neg=0, invalid=762 iter 0, gcam->neg = 6 after 2 iterations, nbhd size=0, neg = 0 0307: dt=38.400000, rms=0.515 (1.200%), neg=0, invalid=762 0308: dt=11.200000, rms=0.513 (0.252%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0309: dt=44.800000, rms=0.512 (0.215%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0310: dt=44.800000, rms=0.511 (0.197%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0311: dt=44.800000, rms=0.509 (0.456%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 8 iterations, nbhd size=1, neg = 0 0312: dt=44.800000, rms=0.507 (0.423%), neg=0, invalid=762 iter 0, gcam->neg = 13 after 3 iterations, nbhd size=0, neg = 0 0313: dt=44.800000, rms=0.505 (0.378%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 2 iterations, nbhd size=0, neg = 0 0314: dt=44.800000, rms=0.503 (0.327%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 14 iterations, nbhd size=1, neg = 0 0315: dt=44.800000, rms=0.503 (0.121%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0316: dt=44.800000, rms=0.501 (0.278%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0317: dt=44.800000, rms=0.500 (0.267%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 11 iterations, nbhd size=1, neg = 0 0318: dt=44.800000, rms=0.499 (0.110%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 9 iterations, nbhd size=1, neg = 0 0319: dt=44.800000, rms=0.499 (0.119%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0320: dt=44.800000, rms=0.497 (0.230%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 2 iterations, nbhd size=0, neg = 0 0321: dt=44.800000, rms=0.497 (0.089%), neg=0, invalid=762 0322: dt=44.800000, rms=0.496 (0.139%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0323: dt=44.800000, rms=0.496 (0.037%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 7 iterations, nbhd size=1, neg = 0 0324: dt=44.800000, rms=0.496 (0.030%), neg=0, invalid=762 0325: dt=11.200000, rms=0.495 (0.151%), neg=0, invalid=762 0326: dt=19.200000, rms=0.495 (0.059%), neg=0, invalid=762 0327: dt=19.200000, rms=0.495 (0.041%), neg=0, invalid=762 0328: dt=19.200000, rms=0.495 (0.011%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0329: dt=19.200000, rms=0.495 (0.020%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0330: dt=19.200000, rms=0.494 (0.032%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0331: dt=19.200000, rms=0.494 (0.023%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.500, neg=0, invalid=762 0332: dt=0.000176, rms=0.499 (0.147%), neg=0, invalid=762 0333: dt=0.000000, rms=0.499 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.500, neg=0, invalid=762 0334: dt=1.008000, rms=0.499 (0.154%), neg=0, invalid=762 0335: dt=1.008000, rms=0.499 (0.005%), neg=0, invalid=762 0336: dt=1.008000, rms=0.499 (0.002%), neg=0, invalid=762 0337: dt=1.008000, rms=0.499 (-0.008%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.509, neg=0, invalid=762 0338: dt=0.448000, rms=0.508 (0.216%), neg=0, invalid=762 0339: dt=0.384000, rms=0.508 (0.019%), neg=0, invalid=762 0340: dt=0.384000, rms=0.508 (-0.010%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.508, neg=0, invalid=762 0341: dt=1.792000, rms=0.505 (0.553%), neg=0, invalid=762 0342: dt=1.792000, rms=0.505 (0.155%), neg=0, invalid=762 0343: dt=1.792000, rms=0.504 (0.091%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0344: dt=1.792000, rms=0.504 (0.026%), neg=0, invalid=762 0345: dt=1.792000, rms=0.504 (-0.041%), 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=0.500, neg=0, invalid=762 iter 0, gcam->neg = 724 after 11 iterations, nbhd size=1, neg = 0 0346: dt=2.061839, rms=0.468 (6.390%), neg=0, invalid=762 0347: dt=0.064000, rms=0.468 (0.036%), neg=0, invalid=762 0348: dt=0.064000, rms=0.468 (-0.042%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.469, neg=0, invalid=762 0349: dt=0.112000, rms=0.468 (0.312%), neg=0, invalid=762 0350: dt=0.028000, rms=0.468 (0.013%), neg=0, invalid=762 0351: dt=0.028000, rms=0.468 (-0.004%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.455, neg=0, invalid=762 0352: dt=0.000000, rms=0.455 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.455, neg=0, invalid=762 0353: dt=32.368000, rms=0.455 (0.016%), neg=0, invalid=762 0354: dt=32.368000, rms=0.455 (0.003%), neg=0, invalid=762 0355: dt=32.368000, rms=0.455 (0.001%), neg=0, invalid=762 0356: dt=32.368000, rms=0.455 (-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=0.455, neg=0, invalid=762 0357: dt=0.000000, rms=0.455 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.455, neg=0, invalid=762 0358: dt=36.288000, rms=0.455 (0.034%), neg=0, invalid=762 0359: dt=82.944000, rms=0.454 (0.022%), neg=0, invalid=762 0360: dt=82.944000, rms=0.454 (0.026%), neg=0, invalid=762 0361: dt=82.944000, rms=0.454 (0.017%), neg=0, invalid=762 0362: dt=82.944000, rms=0.454 (0.003%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.455, neg=0, invalid=762 0363: dt=1.200000, rms=0.455 (0.003%), neg=0, invalid=762 0364: dt=0.175000, rms=0.455 (0.000%), neg=0, invalid=762 0365: dt=0.175000, rms=0.455 (0.000%), neg=0, invalid=762 0366: dt=0.175000, rms=0.455 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.455, neg=0, invalid=762 0367: dt=87.780167, rms=0.452 (0.742%), neg=0, invalid=762 0368: dt=11.200000, rms=0.451 (0.125%), neg=0, invalid=762 0369: dt=11.200000, rms=0.451 (0.050%), neg=0, invalid=762 0370: dt=11.200000, rms=0.450 (0.058%), neg=0, invalid=762 0371: dt=11.200000, rms=0.450 (0.057%), neg=0, invalid=762 0372: dt=11.200000, rms=0.450 (0.078%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0373: dt=11.200000, rms=0.449 (0.103%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 3 iterations, nbhd size=0, neg = 0 0374: dt=11.200000, rms=0.449 (0.113%), neg=0, invalid=762 0375: dt=11.200000, rms=0.448 (0.115%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0376: dt=11.200000, rms=0.448 (0.098%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0377: dt=44.800000, rms=0.448 (0.033%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.451, neg=0, invalid=762 0378: dt=0.000000, rms=0.451 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.451, neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0379: dt=14.924370, rms=0.449 (0.335%), neg=0, invalid=762 iter 0, gcam->neg = 14 after 9 iterations, nbhd size=1, neg = 0 0380: dt=34.998296, rms=0.447 (0.542%), neg=0, invalid=762 0381: dt=5.043478, rms=0.446 (0.125%), neg=0, invalid=762 0382: dt=5.043478, rms=0.446 (0.030%), neg=0, invalid=762 0383: dt=5.043478, rms=0.446 (0.023%), neg=0, invalid=762 0384: dt=5.043478, rms=0.446 (0.039%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0385: dt=5.043478, rms=0.446 (0.094%), neg=0, invalid=762 0386: dt=5.043478, rms=0.445 (0.132%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0387: dt=5.043478, rms=0.444 (0.129%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 0388: dt=5.043478, rms=0.444 (0.106%), neg=0, invalid=762 0389: dt=5.043478, rms=0.444 (0.086%), neg=0, invalid=762 0390: dt=0.000141, rms=0.444 (0.000%), neg=0, invalid=762 0391: dt=0.000141, rms=0.444 (-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=0.449, neg=0, invalid=762 0392: dt=0.000000, rms=0.449 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.449, neg=0, invalid=762 0393: dt=0.000000, rms=0.449 (0.000%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.440, neg=0, invalid=762 iter 0, gcam->neg = 376 after 15 iterations, nbhd size=1, neg = 0 0394: dt=1.344846, rms=0.431 (1.974%), neg=0, invalid=762 0395: dt=0.000023, rms=0.431 (0.000%), neg=0, invalid=762 0396: dt=0.000023, rms=0.431 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.431, neg=0, invalid=762 0397: dt=0.201550, rms=0.430 (0.284%), neg=0, invalid=762 0398: dt=0.320000, rms=0.429 (0.195%), neg=0, invalid=762 0399: dt=0.320000, rms=0.428 (0.314%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0400: dt=0.320000, rms=0.426 (0.378%), neg=0, invalid=762 iter 0, gcam->neg = 82 after 11 iterations, nbhd size=1, neg = 0 0401: dt=0.320000, rms=0.426 (0.077%), neg=0, invalid=762 iter 0, gcam->neg = 16 after 2 iterations, nbhd size=0, neg = 0 0402: dt=0.320000, rms=0.425 (0.207%), neg=0, invalid=762 iter 0, gcam->neg = 31 after 9 iterations, nbhd size=1, neg = 0 0403: dt=0.320000, rms=0.425 (0.034%), neg=0, invalid=762 iter 0, gcam->neg = 29 after 8 iterations, nbhd size=1, neg = 0 0404: dt=0.320000, rms=0.425 (-0.070%), neg=0, invalid=762 0405: dt=0.320000, rms=0.425 (0.058%), neg=0, invalid=762 0406: dt=0.112000, rms=0.425 (0.008%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 1 hours, 32 minutes and 28 seconds. mri_ca_register utimesec 7045.430110 mri_ca_register stimesec 9.594475 mri_ca_register ru_maxrss 1336280 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 4687332 mri_ca_register ru_majflt 0 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 0 mri_ca_register ru_oublock 0 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 24633 mri_ca_register ru_nivcsw 361927 FSRUNTIME@ mri_ca_register 1.5410 hours 4 threads #-------------------------------------- #@# SubCort Seg Thu Oct 3 12:01:33 BST 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 zappst-Q170M-C machine x86_64 setenv SUBJECTS_DIR /mnt/8E74B1C874B1B377/FreeSurfer/subjects cd /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 7.48 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 = 0.10802 (26) Left_Lateral_Ventricle (4): linear fit = 1.36 x + 0.0 (441 voxels, overlap=0.761) Left_Lateral_Ventricle (4): linear fit = 1.36 x + 0.0 (441 voxels, peak = 27), gca=27.1 gca peak = 0.17677 (13) mri peak = 0.12299 (25) Right_Lateral_Ventricle (43): linear fit = 1.82 x + 0.0 (420 voxels, overlap=0.306) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (420 voxels, peak = 24), gca=19.5 gca peak = 0.28129 (95) mri peak = 0.10606 (103) Right_Pallidum (52): linear fit = 1.08 x + 0.0 (657 voxels, overlap=0.107) Right_Pallidum (52): linear fit = 1.08 x + 0.0 (657 voxels, peak = 102), gca=102.1 gca peak = 0.16930 (96) mri peak = 0.10765 (106) Left_Pallidum (13): linear fit = 1.10 x + 0.0 (704 voxels, overlap=0.199) Left_Pallidum (13): linear fit = 1.10 x + 0.0 (704 voxels, peak = 105), gca=105.1 gca peak = 0.24553 (55) mri peak = 0.08081 (68) Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (492 voxels, overlap=0.584) Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (492 voxels, peak = 64), gca=63.5 gca peak = 0.30264 (59) mri peak = 0.07353 (64) Left_Hippocampus (17): linear fit = 1.13 x + 0.0 (751 voxels, overlap=0.718) Left_Hippocampus (17): linear fit = 1.13 x + 0.0 (751 voxels, peak = 67), gca=67.0 gca peak = 0.07580 (103) mri peak = 0.08147 (101) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (43149 voxels, overlap=0.789) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (43149 voxels, peak = 102), gca=102.5 gca peak = 0.07714 (104) mri peak = 0.07008 (98) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (47481 voxels, overlap=0.835) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (47481 voxels, peak = 103), gca=103.5 gca peak = 0.09712 (58) mri peak = 0.03723 (65) Left_Cerebral_Cortex (3): linear fit = 1.18 x + 0.0 (18156 voxels, overlap=0.275) Left_Cerebral_Cortex (3): linear fit = 1.18 x + 0.0 (18156 voxels, peak = 69), gca=68.7 gca peak = 0.11620 (58) mri peak = 0.03429 (72) Right_Cerebral_Cortex (42): linear fit = 1.29 x + 0.0 (17221 voxels, overlap=0.003) Right_Cerebral_Cortex (42): linear fit = 1.29 x + 0.0 (17221 voxels, peak = 75), gca=75.1 gca peak = 0.30970 (66) mri peak = 0.10100 (79) Right_Caudate (50): linear fit = 1.14 x + 0.0 (1094 voxels, overlap=0.030) Right_Caudate (50): linear fit = 1.14 x + 0.0 (1094 voxels, peak = 76), gca=75.6 gca peak = 0.15280 (69) mri peak = 0.11130 (81) Left_Caudate (11): linear fit = 1.10 x + 0.0 (895 voxels, overlap=0.507) Left_Caudate (11): linear fit = 1.10 x + 0.0 (895 voxels, peak = 76), gca=75.6 gca peak = 0.13902 (56) mri peak = 0.04841 (77) Left_Cerebellum_Cortex (8): linear fit = 1.34 x + 0.0 (16760 voxels, overlap=0.002) Left_Cerebellum_Cortex (8): linear fit = 1.34 x + 0.0 (16760 voxels, peak = 75), gca=74.8 gca peak = 0.14777 (55) mri peak = 0.05670 (80) Right_Cerebellum_Cortex (47): linear fit = 1.42 x + 0.0 (21555 voxels, overlap=0.001) Right_Cerebellum_Cortex (47): linear fit = 1.42 x + 0.0 (21555 voxels, peak = 78), gca=78.4 gca peak = 0.16765 (84) mri peak = 0.07433 (85) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (6113 voxels, overlap=0.904) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (6113 voxels, peak = 86), gca=86.1 gca peak = 0.18739 (84) mri peak = 0.06741 (87) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (7205 voxels, overlap=0.802) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (7205 voxels, peak = 87), gca=86.9 gca peak = 0.29869 (57) mri peak = 0.08680 (74) Left_Amygdala (18): linear fit = 1.28 x + 0.0 (265 voxels, overlap=0.073) Left_Amygdala (18): linear fit = 1.28 x + 0.0 (265 voxels, peak = 73), gca=73.2 gca peak = 0.33601 (57) mri peak = 0.08553 (60) Right_Amygdala (54): linear fit = 1.18 x + 0.0 (152 voxels, overlap=0.629) Right_Amygdala (54): linear fit = 1.18 x + 0.0 (152 voxels, peak = 68), gca=67.5 gca peak = 0.11131 (90) mri peak = 0.07721 (90) Left_Thalamus_Proper (10): linear fit = 1.03 x + 0.0 (3965 voxels, overlap=0.835) Left_Thalamus_Proper (10): linear fit = 1.03 x + 0.0 (3965 voxels, peak = 93), gca=93.1 gca peak = 0.11793 (83) mri peak = 0.07639 (93) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (4346 voxels, overlap=0.309) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (4346 voxels, peak = 93), gca=92.5 gca peak = 0.08324 (81) mri peak = 0.09338 (88) Left_Putamen (12): linear fit = 1.12 x + 0.0 (1613 voxels, overlap=0.294) Left_Putamen (12): linear fit = 1.12 x + 0.0 (1613 voxels, peak = 91), gca=91.1 gca peak = 0.10360 (77) mri peak = 0.08293 (84) Right_Putamen (51): linear fit = 1.12 x + 0.0 (1541 voxels, overlap=0.369) Right_Putamen (51): linear fit = 1.12 x + 0.0 (1541 voxels, peak = 87), gca=86.6 gca peak = 0.08424 (78) mri peak = 0.05753 (88) Brain_Stem (16): linear fit = 1.12 x + 0.0 (8792 voxels, overlap=0.477) Brain_Stem (16): linear fit = 1.12 x + 0.0 (8792 voxels, peak = 88), gca=87.8 gca peak = 0.12631 (89) mri peak = 0.07301 (103) Right_VentralDC (60): linear fit = 1.18 x + 0.0 (1174 voxels, overlap=0.016) Right_VentralDC (60): linear fit = 1.18 x + 0.0 (1174 voxels, peak = 105), gca=105.5 gca peak = 0.14500 (87) mri peak = 0.08020 (105) Left_VentralDC (28): linear fit = 1.20 x + 0.0 (1326 voxels, overlap=0.030) Left_VentralDC (28): linear fit = 1.20 x + 0.0 (1326 voxels, peak = 104), gca=104.0 gca peak = 0.14975 (24) mri peak = 0.14721 (26) gca peak = 0.19357 (14) mri peak = 0.12172 (17) Fourth_Ventricle (15): linear fit = 1.17 x + 0.0 (249 voxels, overlap=0.846) Fourth_Ventricle (15): linear fit = 1.17 x + 0.0 (249 voxels, peak = 16), gca=16.4 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 1.00000 (94) gca peak Third_Ventricle = 0.14975 (24) gca peak CSF = 0.23379 (36) gca peak Left_Accumbens_area = 0.70037 (62) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.24655 (23) gca peak Right_Accumbens_area = 0.45042 (65) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.65475 (32) gca peak WM_hypointensities = 0.07854 (76) gca peak non_WM_hypointensities = 0.08491 (43) gca peak Optic_Chiasm = 0.71127 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.21 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.34 x + 0.0 Left_Pallidum too bright - rescaling by 0.950 (from 1.095) to 99.9 (was 105.1) Right_Pallidum too bright - rescaling by 0.978 (from 1.075) to 99.9 (was 102.1) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.13785 (25) mri peak = 0.10802 (26) Left_Lateral_Ventricle (4): linear fit = 0.90 x + 0.0 (441 voxels, overlap=0.866) Left_Lateral_Ventricle (4): linear fit = 0.90 x + 0.0 (441 voxels, peak = 23), gca=22.6 gca peak = 0.14095 (19) mri peak = 0.12299 (25) Right_Lateral_Ventricle (43): linear fit = 1.24 x + 0.0 (420 voxels, overlap=0.699) Right_Lateral_Ventricle (43): linear fit = 1.24 x + 0.0 (420 voxels, peak = 23), gca=23.5 gca peak = 0.23293 (99) mri peak = 0.10606 (103) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (657 voxels, overlap=1.006) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (657 voxels, peak = 100), gca=100.5 gca peak = 0.15494 (99) mri peak = 0.10765 (106) Left_Pallidum (13): linear fit = 1.03 x + 0.0 (704 voxels, overlap=0.711) Left_Pallidum (13): linear fit = 1.03 x + 0.0 (704 voxels, peak = 102), gca=102.5 gca peak = 0.23345 (64) mri peak = 0.08081 (68) Right_Hippocampus (53): linear fit = 0.98 x + 0.0 (492 voxels, overlap=0.894) Right_Hippocampus (53): linear fit = 0.98 x + 0.0 (492 voxels, peak = 62), gca=62.4 gca peak = 0.28259 (67) mri peak = 0.07353 (64) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (751 voxels, overlap=1.008) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (751 voxels, peak = 66), gca=66.0 gca peak = 0.07862 (102) mri peak = 0.08147 (101) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (43149 voxels, overlap=0.786) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (43149 voxels, peak = 101), gca=101.5 gca peak = 0.08045 (104) mri peak = 0.07008 (98) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (47481 voxels, overlap=0.816) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (47481 voxels, peak = 103), gca=103.5 gca peak = 0.08213 (69) mri peak = 0.03723 (65) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (18156 voxels, overlap=0.873) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (18156 voxels, peak = 68), gca=68.0 gca peak = 0.09071 (75) mri peak = 0.03429 (72) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (17221 voxels, overlap=0.934) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (17221 voxels, peak = 74), gca=73.9 gca peak = 0.24454 (76) mri peak = 0.10100 (79) Right_Caudate (50): linear fit = 1.01 x + 0.0 (1094 voxels, overlap=1.002) Right_Caudate (50): linear fit = 1.01 x + 0.0 (1094 voxels, peak = 77), gca=77.1 gca peak = 0.12819 (75) mri peak = 0.11130 (81) Left_Caudate (11): linear fit = 1.00 x + 0.0 (895 voxels, overlap=0.909) Left_Caudate (11): linear fit = 1.00 x + 0.0 (895 voxels, peak = 75), gca=75.0 gca peak = 0.10548 (75) mri peak = 0.04841 (77) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (16760 voxels, overlap=0.987) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (16760 voxels, peak = 75), gca=74.6 gca peak = 0.10587 (78) mri peak = 0.05670 (80) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (21555 voxels, overlap=0.961) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (21555 voxels, peak = 78), gca=77.6 gca peak = 0.15814 (86) mri peak = 0.07433 (85) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6113 voxels, overlap=0.963) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6113 voxels, peak = 86), gca=85.6 gca peak = 0.19467 (87) mri peak = 0.06741 (87) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (7205 voxels, overlap=0.952) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (7205 voxels, peak = 87), gca=86.6 gca peak = 0.27472 (73) mri peak = 0.08680 (74) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (265 voxels, overlap=1.018) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (265 voxels, peak = 73), gca=73.0 gca peak = 0.29287 (67) mri peak = 0.08553 (60) Right_Amygdala (54): linear fit = 0.88 x + 0.0 (152 voxels, overlap=0.989) Right_Amygdala (54): linear fit = 0.88 x + 0.0 (152 voxels, peak = 59), gca=59.3 gca peak = 0.10695 (91) mri peak = 0.07721 (90) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3965 voxels, overlap=0.935) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3965 voxels, peak = 91), gca=90.5 gca peak = 0.10626 (90) mri peak = 0.07639 (93) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (4346 voxels, overlap=0.917) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (4346 voxels, peak = 91), gca=91.3 gca peak = 0.09344 (91) mri peak = 0.09338 (88) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1613 voxels, overlap=0.800) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1613 voxels, peak = 91), gca=90.5 gca peak = 0.08153 (84) mri peak = 0.08293 (84) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1541 voxels, overlap=0.776) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1541 voxels, peak = 83), gca=82.7 gca peak = 0.07670 (88) mri peak = 0.05753 (88) Brain_Stem (16): linear fit = 1.00 x + 0.0 (8792 voxels, overlap=0.895) Brain_Stem (16): linear fit = 1.00 x + 0.0 (8792 voxels, peak = 88), gca=88.4 gca peak = 0.10234 (104) mri peak = 0.07301 (103) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1174 voxels, overlap=0.838) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1174 voxels, peak = 105), gca=104.5 gca peak = 0.18670 (102) mri peak = 0.08020 (105) Left_VentralDC (28): linear fit = 0.98 x + 0.0 (1326 voxels, overlap=0.934) Left_VentralDC (28): linear fit = 0.98 x + 0.0 (1326 voxels, peak = 99), gca=99.5 gca peak = 0.12656 (34) mri peak = 0.14721 (26) gca peak = 0.17279 (17) mri peak = 0.12172 (17) Fourth_Ventricle (15): linear fit = 0.94 x + 0.0 (249 voxels, overlap=0.767) Fourth_Ventricle (15): linear fit = 0.94 x + 0.0 (249 voxels, peak = 16), gca=15.9 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.15127 (30) gca peak Left_Thalamus = 0.36646 (101) gca peak Third_Ventricle = 0.12656 (34) gca peak CSF = 0.23909 (49) gca peak Left_Accumbens_area = 0.80018 (68) gca peak Left_undetermined = 0.96707 (31) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.11873 (35) gca peak Right_Inf_Lat_Vent = 0.18678 (27) gca peak Right_Accumbens_area = 0.33779 (74) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14506 (37) gca peak Fifth_Ventricle = 0.86987 (42) gca peak WM_hypointensities = 0.08906 (76) gca peak non_WM_hypointensities = 0.11534 (54) gca peak Optic_Chiasm = 0.61145 (75) not using caudate to estimate GM means estimating mean gm scale to be 0.97 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.02 x + 0.0 Left_Pallidum too bright - rescaling by 0.970 (from 1.035) to 99.4 (was 102.5) Right_Pallidum too bright - rescaling by 0.989 (from 1.015) to 99.4 (was 100.5) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 115428 voxels changed in iteration 0 of unlikely voxel relabeling 691 voxels changed in iteration 1 of unlikely voxel relabeling 13 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 89339 gm and wm labels changed (%24 to gray, %76 to white out of all changed labels) 490 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 99261 changed. image ll: -2.191, PF=0.500 pass 2: 27000 changed. image ll: -2.189, PF=0.500 pass 3: 7057 changed. pass 4: 2272 changed. 93112 voxels changed in iteration 0 of unlikely voxel relabeling 1106 voxels changed in iteration 1 of unlikely voxel relabeling 134 voxels changed in iteration 2 of unlikely voxel relabeling 30 voxels changed in iteration 3 of unlikely voxel relabeling 3 voxels changed in iteration 4 of unlikely voxel relabeling 10236 voxels changed in iteration 0 of unlikely voxel relabeling 141 voxels changed in iteration 1 of unlikely voxel relabeling 7 voxels changed in iteration 2 of unlikely voxel relabeling 1 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 9084 voxels changed in iteration 0 of unlikely voxel relabeling 120 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 6799 voxels changed in iteration 0 of unlikely voxel relabeling 38 voxels changed in iteration 1 of unlikely voxel relabeling 5 voxels changed in iteration 2 of unlikely voxel relabeling 11 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 2795.971291 mri_ca_label stimesec 0.999961 mri_ca_label ru_maxrss 2109440 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 701628 mri_ca_label ru_majflt 14 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 2496 mri_ca_label ru_oublock 0 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 834 mri_ca_label ru_nivcsw 17389 auto-labeling took 45 minutes and 49 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/transforms/cc_up.lta S131032017_Supine will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/transforms/cc_up.lta reading aseg from /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/aseg.auto_noCCseg.mgz reading norm from /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/norm.mgz 42460 voxels in left wm, 35414 in right wm, xrange [122, 130] searching rotation angles z=[-3 11], y=[-8 6] searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.2 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.2 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.2 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.0 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.8 searching scale 1 Z rot 4.0 searching scale 1 Z rot 4.3 searching scale 1 Z rot 4.5 searching scale 1 Z rot 4.8 searching scale 1 Z rot 5.0 searching scale 1 Z rot 5.3 searching scale 1 Z rot 5.5 searching scale 1 Z rot 5.8 searching scale 1 Z rot 6.0 searching scale 1 Z rot 6.3 searching scale 1 Z rot 6.5 searching scale 1 Z rot 6.8 searching scale 1 Z rot 7.0 searching scale 1 Z rot 7.3 searching scale 1 Z rot 7.5 searching scale 1 Z rot 7.8 searching scale 1 Z rot 8.0 searching scale 1 Z rot 8.3 searching scale 1 Z rot 8.5 searching scale 1 Z rot 8.8 searching scale 1 Z rot 9.0 searching scale 1 Z rot 9.3 global minimum found at slice 125.0, rotations (-0.51, 2.51) final transformation (x=125.0, yr=-0.506, zr=2.508): 0.99900 -0.04376 -0.00883 8.90232; 0.04376 0.99904 -0.00039 15.68034; 0.00884 0.00000 0.99996 2.89990; 0.00000 0.00000 0.00000 1.00000; updating x range to be [126, 130] in xformed coordinates best xformed slice 128 cc center is found at 128 107 124 eigenvectors: -0.00112 0.00099 1.00000; 0.06559 -0.99785 0.00106; 0.99785 0.06559 0.00105; writing aseg with callosum to /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/aseg.auto.mgz... corpus callosum segmentation took 0.4 minutes #-------------------------------------- #@# Merge ASeg Thu Oct 3 12:47:50 BST 2019 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Thu Oct 3 12:47:50 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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... 2151 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 109 gm peak at 71 (71), valley at 29 (29) csf peak at 35, setting threshold to 59 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 70 (70), valley at 28 (28) csf peak at 36, setting threshold to 58 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 1 minutes and 54 seconds. #-------------------------------------------- #@# Mask BFS Thu Oct 3 12:49:45 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1607593 voxels in mask (pct= 9.58) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Thu Oct 3 12:49:46 BST 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 (105.0): 105.5 +- 6.3 [79.0 --> 125.0] GM (70.0) : 67.7 +- 11.0 [30.0 --> 95.0] setting bottom of white matter range to 78.7 setting top of gray matter range to 89.6 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... 17007 sparsely connected voxels removed... thickening thin strands.... 20 segments, 5061 filled 6273 bright non-wm voxels segmented. 7863 diagonally connected voxels added... white matter segmentation took 1.1 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 0.31 minutes reading wm segmentation from wm.seg.mgz... 377 voxels added to wm to prevent paths from MTL structures to cortex 4195 additional wm voxels added 0 additional wm voxels added SEG EDIT: 37089 voxels turned on, 51309 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 98 new 98 115,126,128 old 98 new 98 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 42 found - 42 modified | TOTAL: 42 pass 2 (xy+): 0 found - 42 modified | TOTAL: 42 pass 1 (xy-): 44 found - 44 modified | TOTAL: 86 pass 2 (xy-): 0 found - 44 modified | TOTAL: 86 pass 1 (yz+): 45 found - 45 modified | TOTAL: 131 pass 2 (yz+): 0 found - 45 modified | TOTAL: 131 pass 1 (yz-): 57 found - 57 modified | TOTAL: 188 pass 2 (yz-): 0 found - 57 modified | TOTAL: 188 pass 1 (xz+): 47 found - 47 modified | TOTAL: 235 pass 2 (xz+): 0 found - 47 modified | TOTAL: 235 pass 1 (xz-): 42 found - 42 modified | TOTAL: 277 pass 2 (xz-): 0 found - 42 modified | TOTAL: 277 Iteration Number : 1 pass 1 (+++): 61 found - 61 modified | TOTAL: 61 pass 2 (+++): 0 found - 61 modified | TOTAL: 61 pass 1 (+++): 34 found - 34 modified | TOTAL: 95 pass 2 (+++): 0 found - 34 modified | TOTAL: 95 pass 1 (+++): 76 found - 76 modified | TOTAL: 171 pass 2 (+++): 0 found - 76 modified | TOTAL: 171 pass 1 (+++): 71 found - 71 modified | TOTAL: 242 pass 2 (+++): 0 found - 71 modified | TOTAL: 242 Iteration Number : 1 pass 1 (++): 215 found - 215 modified | TOTAL: 215 pass 2 (++): 0 found - 215 modified | TOTAL: 215 pass 1 (+-): 252 found - 252 modified | TOTAL: 467 pass 2 (+-): 0 found - 252 modified | TOTAL: 467 pass 1 (--): 203 found - 203 modified | TOTAL: 670 pass 2 (--): 1 found - 204 modified | TOTAL: 671 pass 3 (--): 0 found - 204 modified | TOTAL: 671 pass 1 (-+): 207 found - 207 modified | TOTAL: 878 pass 2 (-+): 0 found - 207 modified | TOTAL: 878 Iteration Number : 2 pass 1 (xy+): 11 found - 11 modified | TOTAL: 11 pass 2 (xy+): 0 found - 11 modified | TOTAL: 11 pass 1 (xy-): 12 found - 12 modified | TOTAL: 23 pass 2 (xy-): 0 found - 12 modified | TOTAL: 23 pass 1 (yz+): 23 found - 23 modified | TOTAL: 46 pass 2 (yz+): 0 found - 23 modified | TOTAL: 46 pass 1 (yz-): 13 found - 13 modified | TOTAL: 59 pass 2 (yz-): 0 found - 13 modified | TOTAL: 59 pass 1 (xz+): 16 found - 16 modified | TOTAL: 75 pass 2 (xz+): 0 found - 16 modified | TOTAL: 75 pass 1 (xz-): 14 found - 14 modified | TOTAL: 89 pass 2 (xz-): 0 found - 14 modified | TOTAL: 89 Iteration Number : 2 pass 1 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 pass 1 (+++): 2 found - 2 modified | TOTAL: 6 pass 2 (+++): 0 found - 2 modified | TOTAL: 6 pass 1 (+++): 6 found - 6 modified | TOTAL: 12 pass 2 (+++): 0 found - 6 modified | TOTAL: 12 pass 1 (+++): 1 found - 1 modified | TOTAL: 13 pass 2 (+++): 0 found - 1 modified | TOTAL: 13 Iteration Number : 2 pass 1 (++): 6 found - 6 modified | TOTAL: 6 pass 2 (++): 0 found - 6 modified | TOTAL: 6 pass 1 (+-): 11 found - 11 modified | TOTAL: 17 pass 2 (+-): 0 found - 11 modified | TOTAL: 17 pass 1 (--): 9 found - 9 modified | TOTAL: 26 pass 2 (--): 0 found - 9 modified | TOTAL: 26 pass 1 (-+): 2 found - 2 modified | TOTAL: 28 pass 2 (-+): 0 found - 2 modified | TOTAL: 28 Iteration Number : 3 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+): 4 found - 4 modified | TOTAL: 6 pass 2 (yz+): 0 found - 4 modified | TOTAL: 6 pass 1 (yz-): 1 found - 1 modified | TOTAL: 7 pass 2 (yz-): 0 found - 1 modified | TOTAL: 7 pass 1 (xz+): 1 found - 1 modified | TOTAL: 8 pass 2 (xz+): 0 found - 1 modified | TOTAL: 8 pass 1 (xz-): 0 found - 0 modified | TOTAL: 8 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 (+-): 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 : 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 = 1536 (out of 544452: 0.282119) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Thu Oct 3 12:51:14 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.07379 -0.03619 -0.03506 1.05688; 0.04463 1.04088 0.14862 -37.39441; 0.03214 -0.18045 0.92901 12.28946; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.07379 -0.03619 -0.03506 1.05688; 0.04463 1.04088 0.14862 -37.39441; 0.03214 -0.18045 0.92901 12.28946; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1363 (min = 350, max = 1400), aspect = 0.63 (min = 0.10, max = 0.75) no need to search using seed (126, 123, 151), TAL = (2.0, 23.0, 5.0) talairach voxel to voxel transform 0.92885 0.03734 0.02908 0.05724; -0.03429 0.93342 -0.15062 36.79187; -0.03880 0.18002 1.04615 -6.08401; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (126, 123, 151) --> (2.0, 23.0, 5.0) done. writing output to filled.mgz... filling took 0.4 minutes talairach cc position changed to (2.00, 23.00, 5.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, 23.00, 5.00) SRC: (109.36, 125.15, 169.84) search lh wm seed point around talairach space (-16.00, 23.00, 5.00), SRC: (142.80, 123.92, 168.44) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Thu Oct 3 12:51:38 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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-): 2 found - 2 modified | TOTAL: 4 pass 2 (xy-): 0 found - 2 modified | TOTAL: 4 pass 1 (yz+): 1 found - 1 modified | TOTAL: 5 pass 2 (yz+): 0 found - 1 modified | TOTAL: 5 pass 1 (yz-): 0 found - 0 modified | TOTAL: 5 pass 1 (xz+): 0 found - 0 modified | TOTAL: 5 pass 1 (xz-): 0 found - 0 modified | TOTAL: 5 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 1 found - 1 modified | TOTAL: 2 pass 2 (-+): 0 found - 1 modified | TOTAL: 2 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 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 = 7 (out of 260951: 0.002682) 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 40: 31 vertices, 40 faces slice 50: 2972 vertices, 3122 faces slice 60: 9197 vertices, 9473 faces slice 70: 17978 vertices, 18292 faces slice 80: 28750 vertices, 29175 faces slice 90: 40981 vertices, 41492 faces slice 100: 53613 vertices, 54029 faces slice 110: 66281 vertices, 66748 faces slice 120: 78957 vertices, 79453 faces slice 130: 91671 vertices, 92196 faces slice 140: 104680 vertices, 105234 faces slice 150: 117555 vertices, 118107 faces slice 160: 128287 vertices, 128761 faces slice 170: 138296 vertices, 138769 faces slice 180: 146872 vertices, 147277 faces slice 190: 153707 vertices, 154067 faces slice 200: 159372 vertices, 159696 faces slice 210: 163130 vertices, 163354 faces slice 220: 163414 vertices, 163574 faces slice 230: 163414 vertices, 163574 faces slice 240: 163414 vertices, 163574 faces slice 250: 163414 vertices, 163574 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... 163414 voxel in cpt #1: X=-160 [v=163414,e=490722,f=327148] located at (-25.406954, -5.952826, 10.897169) For the whole surface: X=-160 [v=163414,e=490722,f=327148] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Thu Oct 3 12:51:41 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 1 found - 1 modified | TOTAL: 2 pass 2 (xy-): 0 found - 1 modified | TOTAL: 2 pass 1 (yz+): 0 found - 0 modified | TOTAL: 2 pass 1 (yz-): 4 found - 4 modified | TOTAL: 6 pass 2 (yz-): 0 found - 4 modified | TOTAL: 6 pass 1 (xz+): 0 found - 0 modified | TOTAL: 6 pass 1 (xz-): 0 found - 0 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-): 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 = 7 (out of 270749: 0.002585) 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 40: 160 vertices, 194 faces slice 50: 3370 vertices, 3534 faces slice 60: 10065 vertices, 10336 faces slice 70: 18654 vertices, 18990 faces slice 80: 29250 vertices, 29652 faces slice 90: 40940 vertices, 41429 faces slice 100: 53920 vertices, 54385 faces slice 110: 66522 vertices, 67018 faces slice 120: 80012 vertices, 80521 faces slice 130: 93180 vertices, 93686 faces slice 140: 106056 vertices, 106609 faces slice 150: 118783 vertices, 119306 faces slice 160: 129350 vertices, 129811 faces slice 170: 138037 vertices, 138445 faces slice 180: 146047 vertices, 146465 faces slice 190: 153818 vertices, 154251 faces slice 200: 159915 vertices, 160292 faces slice 210: 164243 vertices, 164503 faces slice 220: 164808 vertices, 164972 faces slice 230: 164808 vertices, 164972 faces slice 240: 164808 vertices, 164972 faces slice 250: 164808 vertices, 164972 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... 164808 voxel in cpt #1: X=-164 [v=164808,e=494916,f=329944] located at (29.889338, -5.744151, 9.708776) For the whole surface: X=-164 [v=164808,e=494916,f=329944] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Thu Oct 3 12:51:44 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix #-------------------------------------------- #@# Smooth1 rh Thu Oct 3 12:51:44 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix Waiting for PID 27158 of (27158 27161) to complete... Waiting for PID 27161 of (27158 27161) 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 (27158 27161) completed and logs appended. #-------------------------------------------- #@# Inflation1 lh Thu Oct 3 12:51:49 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix #-------------------------------------------- #@# Inflation1 rh Thu Oct 3 12:51:49 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Waiting for PID 27206 of (27206 27209) to complete... Waiting for PID 27209 of (27206 27209) 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 = 47.7 mm, total surface area = 83242 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.5 minutes step 000: RMS=0.167 (target=0.015) step 005: RMS=0.127 (target=0.015) step 010: RMS=0.099 (target=0.015) step 015: RMS=0.086 (target=0.015) step 020: RMS=0.077 (target=0.015) step 025: RMS=0.070 (target=0.015) step 030: RMS=0.064 (target=0.015) step 035: RMS=0.060 (target=0.015) step 040: RMS=0.056 (target=0.015) step 045: RMS=0.055 (target=0.015) step 050: RMS=0.054 (target=0.015) step 055: RMS=0.053 (target=0.015) step 060: RMS=0.053 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 80.539323 mris_inflate stimesec 0.307920 mris_inflate ru_maxrss 257912 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 62846 mris_inflate ru_majflt 7 mris_inflate ru_nswap 0 mris_inflate ru_inblock 968 mris_inflate ru_oublock 0 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 22230 mris_inflate ru_nivcsw 11599 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 48.2 mm, total surface area = 83498 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.5 minutes step 000: RMS=0.170 (target=0.015) step 005: RMS=0.129 (target=0.015) step 010: RMS=0.103 (target=0.015) step 015: RMS=0.091 (target=0.015) step 020: RMS=0.083 (target=0.015) step 025: RMS=0.077 (target=0.015) step 030: RMS=0.072 (target=0.015) step 035: RMS=0.068 (target=0.015) step 040: RMS=0.067 (target=0.015) step 045: RMS=0.065 (target=0.015) step 050: RMS=0.064 (target=0.015) step 055: RMS=0.064 (target=0.015) step 060: RMS=0.064 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 81.543777 mris_inflate stimesec 0.243867 mris_inflate ru_maxrss 259924 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 63366 mris_inflate ru_majflt 4 mris_inflate ru_nswap 0 mris_inflate ru_inblock 704 mris_inflate ru_oublock 0 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 14914 mris_inflate ru_nivcsw 13014 PIDs (27206 27209) completed and logs appended. #-------------------------------------------- #@# QSphere lh Thu Oct 3 12:52:17 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix #-------------------------------------------- #@# QSphere rh Thu Oct 3 12:52:17 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix Waiting for PID 27282 of (27282 27285) to complete... Waiting for PID 27285 of (27282 27285) 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 0.89 +- 0.57 (0.00-->6.90) (max @ vno 59461 --> 60667) face area 0.02 +- 0.03 (-0.30-->0.49) == Number of threads available to mris_sphere for OpenMP = 4 == scaling brain by 0.278... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.758, avgs=0 005/300: dt: 0.9000, rms radial error=177.497, avgs=0 010/300: dt: 0.9000, rms radial error=176.937, avgs=0 015/300: dt: 0.9000, rms radial error=176.202, avgs=0 020/300: dt: 0.9000, rms radial error=175.364, avgs=0 025/300: dt: 0.9000, rms radial error=174.468, avgs=0 030/300: dt: 0.9000, rms radial error=173.538, avgs=0 035/300: dt: 0.9000, rms radial error=172.591, avgs=0 040/300: dt: 0.9000, rms radial error=171.636, avgs=0 045/300: dt: 0.9000, rms radial error=170.677, avgs=0 050/300: dt: 0.9000, rms radial error=169.719, avgs=0 055/300: dt: 0.9000, rms radial error=168.764, avgs=0 060/300: dt: 0.9000, rms radial error=167.818, avgs=0 065/300: dt: 0.9000, rms radial error=166.877, avgs=0 070/300: dt: 0.9000, rms radial error=165.940, avgs=0 075/300: dt: 0.9000, rms radial error=165.009, avgs=0 080/300: dt: 0.9000, rms radial error=164.082, avgs=0 085/300: dt: 0.9000, rms radial error=163.161, avgs=0 090/300: dt: 0.9000, rms radial error=162.245, avgs=0 095/300: dt: 0.9000, rms radial error=161.334, avgs=0 100/300: dt: 0.9000, rms radial error=160.428, avgs=0 105/300: dt: 0.9000, rms radial error=159.527, avgs=0 110/300: dt: 0.9000, rms radial error=158.630, avgs=0 115/300: dt: 0.9000, rms radial error=157.739, avgs=0 120/300: dt: 0.9000, rms radial error=156.853, avgs=0 125/300: dt: 0.9000, rms radial error=155.971, avgs=0 130/300: dt: 0.9000, rms radial error=155.095, avgs=0 135/300: dt: 0.9000, rms radial error=154.223, avgs=0 140/300: dt: 0.9000, rms radial error=153.356, avgs=0 145/300: dt: 0.9000, rms radial error=152.494, avgs=0 150/300: dt: 0.9000, rms radial error=151.637, avgs=0 155/300: dt: 0.9000, rms radial error=150.784, avgs=0 160/300: dt: 0.9000, rms radial error=149.937, avgs=0 165/300: dt: 0.9000, rms radial error=149.094, avgs=0 170/300: dt: 0.9000, rms radial error=148.257, avgs=0 175/300: dt: 0.9000, rms radial error=147.422, avgs=0 180/300: dt: 0.9000, rms radial error=146.592, avgs=0 185/300: dt: 0.9000, rms radial error=145.768, avgs=0 190/300: dt: 0.9000, rms radial error=144.946, avgs=0 195/300: dt: 0.9000, rms radial error=144.129, avgs=0 200/300: dt: 0.9000, rms radial error=143.315, avgs=0 205/300: dt: 0.9000, rms radial error=142.507, avgs=0 210/300: dt: 0.9000, rms radial error=141.702, avgs=0 215/300: dt: 0.9000, rms radial error=140.902, avgs=0 220/300: dt: 0.9000, rms radial error=140.106, avgs=0 225/300: dt: 0.9000, rms radial error=139.315, avgs=0 230/300: dt: 0.9000, rms radial error=138.528, avgs=0 235/300: dt: 0.9000, rms radial error=137.749, avgs=0 240/300: dt: 0.9000, rms radial error=136.969, avgs=0 245/300: dt: 0.9000, rms radial error=136.195, avgs=0 250/300: dt: 0.9000, rms radial error=135.427, avgs=0 255/300: dt: 0.9000, rms radial error=134.662, avgs=0 260/300: dt: 0.9000, rms radial error=133.902, avgs=0 265/300: dt: 0.9000, rms radial error=133.146, avgs=0 270/300: dt: 0.9000, rms radial error=132.394, avgs=0 275/300: dt: 0.9000, rms radial error=131.646, avgs=0 280/300: dt: 0.9000, rms radial error=130.903, avgs=0 285/300: dt: 0.9000, rms radial error=130.164, avgs=0 290/300: dt: 0.9000, rms radial error=129.429, avgs=0 295/300: dt: 0.9000, rms radial error=128.698, avgs=0 300/300: dt: 0.9000, rms radial error=127.971, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 19901.22 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 = 3658.17 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00006 epoch 3 (K=160.0), pass 1, starting sse = 468.95 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/11 = 0.00456 epoch 4 (K=640.0), pass 1, starting sse = 41.92 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/11 = 0.00578 final distance error %29.79 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.04 hours mris_sphere utimesec 392.593314 mris_sphere stimesec 0.416018 mris_sphere ru_maxrss 258036 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 62870 mris_sphere ru_majflt 13 mris_sphere ru_nswap 0 mris_sphere ru_inblock 1928 mris_sphere ru_oublock 0 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 20746 mris_sphere ru_nivcsw 41158 FSRUNTIME@ mris_sphere 0.0402 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 0.88 +- 0.58 (0.00-->9.20) (max @ vno 63374 --> 64719) face area 0.02 +- 0.03 (-0.15-->0.76) == Number of threads available to mris_sphere for OpenMP = 4 == scaling brain by 0.276... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.695, avgs=0 005/300: dt: 0.9000, rms radial error=177.433, avgs=0 010/300: dt: 0.9000, rms radial error=176.870, avgs=0 015/300: dt: 0.9000, rms radial error=176.131, avgs=0 020/300: dt: 0.9000, rms radial error=175.288, avgs=0 025/300: dt: 0.9000, rms radial error=174.386, avgs=0 030/300: dt: 0.9000, rms radial error=173.457, avgs=0 035/300: dt: 0.9000, rms radial error=172.510, avgs=0 040/300: dt: 0.9000, rms radial error=171.556, avgs=0 045/300: dt: 0.9000, rms radial error=170.600, avgs=0 050/300: dt: 0.9000, rms radial error=169.645, avgs=0 055/300: dt: 0.9000, rms radial error=168.691, avgs=0 060/300: dt: 0.9000, rms radial error=167.746, avgs=0 065/300: dt: 0.9000, rms radial error=166.806, avgs=0 070/300: dt: 0.9000, rms radial error=165.870, avgs=0 075/300: dt: 0.9000, rms radial error=164.940, avgs=0 080/300: dt: 0.9000, rms radial error=164.015, avgs=0 085/300: dt: 0.9000, rms radial error=163.091, avgs=0 090/300: dt: 0.9000, rms radial error=162.176, avgs=0 095/300: dt: 0.9000, rms radial error=161.267, avgs=0 100/300: dt: 0.9000, rms radial error=160.361, avgs=0 105/300: dt: 0.9000, rms radial error=159.460, avgs=0 110/300: dt: 0.9000, rms radial error=158.565, avgs=0 115/300: dt: 0.9000, rms radial error=157.675, avgs=0 120/300: dt: 0.9000, rms radial error=156.787, avgs=0 125/300: dt: 0.9000, rms radial error=155.908, avgs=0 130/300: dt: 0.9000, rms radial error=155.030, avgs=0 135/300: dt: 0.9000, rms radial error=154.158, avgs=0 140/300: dt: 0.9000, rms radial error=153.291, avgs=0 145/300: dt: 0.9000, rms radial error=152.430, avgs=0 150/300: dt: 0.9000, rms radial error=151.575, avgs=0 155/300: dt: 0.9000, rms radial error=150.723, avgs=0 160/300: dt: 0.9000, rms radial error=149.876, avgs=0 165/300: dt: 0.9000, rms radial error=149.034, avgs=0 170/300: dt: 0.9000, rms radial error=148.195, avgs=0 175/300: dt: 0.9000, rms radial error=147.363, avgs=0 180/300: dt: 0.9000, rms radial error=146.535, avgs=0 185/300: dt: 0.9000, rms radial error=145.711, avgs=0 190/300: dt: 0.9000, rms radial error=144.891, avgs=0 195/300: dt: 0.9000, rms radial error=144.076, avgs=0 200/300: dt: 0.9000, rms radial error=143.266, avgs=0 205/300: dt: 0.9000, rms radial error=142.460, avgs=0 210/300: dt: 0.9000, rms radial error=141.658, avgs=0 215/300: dt: 0.9000, rms radial error=140.861, avgs=0 220/300: dt: 0.9000, rms radial error=140.068, avgs=0 225/300: dt: 0.9000, rms radial error=139.279, avgs=0 230/300: dt: 0.9000, rms radial error=138.495, avgs=0 235/300: dt: 0.9000, rms radial error=137.715, avgs=0 240/300: dt: 0.9000, rms radial error=136.940, avgs=0 245/300: dt: 0.9000, rms radial error=136.169, avgs=0 250/300: dt: 0.9000, rms radial error=135.402, avgs=0 255/300: dt: 0.9000, rms radial error=134.639, avgs=0 260/300: dt: 0.9000, rms radial error=133.881, avgs=0 265/300: dt: 0.9000, rms radial error=133.127, avgs=0 270/300: dt: 0.9000, rms radial error=132.377, avgs=0 275/300: dt: 0.9000, rms radial error=131.631, avgs=0 280/300: dt: 0.9000, rms radial error=130.890, avgs=0 285/300: dt: 0.9000, rms radial error=130.152, avgs=0 290/300: dt: 0.9000, rms radial error=129.419, avgs=0 295/300: dt: 0.9000, rms radial error=128.690, avgs=0 300/300: dt: 0.9000, rms radial error=127.965, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 20133.68 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00009 epoch 2 (K=40.0), pass 1, starting sse = 3737.16 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00005 epoch 3 (K=160.0), pass 1, starting sse = 497.62 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.03/10 = 0.00285 epoch 4 (K=640.0), pass 1, starting sse = 54.06 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/11 = 0.00568 final distance error %30.81 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.04 hours mris_sphere utimesec 383.332086 mris_sphere stimesec 0.507819 mris_sphere ru_maxrss 259992 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 63387 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 64 mris_sphere ru_oublock 0 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 26717 mris_sphere ru_nivcsw 39779 FSRUNTIME@ mris_sphere 0.0394 hours 1 threads PIDs (27282 27285) completed and logs appended. #-------------------------------------------- #@# Fix Topology Copy lh Thu Oct 3 12:54:42 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Thu Oct 3 12:54:42 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Thu Oct 3 12:54:42 BST 2019 mris_fix_topology -rusage /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 S131032017_Supine lh #@# Fix Topology rh Thu Oct 3 12:54:42 BST 2019 mris_fix_topology -rusage /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 S131032017_Supine rh Waiting for PID 27450 of (27450 27453) to complete... Waiting for PID 27453 of (27450 27453) to complete... mris_fix_topology -rusage /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 S131032017_Supine 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=-160 (nv=163414, nf=327148, ne=490722, g=81) 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... 13182 ambiguous faces found in tessellation segmenting defects... 73 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 8 into 6 -merging segment 59 into 50 71 defects to be corrected 0 vertices coincident reading input surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.5316 (-4.7658) -vertex loglikelihood: -6.5269 (-3.2634) -normal dot loglikelihood: -3.5689 (-3.5689) -quad curv loglikelihood: -6.6031 (-3.3016) Total Loglikelihood : -26.2306 CORRECTING DEFECT 0 (vertices=1156, convex hull=696, v0=17948) XL defect detected... After retessellation of defect 0 (v0=17948), euler #=-64 (155872,465092,309156) : difference with theory (-68) = -4 CORRECTING DEFECT 1 (vertices=350, convex hull=338, v0=25130) After retessellation of defect 1 (v0=25130), euler #=-63 (156012,465673,309598) : difference with theory (-67) = -4 CORRECTING DEFECT 2 (vertices=83, convex hull=69, v0=29597) After retessellation of defect 2 (v0=29597), euler #=-62 (156029,465754,309663) : difference with theory (-66) = -4 CORRECTING DEFECT 3 (vertices=23, convex hull=55, v0=31120) After retessellation of defect 3 (v0=31120), euler #=-61 (156039,465800,309700) : difference with theory (-65) = -4 CORRECTING DEFECT 4 (vertices=71, convex hull=47, v0=34999) After retessellation of defect 4 (v0=34999), euler #=-60 (156045,465832,309727) : difference with theory (-64) = -4 CORRECTING DEFECT 5 (vertices=39, convex hull=69, v0=44584) After retessellation of defect 5 (v0=44584), euler #=-59 (156063,465915,309793) : difference with theory (-63) = -4 CORRECTING DEFECT 6 (vertices=174, convex hull=157, v0=45081) After retessellation of defect 6 (v0=45081), euler #=-57 (156094,466078,309927) : difference with theory (-62) = -5 CORRECTING DEFECT 7 (vertices=22, convex hull=18, v0=45699) After retessellation of defect 7 (v0=45699), euler #=-56 (156095,466086,309935) : difference with theory (-61) = -5 CORRECTING DEFECT 8 (vertices=25, convex hull=28, v0=52012) After retessellation of defect 8 (v0=52012), euler #=-55 (156098,466104,309951) : difference with theory (-60) = -5 CORRECTING DEFECT 9 (vertices=75, convex hull=66, v0=52148) After retessellation of defect 9 (v0=52148), euler #=-54 (156128,466222,310040) : difference with theory (-59) = -5 CORRECTING DEFECT 10 (vertices=49, convex hull=36, v0=52323) After retessellation of defect 10 (v0=52323), euler #=-53 (156134,466259,310072) : difference with theory (-58) = -5 CORRECTING DEFECT 11 (vertices=434, convex hull=248, v0=57183) normal vector of length zero at vertex 157786 with 4 faces normal vector of length zero at vertex 157786 with 4 faces normal vector of length zero at vertex 157786 with 4 faces normal vector of length zero at vertex 157846 with 4 faces normal vector of length zero at vertex 157846 with 4 faces normal vector of length zero at vertex 157846 with 4 faces After retessellation of defect 11 (v0=57183), euler #=-55 (156280,466840,310505) : difference with theory (-57) = -2 CORRECTING DEFECT 12 (vertices=77, convex hull=92, v0=58632) After retessellation of defect 12 (v0=58632), euler #=-54 (156330,467034,310650) : difference with theory (-56) = -2 CORRECTING DEFECT 13 (vertices=150, convex hull=105, v0=59546) After retessellation of defect 13 (v0=59546), euler #=-53 (156357,467163,310753) : difference with theory (-55) = -2 CORRECTING DEFECT 14 (vertices=159, convex hull=171, v0=60259) After retessellation of defect 14 (v0=60259), euler #=-52 (156415,467419,310952) : difference with theory (-54) = -2 CORRECTING DEFECT 15 (vertices=90, convex hull=30, v0=63658) After retessellation of defect 15 (v0=63658), euler #=-51 (156422,467454,310981) : difference with theory (-53) = -2 CORRECTING DEFECT 16 (vertices=110, convex hull=33, v0=65729) After retessellation of defect 16 (v0=65729), euler #=-50 (156434,467499,311015) : difference with theory (-52) = -2 CORRECTING DEFECT 17 (vertices=94, convex hull=51, v0=66147) After retessellation of defect 17 (v0=66147), euler #=-49 (156440,467535,311046) : difference with theory (-51) = -2 CORRECTING DEFECT 18 (vertices=32, convex hull=58, v0=69431) After retessellation of defect 18 (v0=69431), euler #=-48 (156461,467621,311112) : difference with theory (-50) = -2 CORRECTING DEFECT 19 (vertices=55, convex hull=44, v0=70775) After retessellation of defect 19 (v0=70775), euler #=-47 (156474,467676,311155) : difference with theory (-49) = -2 CORRECTING DEFECT 20 (vertices=31, convex hull=56, v0=71949) After retessellation of defect 20 (v0=71949), euler #=-46 (156493,467757,311218) : difference with theory (-48) = -2 CORRECTING DEFECT 21 (vertices=57, convex hull=81, v0=74267) After retessellation of defect 21 (v0=74267), euler #=-45 (156524,467882,311313) : difference with theory (-47) = -2 CORRECTING DEFECT 22 (vertices=6, convex hull=21, v0=74400) After retessellation of defect 22 (v0=74400), euler #=-44 (156526,467894,311324) : difference with theory (-46) = -2 CORRECTING DEFECT 23 (vertices=92, convex hull=89, v0=75055) After retessellation of defect 23 (v0=75055), euler #=-43 (156568,468061,311450) : difference with theory (-45) = -2 CORRECTING DEFECT 24 (vertices=25, convex hull=31, v0=78704) After retessellation of defect 24 (v0=78704), euler #=-42 (156575,468090,311473) : difference with theory (-44) = -2 CORRECTING DEFECT 25 (vertices=32, convex hull=64, v0=80111) After retessellation of defect 25 (v0=80111), euler #=-42 (156593,468175,311540) : difference with theory (-43) = -1 CORRECTING DEFECT 26 (vertices=39, convex hull=76, v0=80304) After retessellation of defect 26 (v0=80304), euler #=-41 (156618,468282,311623) : difference with theory (-42) = -1 CORRECTING DEFECT 27 (vertices=69, convex hull=107, v0=81293) After retessellation of defect 27 (v0=81293), euler #=-40 (156657,468445,311748) : difference with theory (-41) = -1 CORRECTING DEFECT 28 (vertices=36, convex hull=36, v0=83456) After retessellation of defect 28 (v0=83456), euler #=-39 (156669,468493,311785) : difference with theory (-40) = -1 CORRECTING DEFECT 29 (vertices=8, convex hull=20, v0=85319) After retessellation of defect 29 (v0=85319), euler #=-38 (156672,468506,311796) : difference with theory (-39) = -1 CORRECTING DEFECT 30 (vertices=75, convex hull=86, v0=88848) After retessellation of defect 30 (v0=88848), euler #=-37 (156707,468650,311906) : difference with theory (-38) = -1 CORRECTING DEFECT 31 (vertices=201, convex hull=79, v0=89199) After retessellation of defect 31 (v0=89199), euler #=-36 (156716,468712,311960) : difference with theory (-37) = -1 CORRECTING DEFECT 32 (vertices=75, convex hull=41, v0=91026) After retessellation of defect 32 (v0=91026), euler #=-35 (156736,468787,312016) : difference with theory (-36) = -1 CORRECTING DEFECT 33 (vertices=33, convex hull=31, v0=91146) After retessellation of defect 33 (v0=91146), euler #=-34 (156743,468817,312040) : difference with theory (-35) = -1 CORRECTING DEFECT 34 (vertices=31, convex hull=62, v0=92478) After retessellation of defect 34 (v0=92478), euler #=-33 (156759,468889,312097) : difference with theory (-34) = -1 CORRECTING DEFECT 35 (vertices=43, convex hull=82, v0=92736) After retessellation of defect 35 (v0=92736), euler #=-32 (156785,468995,312178) : difference with theory (-33) = -1 CORRECTING DEFECT 36 (vertices=25, convex hull=42, v0=95440) After retessellation of defect 36 (v0=95440), euler #=-31 (156788,469018,312199) : difference with theory (-32) = -1 CORRECTING DEFECT 37 (vertices=28, convex hull=58, v0=95519) After retessellation of defect 37 (v0=95519), euler #=-30 (156797,469070,312243) : difference with theory (-31) = -1 CORRECTING DEFECT 38 (vertices=29, convex hull=71, v0=98014) After retessellation of defect 38 (v0=98014), euler #=-29 (156806,469127,312292) : difference with theory (-30) = -1 CORRECTING DEFECT 39 (vertices=5, convex hull=32, v0=98923) After retessellation of defect 39 (v0=98923), euler #=-28 (156806,469134,312300) : difference with theory (-29) = -1 CORRECTING DEFECT 40 (vertices=42, convex hull=97, v0=102104) After retessellation of defect 40 (v0=102104), euler #=-27 (156815,469198,312356) : difference with theory (-28) = -1 CORRECTING DEFECT 41 (vertices=24, convex hull=41, v0=104290) After retessellation of defect 41 (v0=104290), euler #=-26 (156817,469218,312375) : difference with theory (-27) = -1 CORRECTING DEFECT 42 (vertices=26, convex hull=34, v0=104519) After retessellation of defect 42 (v0=104519), euler #=-25 (156824,469250,312401) : difference with theory (-26) = -1 CORRECTING DEFECT 43 (vertices=63, convex hull=99, v0=105995) After retessellation of defect 43 (v0=105995), euler #=-24 (156853,469378,312501) : difference with theory (-25) = -1 CORRECTING DEFECT 44 (vertices=34, convex hull=66, v0=107342) After retessellation of defect 44 (v0=107342), euler #=-23 (156861,469426,312542) : difference with theory (-24) = -1 CORRECTING DEFECT 45 (vertices=26, convex hull=73, v0=107681) After retessellation of defect 45 (v0=107681), euler #=-22 (156878,469504,312604) : difference with theory (-23) = -1 CORRECTING DEFECT 46 (vertices=150, convex hull=135, v0=108222) After retessellation of defect 46 (v0=108222), euler #=-22 (156900,469638,312716) : difference with theory (-22) = 0 CORRECTING DEFECT 47 (vertices=58, convex hull=53, v0=109783) After retessellation of defect 47 (v0=109783), euler #=-22 (156916,469714,312776) : difference with theory (-21) = 1 CORRECTING DEFECT 48 (vertices=44, convex hull=33, v0=111704) After retessellation of defect 48 (v0=111704), euler #=-21 (156920,469739,312798) : difference with theory (-20) = 1 CORRECTING DEFECT 49 (vertices=782, convex hull=671, v0=113431) L defect detected... After retessellation of defect 49 (v0=113431), euler #=-19 (157230,471008,313759) : difference with theory (-19) = 0 CORRECTING DEFECT 50 (vertices=5, convex hull=24, v0=114203) After retessellation of defect 50 (v0=114203), euler #=-18 (157231,471017,313768) : difference with theory (-18) = 0 CORRECTING DEFECT 51 (vertices=64, convex hull=84, v0=116070) After retessellation of defect 51 (v0=116070), euler #=-17 (157258,471131,313856) : difference with theory (-17) = 0 CORRECTING DEFECT 52 (vertices=25, convex hull=26, v0=116233) After retessellation of defect 52 (v0=116233), euler #=-16 (157262,471151,313873) : difference with theory (-16) = 0 CORRECTING DEFECT 53 (vertices=11, convex hull=23, v0=118747) After retessellation of defect 53 (v0=118747), euler #=-15 (157263,471161,313883) : difference with theory (-15) = 0 CORRECTING DEFECT 54 (vertices=477, convex hull=280, v0=118764) After retessellation of defect 54 (v0=118764), euler #=-14 (157310,471437,314113) : difference with theory (-14) = 0 CORRECTING DEFECT 55 (vertices=285, convex hull=171, v0=121907) After retessellation of defect 55 (v0=121907), euler #=-13 (157380,471726,314333) : difference with theory (-13) = 0 CORRECTING DEFECT 56 (vertices=1090, convex hull=237, v0=124045) After retessellation of defect 56 (v0=124045), euler #=-12 (157454,472064,314598) : difference with theory (-12) = 0 CORRECTING DEFECT 57 (vertices=16, convex hull=29, v0=127011) After retessellation of defect 57 (v0=127011), euler #=-11 (157459,472090,314620) : difference with theory (-11) = 0 CORRECTING DEFECT 58 (vertices=129, convex hull=73, v0=134273) After retessellation of defect 58 (v0=134273), euler #=-10 (157476,472171,314685) : difference with theory (-10) = 0 CORRECTING DEFECT 59 (vertices=22, convex hull=64, v0=134308) After retessellation of defect 59 (v0=134308), euler #=-9 (157489,472234,314736) : difference with theory (-9) = 0 CORRECTING DEFECT 60 (vertices=5, convex hull=24, v0=138244) After retessellation of defect 60 (v0=138244), euler #=-8 (157491,472246,314747) : difference with theory (-8) = 0 CORRECTING DEFECT 61 (vertices=50, convex hull=93, v0=139458) After retessellation of defect 61 (v0=139458), euler #=-7 (157524,472389,314858) : difference with theory (-7) = 0 CORRECTING DEFECT 62 (vertices=47, convex hull=75, v0=143503) After retessellation of defect 62 (v0=143503), euler #=-6 (157546,472486,314934) : difference with theory (-6) = 0 CORRECTING DEFECT 63 (vertices=11, convex hull=26, v0=145824) After retessellation of defect 63 (v0=145824), euler #=-5 (157549,472502,314948) : difference with theory (-5) = 0 CORRECTING DEFECT 64 (vertices=8, convex hull=18, v0=146842) After retessellation of defect 64 (v0=146842), euler #=-4 (157550,472511,314957) : difference with theory (-4) = 0 CORRECTING DEFECT 65 (vertices=42, convex hull=66, v0=148189) After retessellation of defect 65 (v0=148189), euler #=-3 (157568,472590,315019) : difference with theory (-3) = 0 CORRECTING DEFECT 66 (vertices=66, convex hull=84, v0=155737) After retessellation of defect 66 (v0=155737), euler #=-2 (157588,472685,315095) : difference with theory (-2) = 0 CORRECTING DEFECT 67 (vertices=32, convex hull=69, v0=161258) After retessellation of defect 67 (v0=161258), euler #=-1 (157601,472751,315149) : difference with theory (-1) = 0 CORRECTING DEFECT 68 (vertices=24, convex hull=32, v0=161543) After retessellation of defect 68 (v0=161543), euler #=0 (157605,472773,315168) : difference with theory (0) = 0 CORRECTING DEFECT 69 (vertices=57, convex hull=49, v0=163083) After retessellation of defect 69 (v0=163083), euler #=1 (157613,472816,315204) : difference with theory (1) = 0 CORRECTING DEFECT 70 (vertices=16, convex hull=46, v0=163203) After retessellation of defect 70 (v0=163203), euler #=2 (157621,472857,315238) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.26 (0.00-->11.97) (max @ vno 124334 --> 125997) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.26 (0.00-->11.97) (max @ vno 124334 --> 125997) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 231 mutations (33.4%), 461 crossovers (66.6%), 452 vertices were eliminated building final representation... 5793 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=157621, nf=315238, ne=472857, g=0) writing corrected surface to /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 41.7 minutes 0 defective edges removing intersecting faces 000: 653 intersecting 001: 35 intersecting 002: 3 intersecting mris_fix_topology utimesec 2510.674301 mris_fix_topology stimesec 0.427985 mris_fix_topology ru_maxrss 540104 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 140049 mris_fix_topology ru_majflt 6 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 1192 mris_fix_topology ru_oublock 0 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 5715 mris_fix_topology ru_nivcsw 18593 FSRUNTIME@ mris_fix_topology lh 0.6954 hours 1 threads mris_fix_topology -rusage /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 S131032017_Supine 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=-164 (nv=164808, nf=329944, ne=494916, g=83) 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 15 iterations marking ambiguous vertices... 20693 ambiguous faces found in tessellation segmenting defects... 98 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 30 into 25 -merging segment 33 into 25 -merging segment 37 into 27 -merging segment 63 into 49 -merging segment 62 into 49 -merging segment 77 into 74 -merging segment 83 into 81 91 defects to be corrected 0 vertices coincident reading input surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.7006 (-4.8503) -vertex loglikelihood: -6.5261 (-3.2631) -normal dot loglikelihood: -3.5471 (-3.5471) -quad curv loglikelihood: -6.2211 (-3.1106) Total Loglikelihood : -25.9949 CORRECTING DEFECT 0 (vertices=46, convex hull=75, v0=120) After retessellation of defect 0 (v0=120), euler #=-89 (152915,455546,302542) : difference with theory (-88) = 1 CORRECTING DEFECT 1 (vertices=42, convex hull=66, v0=14831) After retessellation of defect 1 (v0=14831), euler #=-88 (152941,455650,302621) : difference with theory (-87) = 1 CORRECTING DEFECT 2 (vertices=24, convex hull=27, v0=19571) After retessellation of defect 2 (v0=19571), euler #=-87 (152942,455666,302637) : difference with theory (-86) = 1 CORRECTING DEFECT 3 (vertices=280, convex hull=108, v0=21417) After retessellation of defect 3 (v0=21417), euler #=-86 (153000,455888,302802) : difference with theory (-85) = 1 CORRECTING DEFECT 4 (vertices=64, convex hull=32, v0=23676) After retessellation of defect 4 (v0=23676), euler #=-85 (153003,455906,302818) : difference with theory (-84) = 1 CORRECTING DEFECT 5 (vertices=103, convex hull=103, v0=25532) After retessellation of defect 5 (v0=25532), euler #=-84 (153051,456092,302957) : difference with theory (-83) = 1 CORRECTING DEFECT 6 (vertices=45, convex hull=36, v0=27829) After retessellation of defect 6 (v0=27829), euler #=-83 (153056,456119,302980) : difference with theory (-82) = 1 CORRECTING DEFECT 7 (vertices=73, convex hull=51, v0=28780) After retessellation of defect 7 (v0=28780), euler #=-82 (153078,456202,303042) : difference with theory (-81) = 1 CORRECTING DEFECT 8 (vertices=366, convex hull=338, v0=29180) After retessellation of defect 8 (v0=29180), euler #=-81 (153118,456489,303290) : difference with theory (-80) = 1 CORRECTING DEFECT 9 (vertices=50, convex hull=75, v0=29991) After retessellation of defect 9 (v0=29991), euler #=-80 (153129,456554,303345) : difference with theory (-79) = 1 CORRECTING DEFECT 10 (vertices=65, convex hull=49, v0=32115) After retessellation of defect 10 (v0=32115), euler #=-79 (153136,456588,303373) : difference with theory (-78) = 1 CORRECTING DEFECT 11 (vertices=36, convex hull=82, v0=35938) After retessellation of defect 11 (v0=35938), euler #=-78 (153157,456684,303449) : difference with theory (-77) = 1 CORRECTING DEFECT 12 (vertices=27, convex hull=21, v0=37110) After retessellation of defect 12 (v0=37110), euler #=-77 (153157,456693,303459) : difference with theory (-76) = 1 CORRECTING DEFECT 13 (vertices=22, convex hull=26, v0=39510) After retessellation of defect 13 (v0=39510), euler #=-76 (153161,456714,303477) : difference with theory (-75) = 1 CORRECTING DEFECT 14 (vertices=87, convex hull=49, v0=40454) After retessellation of defect 14 (v0=40454), euler #=-75 (153169,456753,303509) : difference with theory (-74) = 1 CORRECTING DEFECT 15 (vertices=24, convex hull=70, v0=40530) After retessellation of defect 15 (v0=40530), euler #=-74 (153182,456820,303564) : difference with theory (-73) = 1 CORRECTING DEFECT 16 (vertices=34, convex hull=43, v0=40670) After retessellation of defect 16 (v0=40670), euler #=-73 (153192,456867,303602) : difference with theory (-72) = 1 CORRECTING DEFECT 17 (vertices=49, convex hull=29, v0=40737) After retessellation of defect 17 (v0=40737), euler #=-72 (153196,456889,303621) : difference with theory (-71) = 1 CORRECTING DEFECT 18 (vertices=89, convex hull=77, v0=41198) After retessellation of defect 18 (v0=41198), euler #=-71 (153209,456965,303685) : difference with theory (-70) = 1 CORRECTING DEFECT 19 (vertices=109, convex hull=81, v0=44826) After retessellation of defect 19 (v0=44826), euler #=-71 (153235,457080,303774) : difference with theory (-69) = 2 CORRECTING DEFECT 20 (vertices=19, convex hull=66, v0=45763) After retessellation of defect 20 (v0=45763), euler #=-70 (153246,457138,303822) : difference with theory (-68) = 2 CORRECTING DEFECT 21 (vertices=271, convex hull=112, v0=48634) After retessellation of defect 21 (v0=48634), euler #=-69 (153300,457347,303978) : difference with theory (-67) = 2 CORRECTING DEFECT 22 (vertices=33, convex hull=25, v0=49490) After retessellation of defect 22 (v0=49490), euler #=-68 (153302,457360,303990) : difference with theory (-66) = 2 CORRECTING DEFECT 23 (vertices=1961, convex hull=621, v0=50090) XL defect detected... After retessellation of defect 23 (v0=50090), euler #=-68 (153559,458437,304810) : difference with theory (-65) = 3 CORRECTING DEFECT 24 (vertices=16, convex hull=25, v0=50625) After retessellation of defect 24 (v0=50625), euler #=-67 (153560,458453,304826) : difference with theory (-64) = 3 CORRECTING DEFECT 25 (vertices=406, convex hull=330, v0=57584) After retessellation of defect 25 (v0=57584), euler #=-64 (153642,458894,305188) : difference with theory (-63) = 1 CORRECTING DEFECT 26 (vertices=711, convex hull=272, v0=58368) After retessellation of defect 26 (v0=58368), euler #=-64 (153680,459155,305411) : difference with theory (-62) = 2 CORRECTING DEFECT 27 (vertices=1506, convex hull=430, v0=60842) L defect detected... After retessellation of defect 27 (v0=60842), euler #=-63 (153929,460128,306136) : difference with theory (-61) = 2 CORRECTING DEFECT 28 (vertices=34, convex hull=82, v0=61150) After retessellation of defect 28 (v0=61150), euler #=-62 (153947,460214,306205) : difference with theory (-60) = 2 CORRECTING DEFECT 29 (vertices=20, convex hull=29, v0=68865) After retessellation of defect 29 (v0=68865), euler #=-61 (153951,460234,306222) : difference with theory (-59) = 2 CORRECTING DEFECT 30 (vertices=9, convex hull=14, v0=70147) After retessellation of defect 30 (v0=70147), euler #=-60 (153952,460240,306228) : difference with theory (-58) = 2 CORRECTING DEFECT 31 (vertices=33, convex hull=47, v0=70260) After retessellation of defect 31 (v0=70260), euler #=-59 (153963,460287,306265) : difference with theory (-57) = 2 CORRECTING DEFECT 32 (vertices=143, convex hull=62, v0=78663) After retessellation of defect 32 (v0=78663), euler #=-58 (153969,460331,306304) : difference with theory (-56) = 2 CORRECTING DEFECT 33 (vertices=20, convex hull=26, v0=83654) After retessellation of defect 33 (v0=83654), euler #=-57 (153973,460348,306318) : difference with theory (-55) = 2 CORRECTING DEFECT 34 (vertices=5, convex hull=25, v0=86141) After retessellation of defect 34 (v0=86141), euler #=-56 (153975,460361,306330) : difference with theory (-54) = 2 CORRECTING DEFECT 35 (vertices=655, convex hull=55, v0=88153) After retessellation of defect 35 (v0=88153), euler #=-55 (153984,460411,306372) : difference with theory (-53) = 2 CORRECTING DEFECT 36 (vertices=6, convex hull=33, v0=88920) After retessellation of defect 36 (v0=88920), euler #=-54 (153987,460430,306389) : difference with theory (-52) = 2 CORRECTING DEFECT 37 (vertices=7, convex hull=26, v0=91581) After retessellation of defect 37 (v0=91581), euler #=-53 (153987,460440,306400) : difference with theory (-51) = 2 CORRECTING DEFECT 38 (vertices=22, convex hull=51, v0=93039) After retessellation of defect 38 (v0=93039), euler #=-52 (153996,460485,306437) : difference with theory (-50) = 2 CORRECTING DEFECT 39 (vertices=25, convex hull=46, v0=95344) After retessellation of defect 39 (v0=95344), euler #=-51 (154009,460537,306477) : difference with theory (-49) = 2 CORRECTING DEFECT 40 (vertices=30, convex hull=40, v0=96755) After retessellation of defect 40 (v0=96755), euler #=-50 (154018,460581,306513) : difference with theory (-48) = 2 CORRECTING DEFECT 41 (vertices=34, convex hull=54, v0=99124) After retessellation of defect 41 (v0=99124), euler #=-49 (154039,460666,306578) : difference with theory (-47) = 2 CORRECTING DEFECT 42 (vertices=27, convex hull=17, v0=99425) After retessellation of defect 42 (v0=99425), euler #=-48 (154042,460678,306588) : difference with theory (-46) = 2 CORRECTING DEFECT 43 (vertices=21, convex hull=33, v0=101603) After retessellation of defect 43 (v0=101603), euler #=-47 (154049,460711,306615) : difference with theory (-45) = 2 CORRECTING DEFECT 44 (vertices=104, convex hull=99, v0=101908) After retessellation of defect 44 (v0=101908), euler #=-46 (154058,460785,306681) : difference with theory (-44) = 2 CORRECTING DEFECT 45 (vertices=48, convex hull=43, v0=102105) After retessellation of defect 45 (v0=102105), euler #=-45 (154065,460823,306713) : difference with theory (-43) = 2 CORRECTING DEFECT 46 (vertices=384, convex hull=234, v0=102125) After retessellation of defect 46 (v0=102125), euler #=-42 (154162,461228,307024) : difference with theory (-42) = 0 CORRECTING DEFECT 47 (vertices=12, convex hull=18, v0=102575) After retessellation of defect 47 (v0=102575), euler #=-41 (154164,461239,307034) : difference with theory (-41) = 0 CORRECTING DEFECT 48 (vertices=5, convex hull=22, v0=103206) After retessellation of defect 48 (v0=103206), euler #=-40 (154165,461249,307044) : difference with theory (-40) = 0 CORRECTING DEFECT 49 (vertices=5, convex hull=26, v0=103329) After retessellation of defect 49 (v0=103329), euler #=-39 (154166,461258,307053) : difference with theory (-39) = 0 CORRECTING DEFECT 50 (vertices=24, convex hull=48, v0=103621) After retessellation of defect 50 (v0=103621), euler #=-38 (154177,461309,307094) : difference with theory (-38) = 0 CORRECTING DEFECT 51 (vertices=56, convex hull=35, v0=104252) After retessellation of defect 51 (v0=104252), euler #=-37 (154182,461338,307119) : difference with theory (-37) = 0 CORRECTING DEFECT 52 (vertices=76, convex hull=105, v0=104541) After retessellation of defect 52 (v0=104541), euler #=-36 (154212,461480,307232) : difference with theory (-36) = 0 CORRECTING DEFECT 53 (vertices=186, convex hull=170, v0=105728) After retessellation of defect 53 (v0=105728), euler #=-35 (154247,461665,307383) : difference with theory (-35) = 0 CORRECTING DEFECT 54 (vertices=211, convex hull=94, v0=105949) After retessellation of defect 54 (v0=105949), euler #=-34 (154292,461843,307517) : difference with theory (-34) = 0 CORRECTING DEFECT 55 (vertices=36, convex hull=31, v0=106564) After retessellation of defect 55 (v0=106564), euler #=-33 (154298,461870,307539) : difference with theory (-33) = 0 CORRECTING DEFECT 56 (vertices=232, convex hull=162, v0=106857) After retessellation of defect 56 (v0=106857), euler #=-32 (154392,462226,307802) : difference with theory (-32) = 0 CORRECTING DEFECT 57 (vertices=111, convex hull=97, v0=107711) After retessellation of defect 57 (v0=107711), euler #=-31 (154420,462352,307901) : difference with theory (-31) = 0 CORRECTING DEFECT 58 (vertices=32, convex hull=67, v0=108169) After retessellation of defect 58 (v0=108169), euler #=-30 (154435,462427,307962) : difference with theory (-30) = 0 CORRECTING DEFECT 59 (vertices=43, convex hull=30, v0=109982) After retessellation of defect 59 (v0=109982), euler #=-29 (154440,462451,307982) : difference with theory (-29) = 0 CORRECTING DEFECT 60 (vertices=22, convex hull=31, v0=113505) After retessellation of defect 60 (v0=113505), euler #=-28 (154446,462478,308004) : difference with theory (-28) = 0 CORRECTING DEFECT 61 (vertices=63, convex hull=92, v0=115111) After retessellation of defect 61 (v0=115111), euler #=-27 (154472,462601,308102) : difference with theory (-27) = 0 CORRECTING DEFECT 62 (vertices=19, convex hull=21, v0=117205) After retessellation of defect 62 (v0=117205), euler #=-26 (154477,462622,308119) : difference with theory (-26) = 0 CORRECTING DEFECT 63 (vertices=509, convex hull=285, v0=117442) After retessellation of defect 63 (v0=117442), euler #=-25 (154567,463024,308432) : difference with theory (-25) = 0 CORRECTING DEFECT 64 (vertices=105, convex hull=44, v0=118322) After retessellation of defect 64 (v0=118322), euler #=-24 (154576,463066,308466) : difference with theory (-24) = 0 CORRECTING DEFECT 65 (vertices=57, convex hull=36, v0=118430) After retessellation of defect 65 (v0=118430), euler #=-23 (154585,463106,308498) : difference with theory (-23) = 0 CORRECTING DEFECT 66 (vertices=35, convex hull=67, v0=122848) After retessellation of defect 66 (v0=122848), euler #=-22 (154602,463178,308554) : difference with theory (-22) = 0 CORRECTING DEFECT 67 (vertices=46, convex hull=35, v0=123633) After retessellation of defect 67 (v0=123633), euler #=-21 (154608,463207,308578) : difference with theory (-21) = 0 CORRECTING DEFECT 68 (vertices=33, convex hull=51, v0=126949) After retessellation of defect 68 (v0=126949), euler #=-20 (154617,463251,308614) : difference with theory (-20) = 0 CORRECTING DEFECT 69 (vertices=117, convex hull=114, v0=127136) After retessellation of defect 69 (v0=127136), euler #=-18 (154645,463383,308720) : difference with theory (-19) = -1 CORRECTING DEFECT 70 (vertices=231, convex hull=160, v0=127228) After retessellation of defect 70 (v0=127228), euler #=-18 (154692,463604,308894) : difference with theory (-18) = 0 CORRECTING DEFECT 71 (vertices=19, convex hull=37, v0=128368) After retessellation of defect 71 (v0=128368), euler #=-17 (154695,463627,308915) : difference with theory (-17) = 0 CORRECTING DEFECT 72 (vertices=38, convex hull=71, v0=130480) After retessellation of defect 72 (v0=130480), euler #=-16 (154705,463683,308962) : difference with theory (-16) = 0 CORRECTING DEFECT 73 (vertices=26, convex hull=47, v0=132045) After retessellation of defect 73 (v0=132045), euler #=-15 (154711,463717,308991) : difference with theory (-15) = 0 CORRECTING DEFECT 74 (vertices=174, convex hull=53, v0=132804) After retessellation of defect 74 (v0=132804), euler #=-14 (154726,463782,309042) : difference with theory (-14) = 0 CORRECTING DEFECT 75 (vertices=37, convex hull=68, v0=132969) After retessellation of defect 75 (v0=132969), euler #=-12 (154741,463858,309105) : difference with theory (-13) = -1 CORRECTING DEFECT 76 (vertices=13, convex hull=28, v0=133697) After retessellation of defect 76 (v0=133697), euler #=-11 (154743,463874,309120) : difference with theory (-12) = -1 CORRECTING DEFECT 77 (vertices=24, convex hull=22, v0=138770) After retessellation of defect 77 (v0=138770), euler #=-10 (154746,463889,309133) : difference with theory (-11) = -1 CORRECTING DEFECT 78 (vertices=17, convex hull=39, v0=138815) After retessellation of defect 78 (v0=138815), euler #=-9 (154750,463912,309153) : difference with theory (-10) = -1 CORRECTING DEFECT 79 (vertices=61, convex hull=72, v0=140253) After retessellation of defect 79 (v0=140253), euler #=-8 (154769,464000,309223) : difference with theory (-9) = -1 CORRECTING DEFECT 80 (vertices=9, convex hull=21, v0=140784) After retessellation of defect 80 (v0=140784), euler #=-7 (154771,464013,309235) : difference with theory (-8) = -1 CORRECTING DEFECT 81 (vertices=426, convex hull=123, v0=141095) After retessellation of defect 81 (v0=141095), euler #=-6 (154816,464213,309391) : difference with theory (-7) = -1 CORRECTING DEFECT 82 (vertices=45, convex hull=88, v0=146779) After retessellation of defect 82 (v0=146779), euler #=-5 (154843,464336,309488) : difference with theory (-6) = -1 CORRECTING DEFECT 83 (vertices=27, convex hull=40, v0=147450) After retessellation of defect 83 (v0=147450), euler #=-4 (154848,464366,309514) : difference with theory (-5) = -1 CORRECTING DEFECT 84 (vertices=169, convex hull=98, v0=149674) After retessellation of defect 84 (v0=149674), euler #=-3 (154872,464480,309605) : difference with theory (-4) = -1 CORRECTING DEFECT 85 (vertices=149, convex hull=78, v0=156419) After retessellation of defect 85 (v0=156419), euler #=-2 (154890,464566,309674) : difference with theory (-3) = -1 CORRECTING DEFECT 86 (vertices=36, convex hull=28, v0=158665) After retessellation of defect 86 (v0=158665), euler #=-1 (154891,464579,309687) : difference with theory (-2) = -1 CORRECTING DEFECT 87 (vertices=29, convex hull=87, v0=159731) After retessellation of defect 87 (v0=159731), euler #=0 (154908,464664,309756) : difference with theory (-1) = -1 CORRECTING DEFECT 88 (vertices=114, convex hull=65, v0=164362) After retessellation of defect 88 (v0=164362), euler #=0 (154926,464754,309828) : difference with theory (0) = 0 CORRECTING DEFECT 89 (vertices=5, convex hull=22, v0=164454) After retessellation of defect 89 (v0=164454), euler #=1 (154927,464762,309836) : difference with theory (1) = 0 CORRECTING DEFECT 90 (vertices=36, convex hull=32, v0=164568) After retessellation of defect 90 (v0=164568), euler #=2 (154929,464781,309854) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.28 (0.03-->19.75) (max @ vno 131086 --> 143056) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.28 (0.03-->19.75) (max @ vno 131086 --> 143056) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 335 mutations (37.2%), 566 crossovers (62.8%), 799 vertices were eliminated building final representation... 9879 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=154929, nf=309854, ne=464781, g=0) writing corrected surface to /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 47.3 minutes 0 defective edges removing intersecting faces 000: 959 intersecting 001: 46 intersecting 002: 12 intersecting 003: 6 intersecting mris_fix_topology utimesec 2842.877107 mris_fix_topology stimesec 0.251999 mris_fix_topology ru_maxrss 549348 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 136581 mris_fix_topology ru_majflt 9 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 1656 mris_fix_topology ru_oublock 0 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 5861 mris_fix_topology ru_nivcsw 10397 FSRUNTIME@ mris_fix_topology rh 0.7877 hours 1 threads PIDs (27450 27453) completed and logs appended. mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 157621 - 472857 + 315238 = 2 --> 0 holes F =2V-4: 315238 = 315242-4 (0) 2E=3F: 945714 = 945714 (0) total defect index = 0 mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 154929 - 464781 + 309854 = 2 --> 0 holes F =2V-4: 309854 = 309858-4 (0) 2E=3F: 929562 = 929562 (0) total defect index = 0 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 178 intersecting 001: 7 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 247 intersecting 001: 25 intersecting 002: 12 intersecting 003: 2 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf lh Thu Oct 3 13:42:07 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs S131032017_Supine lh #-------------------------------------------- #@# Make White Surf rh Thu Oct 3 13:42:07 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs S131032017_Supine rh Waiting for PID 30377 of (30377 30380) to complete... Waiting for PID 30380 of (30377 30380) to complete... mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/filled.mgz... reading volume /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/brain.finalsurfs.mgz... reading volume /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/../mri/aseg.presurf.mgz... reading volume /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/wm.mgz... 31356 bright wm thresholded. 6244 bright non-wm voxels segmented. reading original surface position from /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.orig... computing class statistics... border white: 293236 voxels (1.75%) border gray 355995 voxels (2.12%) WM (99.0): 98.4 +- 9.1 [70.0 --> 110.0] GM (72.0) : 70.6 +- 11.2 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 55.8 (was 70) setting MAX_BORDER_WHITE to 114.1 (was 105) setting MIN_BORDER_WHITE to 67.0 (was 85) setting MAX_CSF to 44.6 (was 40) setting MAX_GRAY to 95.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 55.8 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 33.3 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.23 (0.02-->5.96) (max @ vno 142140 --> 147874) face area 0.27 +- 0.13 (0.00-->3.79) mean absolute distance = 0.71 +- 0.87 4091 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=67+-9.6 mean inside = 94.2, mean outside = 74.6 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group mean border=79.1, 124 (124) missing vertices, mean dist 0.3 [0.6 (%34.0)->0.8 (%66.0))] %64 local maxima, %32 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=zapps, 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 0.91 +- 0.26 (0.07-->7.20) (max @ vno 156261 --> 58377) face area 0.27 +- 0.13 (0.00-->3.46) mean absolute distance = 0.43 +- 0.67 6770 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4099504.0, rms=10.670 001: dt: 0.5000, sse=2330893.8, rms=7.539 (29.342%) 002: dt: 0.5000, sse=1591667.9, rms=5.703 (24.354%) 003: dt: 0.5000, sse=1252018.0, rms=4.623 (18.935%) 004: dt: 0.5000, sse=1096842.8, rms=4.017 (13.121%) 005: dt: 0.5000, sse=1040964.6, rms=3.749 (6.661%) 006: dt: 0.5000, sse=1007412.6, rms=3.611 (3.668%) rms = 3.56, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=998005.6, rms=3.562 (1.360%) 008: dt: 0.2500, sse=824099.1, rms=2.409 (32.370%) 009: dt: 0.2500, sse=757877.6, rms=2.062 (14.406%) 010: dt: 0.2500, sse=746125.2, rms=1.967 (4.598%) 011: dt: 0.2500, sse=738415.6, rms=1.903 (3.271%) rms = 1.87, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=734919.9, rms=1.873 (1.594%) 013: dt: 0.1250, sse=724318.8, rms=1.786 (4.604%) rms = 1.77, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=722669.5, rms=1.769 (0.983%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=83.1, 159 (29) missing vertices, mean dist -0.3 [0.5 (%76.4)->0.3 (%23.6))] %77 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=zapps, 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 0.89 +- 0.26 (0.07-->7.33) (max @ vno 156261 --> 58377) face area 0.34 +- 0.17 (0.00-->4.34) mean absolute distance = 0.28 +- 0.40 4549 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1663104.1, rms=5.398 015: dt: 0.5000, sse=1221980.9, rms=3.765 (30.259%) rms = 3.76, time step reduction 1 of 3 to 0.250... 016: dt: 0.5000, sse=1212512.9, rms=3.764 (0.028%) 017: dt: 0.2500, sse=964603.0, rms=2.422 (35.655%) 018: dt: 0.2500, sse=913273.4, rms=2.063 (14.835%) 019: dt: 0.2500, sse=897307.4, rms=1.886 (8.564%) 020: dt: 0.2500, sse=880542.7, rms=1.728 (8.362%) 021: dt: 0.2500, sse=891288.8, rms=1.661 (3.871%) 022: dt: 0.2500, sse=881758.8, rms=1.591 (4.210%) rms = 1.57, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=881238.6, rms=1.570 (1.337%) 024: dt: 0.1250, sse=876222.6, rms=1.507 (4.044%) rms = 1.50, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=856066.1, rms=1.498 (0.589%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group mean border=86.1, 169 (11) missing vertices, mean dist -0.2 [0.3 (%76.9)->0.3 (%23.1))] %87 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=zapps, 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 0.88 +- 0.26 (0.04-->7.43) (max @ vno 156261 --> 58377) face area 0.33 +- 0.17 (0.00-->4.22) mean absolute distance = 0.20 +- 0.33 3721 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1243729.2, rms=4.044 026: dt: 0.5000, sse=1084952.4, rms=3.142 (22.307%) rms = 3.41, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=900588.6, rms=2.129 (32.225%) 028: dt: 0.2500, sse=850072.5, rms=1.646 (22.687%) 029: dt: 0.2500, sse=836419.5, rms=1.461 (11.225%) rms = 1.44, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=828531.2, rms=1.439 (1.529%) 031: dt: 0.1250, sse=813338.4, rms=1.348 (6.333%) rms = 1.34, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=824912.2, rms=1.342 (0.473%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=87.0, 255 (8) missing vertices, mean dist -0.0 [0.2 (%60.3)->0.2 (%39.7))] %90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=zapps, 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/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.white.preaparc... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=856173.2, rms=1.821 rms = 2.12, time step reduction 1 of 3 to 0.250... 033: dt: 0.2500, sse=797377.2, rms=1.290 (29.166%) 034: dt: 0.2500, sse=785839.1, rms=1.060 (17.858%) rms = 1.09, time step reduction 2 of 3 to 0.125... rms = 1.05, time step reduction 3 of 3 to 0.062... 035: dt: 0.1250, sse=776038.4, rms=1.046 (1.235%) positioning took 0.3 minutes generating cortex label... 16 non-cortical segments detected only using segment with 7876 vertices erasing segment 1 (vno[0] = 64146) erasing segment 2 (vno[0] = 66410) erasing segment 3 (vno[0] = 69902) erasing segment 4 (vno[0] = 74869) erasing segment 5 (vno[0] = 77373) erasing segment 6 (vno[0] = 81234) erasing segment 7 (vno[0] = 84769) erasing segment 8 (vno[0] = 88460) erasing segment 9 (vno[0] = 93299) erasing segment 10 (vno[0] = 103930) erasing segment 11 (vno[0] = 107523) erasing segment 12 (vno[0] = 108366) erasing segment 13 (vno[0] = 112458) erasing segment 14 (vno[0] = 117719) erasing segment 15 (vno[0] = 124889) writing cortex label to /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/label/lh.cortex.label... writing curvature file /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.curv writing smoothed area to lh.area writing curvature file /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.area vertex spacing 0.88 +- 0.27 (0.02-->7.37) (max @ vno 58377 --> 156261) face area 0.32 +- 0.17 (0.00-->4.14) refinement took 3.9 minutes mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/filled.mgz... reading volume /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/brain.finalsurfs.mgz... reading volume /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/../mri/aseg.presurf.mgz... reading volume /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/wm.mgz... 31356 bright wm thresholded. 6244 bright non-wm voxels segmented. reading original surface position from /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.orig... computing class statistics... border white: 293236 voxels (1.75%) border gray 355995 voxels (2.12%) WM (99.0): 98.4 +- 9.1 [70.0 --> 110.0] GM (72.0) : 70.6 +- 11.2 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 55.8 (was 70) setting MAX_BORDER_WHITE to 114.1 (was 105) setting MIN_BORDER_WHITE to 67.0 (was 85) setting MAX_CSF to 44.6 (was 40) setting MAX_GRAY to 95.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 55.8 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 33.3 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.24 (0.01-->8.78) (max @ vno 131086 --> 143056) face area 0.27 +- 0.13 (0.00-->4.81) mean absolute distance = 0.77 +- 0.98 4385 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+-6.1, GM=67+-10.4 mean inside = 94.2, mean outside = 75.1 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=79.6, 108 (108) missing vertices, mean dist 0.3 [0.7 (%35.3)->0.8 (%64.7))] %66 local maxima, %30 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=zapps, 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 0.91 +- 0.27 (0.05-->8.10) (max @ vno 131086 --> 143056) face area 0.27 +- 0.14 (0.00-->4.80) mean absolute distance = 0.45 +- 0.69 6204 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4061427.2, rms=10.693 001: dt: 0.5000, sse=2299729.0, rms=7.531 (29.566%) 002: dt: 0.5000, sse=1560519.6, rms=5.666 (24.760%) 003: dt: 0.5000, sse=1227261.2, rms=4.577 (19.224%) 004: dt: 0.5000, sse=1069318.8, rms=3.943 (13.852%) 005: dt: 0.5000, sse=1005917.2, rms=3.667 (7.007%) 006: dt: 0.5000, sse=969705.1, rms=3.500 (4.540%) rms = 3.46, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=970672.8, rms=3.460 (1.152%) 008: dt: 0.2500, sse=783728.9, rms=2.349 (32.115%) 009: dt: 0.2500, sse=743657.4, rms=2.031 (13.552%) 010: dt: 0.2500, sse=733829.1, rms=1.934 (4.740%) 011: dt: 0.2500, sse=726921.8, rms=1.881 (2.751%) rms = 1.85, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=724011.9, rms=1.847 (1.811%) 013: dt: 0.1250, sse=717098.3, rms=1.787 (3.274%) rms = 1.78, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=716123.2, rms=1.775 (0.631%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=83.4, 172 (39) missing vertices, mean dist -0.3 [0.5 (%75.1)->0.3 (%24.9))] %77 local maxima, %18 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=zapps, 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 0.89 +- 0.26 (0.04-->7.77) (max @ vno 131086 --> 143056) face area 0.35 +- 0.18 (0.00-->7.01) mean absolute distance = 0.30 +- 0.43 4730 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1636953.1, rms=5.358 015: dt: 0.5000, sse=1186520.0, rms=3.668 (31.538%) 016: dt: 0.5000, sse=1184774.1, rms=3.580 (2.410%) 017: dt: 0.5000, sse=1149562.6, rms=3.459 (3.386%) rms = 3.56, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=955141.6, rms=2.421 (29.995%) 019: dt: 0.2500, sse=891638.3, rms=1.897 (21.640%) 020: dt: 0.2500, sse=871857.7, rms=1.695 (10.663%) 021: dt: 0.2500, sse=862973.4, rms=1.616 (4.674%) rms = 1.57, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=856822.4, rms=1.568 (2.947%) 023: dt: 0.1250, sse=851418.7, rms=1.504 (4.072%) rms = 1.50, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=850302.7, rms=1.496 (0.562%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group mean border=86.4, 193 (21) missing vertices, mean dist -0.2 [0.3 (%76.2)->0.3 (%23.8))] %88 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=zapps, 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 0.88 +- 0.26 (0.05-->7.53) (max @ vno 131086 --> 143056) face area 0.33 +- 0.18 (0.00-->7.40) mean absolute distance = 0.22 +- 0.36 4716 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1240027.5, rms=4.058 025: dt: 0.5000, sse=1043907.1, rms=3.026 (25.432%) rms = 3.30, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=887408.8, rms=2.082 (31.186%) 027: dt: 0.2500, sse=847632.2, rms=1.611 (22.618%) 028: dt: 0.2500, sse=819848.3, rms=1.450 (10.041%) rms = 1.43, time step reduction 2 of 3 to 0.125... 029: dt: 0.2500, sse=817745.5, rms=1.427 (1.568%) 030: dt: 0.1250, sse=812167.1, rms=1.347 (5.586%) rms = 1.34, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=808302.9, rms=1.343 (0.301%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=87.3, 217 (15) missing vertices, mean dist -0.0 [0.2 (%60.1)->0.2 (%39.9))] %91 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=zapps, 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/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.white.preaparc... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=840048.5, rms=1.835 rms = 2.05, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=789525.3, rms=1.307 (28.772%) 033: dt: 0.2500, sse=778978.8, rms=1.048 (19.821%) rms = 1.06, time step reduction 2 of 3 to 0.125... rms = 1.04, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=773769.6, rms=1.038 (0.936%) positioning took 0.3 minutes generating cortex label... 20 non-cortical segments detected only using segment with 6612 vertices erasing segment 1 (vno[0] = 60678) erasing segment 2 (vno[0] = 62005) erasing segment 3 (vno[0] = 64062) erasing segment 4 (vno[0] = 80841) erasing segment 5 (vno[0] = 86711) erasing segment 6 (vno[0] = 90753) erasing segment 7 (vno[0] = 93840) erasing segment 8 (vno[0] = 110682) erasing segment 9 (vno[0] = 110703) erasing segment 10 (vno[0] = 111584) erasing segment 11 (vno[0] = 113927) erasing segment 12 (vno[0] = 114194) erasing segment 13 (vno[0] = 114255) erasing segment 14 (vno[0] = 118971) erasing segment 15 (vno[0] = 119844) erasing segment 16 (vno[0] = 121353) erasing segment 17 (vno[0] = 126264) erasing segment 18 (vno[0] = 129236) erasing segment 19 (vno[0] = 132367) writing cortex label to /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/label/rh.cortex.label... writing curvature file /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.curv writing smoothed area to rh.area writing curvature file /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.area vertex spacing 0.88 +- 0.27 (0.02-->7.50) (max @ vno 131086 --> 143056) face area 0.33 +- 0.17 (0.00-->7.50) refinement took 3.8 minutes PIDs (30377 30380) completed and logs appended. #-------------------------------------------- #@# Smooth2 lh Thu Oct 3 13:45:59 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm #-------------------------------------------- #@# Smooth2 rh Thu Oct 3 13:45:59 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm Waiting for PID 30558 of (30558 30561) to complete... Waiting for PID 30561 of (30558 30561) 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 (30558 30561) completed and logs appended. #-------------------------------------------- #@# Inflation2 lh Thu Oct 3 13:46:04 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/scripts mris_inflate -rusage /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated #-------------------------------------------- #@# Inflation2 rh Thu Oct 3 13:46:04 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/scripts mris_inflate -rusage /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Waiting for PID 30608 of (30608 30611) to complete... Waiting for PID 30611 of (30608 30611) to complete... mris_inflate -rusage /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 47.7 mm, total surface area = 90934 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.183 (target=0.015) step 005: RMS=0.128 (target=0.015) step 010: RMS=0.100 (target=0.015) step 015: RMS=0.083 (target=0.015) step 020: RMS=0.069 (target=0.015) step 025: RMS=0.059 (target=0.015) step 030: RMS=0.050 (target=0.015) step 035: RMS=0.042 (target=0.015) step 040: RMS=0.036 (target=0.015) step 045: RMS=0.032 (target=0.015) step 050: RMS=0.030 (target=0.015) step 055: RMS=0.027 (target=0.015) step 060: RMS=0.025 (target=0.015) inflation complete. inflation took 0.5 minutes mris_inflate utimesec 85.003529 mris_inflate stimesec 0.291395 mris_inflate ru_maxrss 249384 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 60729 mris_inflate ru_majflt 1 mris_inflate ru_nswap 0 mris_inflate ru_inblock 232 mris_inflate ru_oublock 0 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 13477 mris_inflate ru_nivcsw 15803 mris_inflate -rusage /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 48.2 mm, total surface area = 90806 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.184 (target=0.015) step 005: RMS=0.129 (target=0.015) step 010: RMS=0.099 (target=0.015) step 015: RMS=0.081 (target=0.015) step 020: RMS=0.068 (target=0.015) step 025: RMS=0.057 (target=0.015) step 030: RMS=0.048 (target=0.015) step 035: RMS=0.040 (target=0.015) step 040: RMS=0.036 (target=0.015) step 045: RMS=0.032 (target=0.015) step 050: RMS=0.029 (target=0.015) step 055: RMS=0.026 (target=0.015) step 060: RMS=0.025 (target=0.015) inflation complete. inflation took 0.5 minutes mris_inflate utimesec 84.905785 mris_inflate stimesec 0.279860 mris_inflate ru_maxrss 245072 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 59679 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 0 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 21622 mris_inflate ru_nivcsw 17030 PIDs (30608 30611) completed and logs appended. #-------------------------------------------- #@# Curv .H and .K lh Thu Oct 3 13:46:36 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 Thu Oct 3 13:46:36 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf reconbatchjobs /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 30702 of (30702 30705 30708 30711 30714 30717 30720 30723 30726 30729 30732 30735) to complete... Waiting for PID 30705 of (30702 30705 30708 30711 30714 30717 30720 30723 30726 30729 30732 30735) to complete... Waiting for PID 30708 of (30702 30705 30708 30711 30714 30717 30720 30723 30726 30729 30732 30735) to complete... Waiting for PID 30711 of (30702 30705 30708 30711 30714 30717 30720 30723 30726 30729 30732 30735) to complete... Waiting for PID 30714 of (30702 30705 30708 30711 30714 30717 30720 30723 30726 30729 30732 30735) to complete... Waiting for PID 30717 of (30702 30705 30708 30711 30714 30717 30720 30723 30726 30729 30732 30735) to complete... Waiting for PID 30720 of (30702 30705 30708 30711 30714 30717 30720 30723 30726 30729 30732 30735) to complete... Waiting for PID 30723 of (30702 30705 30708 30711 30714 30717 30720 30723 30726 30729 30732 30735) to complete... Waiting for PID 30726 of (30702 30705 30708 30711 30714 30717 30720 30723 30726 30729 30732 30735) to complete... Waiting for PID 30729 of (30702 30705 30708 30711 30714 30717 30720 30723 30726 30729 30732 30735) to complete... Waiting for PID 30732 of (30702 30705 30708 30711 30714 30717 30720 30723 30726 30729 30732 30735) to complete... Waiting for PID 30735 of (30702 30705 30708 30711 30714 30717 30720 30723 30726 30729 30732 30735) to complete... mris_curvature -w lh.white.preaparc total integrated curvature = 47.613*4pi (598.317) --> -47 handles ICI = 257.6, FI = 2356.8, variation=37514.932 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 217 vertices thresholded to be in k1 ~ [-0.28 0.22], k2 ~ [-0.12 0.14] total integrated curvature = 0.417*4pi (5.241) --> 1 handles ICI = 1.5, FI = 9.9, variation=172.460 144 vertices thresholded to be in [-0.01 0.02] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 164 vertices thresholded to be in [-0.16 0.12] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.017, std = 0.022 done. mris_curvature -w rh.white.preaparc total integrated curvature = 5.730*4pi (72.010) --> -5 handles ICI = 210.8, FI = 2194.9, variation=34600.658 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 217 vertices thresholded to be in k1 ~ [-0.36 0.25], k2 ~ [-0.13 0.09] total integrated curvature = 0.366*4pi (4.600) --> 1 handles ICI = 1.5, FI = 9.4, variation=166.541 154 vertices thresholded to be in [-0.01 0.02] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 150 vertices thresholded to be in [-0.17 0.13] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.017, std = 0.022 done. PIDs (30702 30705 30708 30711 30714 30717 30720 30723 30726 30729 30732 30735) completed and logs appended. #----------------------------------------- #@# Curvature Stats lh Thu Oct 3 13:47:34 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm S131032017_Supine 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 [ S131032017_Supine/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 [ 325 ] Gb_filter = 0 WARN: S lookup min: -0.237663 WARN: S explicit min: 0.000000 vertex = 430 #----------------------------------------- #@# Curvature Stats rh Thu Oct 3 13:47:37 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm S131032017_Supine 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 [ S131032017_Supine/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 [ 294 ] Gb_filter = 0 WARN: S lookup min: -0.386729 WARN: S explicit min: 0.000000 vertex = 449 WARN: C lookup max: 178.983780 WARN: C explicit max: 122.480614 vertex = 19278 #-------------------------------------------- #@# Sphere lh Thu Oct 3 13:47:39 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/scripts mris_sphere -rusage /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere #-------------------------------------------- #@# Sphere rh Thu Oct 3 13:47:39 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/scripts mris_sphere -rusage /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere Waiting for PID 30927 of (30927 30930) to complete... Waiting for PID 30930 of (30927 30930) to complete... mris_sphere -rusage /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 0.262... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=zapps, 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 %20.75 pass 1: epoch 2 of 3 starting distance error %20.72 unfolding complete - removing small folds... starting distance error %20.64 removing remaining folds... final distance error %20.66 MRISunfold() return, current seed 1234 -01: dt=0.0000, 421 negative triangles 191: dt=0.9900, 421 negative triangles 192: dt=0.9900, 203 negative triangles 193: dt=0.9900, 185 negative triangles 194: dt=0.9900, 156 negative triangles 195: dt=0.9900, 149 negative triangles 196: dt=0.9900, 137 negative triangles 197: dt=0.9900, 127 negative triangles 198: dt=0.9900, 112 negative triangles 199: dt=0.9900, 118 negative triangles 200: dt=0.9900, 98 negative triangles 201: dt=0.9900, 99 negative triangles 202: dt=0.9900, 81 negative triangles 203: dt=0.9900, 84 negative triangles 204: dt=0.9900, 70 negative triangles 205: dt=0.9900, 70 negative triangles 206: dt=0.9900, 66 negative triangles 207: dt=0.9900, 67 negative triangles 208: dt=0.9900, 58 negative triangles 209: dt=0.9900, 61 negative triangles 210: dt=0.9900, 55 negative triangles 211: dt=0.9900, 48 negative triangles 212: dt=0.9900, 52 negative triangles 213: dt=0.9900, 48 negative triangles 214: dt=0.9900, 46 negative triangles 215: dt=0.9900, 39 negative triangles 216: dt=0.9900, 41 negative triangles 217: dt=0.9900, 39 negative triangles 218: dt=0.9900, 39 negative triangles 219: dt=0.9900, 37 negative triangles 220: dt=0.9900, 22 negative triangles 221: dt=0.9900, 26 negative triangles 222: dt=0.9900, 27 negative triangles 223: dt=0.9900, 23 negative triangles 224: dt=0.9900, 20 negative triangles 225: dt=0.9900, 16 negative triangles 226: dt=0.9900, 11 negative triangles 227: dt=0.9900, 12 negative triangles 228: dt=0.9900, 8 negative triangles 229: dt=0.9900, 4 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.43 hours mris_sphere utimesec 4934.526187 mris_sphere stimesec 6.509770 mris_sphere ru_maxrss 345084 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 84685 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 0 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 45191 mris_sphere ru_nivcsw 940133 FSRUNTIME@ mris_sphere 0.4277 hours 1 threads mris_sphere -rusage /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 0.260... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=zapps, 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 %22.31 pass 1: epoch 2 of 3 starting distance error %22.27 unfolding complete - removing small folds... starting distance error %22.08 removing remaining folds... final distance error %22.11 MRISunfold() return, current seed 1234 -01: dt=0.0000, 311 negative triangles 231: dt=0.9900, 311 negative triangles 232: dt=0.9900, 146 negative triangles 233: dt=0.9900, 124 negative triangles 234: dt=0.9900, 117 negative triangles 235: dt=0.9900, 106 negative triangles 236: dt=0.9900, 90 negative triangles 237: dt=0.9900, 83 negative triangles 238: dt=0.9900, 82 negative triangles 239: dt=0.9900, 78 negative triangles 240: dt=0.9900, 79 negative triangles 241: dt=0.9900, 73 negative triangles 242: dt=0.9900, 75 negative triangles 243: dt=0.9900, 72 negative triangles 244: dt=0.9900, 73 negative triangles 245: dt=0.9900, 70 negative triangles 246: dt=0.9900, 70 negative triangles 247: dt=0.9900, 74 negative triangles 248: dt=0.9900, 70 negative triangles 249: dt=0.9900, 67 negative triangles 250: dt=0.9900, 68 negative triangles 251: dt=0.9900, 66 negative triangles 252: dt=0.9900, 64 negative triangles 253: dt=0.9900, 65 negative triangles 254: dt=0.9900, 65 negative triangles 255: dt=0.9900, 64 negative triangles 256: dt=0.9900, 68 negative triangles 257: dt=0.9900, 59 negative triangles 258: dt=0.9900, 57 negative triangles 259: dt=0.9900, 58 negative triangles 260: dt=0.9900, 58 negative triangles 261: dt=0.9900, 57 negative triangles 262: dt=0.9900, 62 negative triangles 263: dt=0.9900, 56 negative triangles 264: dt=0.9900, 58 negative triangles 265: dt=0.9900, 51 negative triangles 266: dt=0.9900, 59 negative triangles 267: dt=0.9900, 50 negative triangles 268: dt=0.9900, 51 negative triangles 269: dt=0.9900, 52 negative triangles 270: dt=0.9900, 51 negative triangles 271: dt=0.9900, 50 negative triangles 272: dt=0.9900, 56 negative triangles 273: dt=0.9900, 55 negative triangles 274: dt=0.9900, 51 negative triangles 275: dt=0.9900, 50 negative triangles 276: dt=0.9900, 56 negative triangles 277: dt=0.9900, 46 negative triangles 278: dt=0.9900, 46 negative triangles 279: dt=0.9900, 48 negative triangles 280: dt=0.9900, 53 negative triangles 281: dt=0.9900, 46 negative triangles 282: dt=0.9900, 50 negative triangles 283: dt=0.9900, 57 negative triangles 284: dt=0.9900, 51 negative triangles 285: dt=0.9900, 42 negative triangles 286: dt=0.9900, 48 negative triangles 287: dt=0.9900, 44 negative triangles 288: dt=0.9900, 44 negative triangles 289: dt=0.9900, 40 negative triangles 290: dt=0.9900, 38 negative triangles 291: dt=0.9900, 41 negative triangles 292: dt=0.9900, 37 negative triangles 293: dt=0.9900, 37 negative triangles 294: dt=0.9900, 37 negative triangles 295: dt=0.9900, 32 negative triangles 296: dt=0.9900, 37 negative triangles 297: dt=0.9900, 36 negative triangles 298: dt=0.9900, 31 negative triangles 299: dt=0.9900, 30 negative triangles 300: dt=0.9900, 27 negative triangles 301: dt=0.9900, 24 negative triangles 302: dt=0.9900, 21 negative triangles 303: dt=0.9900, 15 negative triangles 304: dt=0.9900, 16 negative triangles 305: dt=0.9900, 12 negative triangles 306: dt=0.9900, 11 negative triangles 307: dt=0.9900, 8 negative triangles 308: dt=0.9900, 5 negative triangles 309: dt=0.9900, 4 negative triangles 310: dt=0.9900, 6 negative triangles 311: dt=0.9900, 3 negative triangles 312: dt=0.9900, 2 negative triangles 313: dt=0.9900, 1 negative triangles 314: dt=0.9900, 1 negative triangles 315: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.46 hours mris_sphere utimesec 5309.084718 mris_sphere stimesec 6.829796 mris_sphere ru_maxrss 339704 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 83296 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 0 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 53487 mris_sphere ru_nivcsw 962998 FSRUNTIME@ mris_sphere 0.4566 hours 1 threads PIDs (30927 30930) completed and logs appended. #-------------------------------------------- #@# Surf Reg lh Thu Oct 3 14:15:03 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/scripts mris_register -curv -rusage /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 Thu Oct 3 14:15:03 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/scripts mris_register -curv -rusage /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 32083 of (32083 32086) to complete... Waiting for PID 32086 of (32083 32086) to complete... mris_register -curv -rusage /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/scripts cmdline mris_register -curv -rusage /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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=zapps, 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=zapps, 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 = 5.453 curvature mean = 0.001, std = 0.812 curvature mean = 0.030, std = 0.846 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 16.00) sse = 413238.8, tmin=0.6899 d=32.00 min @ (0.00, 8.00, -8.00) sse = 274882.3, tmin=1.3965 d=16.00 min @ (4.00, 0.00, -4.00) sse = 265304.4, tmin=2.1073 d=8.00 min @ (-2.00, -2.00, 4.00) sse = 254236.9, tmin=2.8278 d=4.00 min @ (0.00, 1.00, -1.00) sse = 250047.9, tmin=3.5561 d=2.00 min @ (0.50, 0.00, -0.50) sse = 249283.9, tmin=4.2869 d=0.50 min @ (0.00, 0.00, 0.12) sse = 249246.0, tmin=6.3244 tol=1.0e+00, sigma=0.5, host=zapps, 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 6.32 min curvature mean = -0.034, std = 0.823 curvature mean = 0.012, std = 0.936 curvature mean = -0.038, std = 0.832 curvature mean = 0.005, std = 0.972 curvature mean = -0.040, std = 0.834 curvature mean = 0.001, std = 0.988 2 Reading smoothwm curvature mean = -0.035, std = 0.463 curvature mean = 0.028, std = 0.247 curvature mean = 0.063, std = 0.213 curvature mean = 0.024, std = 0.305 curvature mean = 0.035, std = 0.337 curvature mean = 0.023, std = 0.332 curvature mean = 0.021, std = 0.438 curvature mean = 0.023, std = 0.342 curvature mean = 0.008, std = 0.528 MRISregister() return, current seed 0 -01: dt=0.0000, 103 negative triangles 121: dt=0.9900, 103 negative triangles expanding nbhd size to 1 122: dt=0.9900, 151 negative triangles 123: dt=0.9900, 106 negative triangles 124: dt=0.9900, 95 negative triangles 125: dt=0.9900, 94 negative triangles 126: dt=0.9900, 91 negative triangles 127: dt=0.9900, 79 negative triangles 128: dt=0.9900, 78 negative triangles 129: dt=0.9900, 70 negative triangles 130: dt=0.9900, 71 negative triangles 131: dt=0.9900, 59 negative triangles 132: dt=0.9900, 53 negative triangles 133: dt=0.9900, 48 negative triangles 134: dt=0.9900, 38 negative triangles 135: dt=0.9900, 35 negative triangles 136: dt=0.9900, 34 negative triangles 137: dt=0.9900, 35 negative triangles 138: dt=0.9900, 27 negative triangles 139: dt=0.9900, 26 negative triangles 140: dt=0.9900, 26 negative triangles 141: dt=0.9900, 21 negative triangles 142: dt=0.9900, 17 negative triangles 143: dt=0.9900, 15 negative triangles 144: dt=0.9900, 14 negative triangles 145: dt=0.9900, 13 negative triangles 146: dt=0.9900, 12 negative triangles 147: dt=0.9900, 8 negative triangles 148: dt=0.9900, 11 negative triangles 149: dt=0.9900, 9 negative triangles 150: dt=0.9900, 8 negative triangles 151: dt=0.9900, 11 negative triangles 152: dt=0.9900, 7 negative triangles 153: dt=0.9900, 7 negative triangles 154: dt=0.9900, 4 negative triangles 155: dt=0.9900, 4 negative triangles 156: dt=0.9900, 2 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 0.84 hours mris_register utimesec 8852.867241 mris_register stimesec 12.053601 mris_register ru_maxrss 302984 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 74065 mris_register ru_majflt 8 mris_register ru_nswap 0 mris_register ru_inblock 6832 mris_register ru_oublock 0 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 41035 mris_register ru_nivcsw 1420117 FSRUNTIME@ mris_register 0.8374 hours 1 threads mris_register -curv -rusage /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/scripts cmdline mris_register -curv -rusage /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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=zapps, 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=zapps, 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 = 5.559 curvature mean = 0.019, std = 0.809 curvature mean = 0.029, std = 0.844 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 0.00, 16.00) sse = 358604.4, tmin=0.6522 d=32.00 min @ (-8.00, -8.00, 0.00) sse = 321969.3, tmin=1.3134 d=16.00 min @ (0.00, 4.00, -4.00) sse = 285531.9, tmin=1.9794 d=8.00 min @ (0.00, 0.00, 2.00) sse = 280091.4, tmin=2.6497 d=4.00 min @ (1.00, 0.00, 0.00) sse = 279893.6, tmin=3.3219 d=2.00 min @ (-0.50, 0.00, -0.50) sse = 279458.1, tmin=3.9932 d=1.00 min @ (0.00, -0.25, 0.00) sse = 279353.7, tmin=4.6655 d=0.50 min @ (0.00, 0.00, 0.12) sse = 279345.7, tmin=5.3371 tol=1.0e+00, sigma=0.5, host=zapps, 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 5.34 min curvature mean = -0.013, std = 0.824 curvature mean = 0.009, std = 0.939 curvature mean = -0.020, std = 0.832 curvature mean = 0.004, std = 0.974 curvature mean = -0.023, std = 0.832 curvature mean = 0.001, std = 0.989 2 Reading smoothwm curvature mean = -0.028, std = 0.324 curvature mean = 0.027, std = 0.243 curvature mean = 0.069, std = 0.305 curvature mean = 0.025, std = 0.298 curvature mean = 0.038, std = 0.481 curvature mean = 0.024, std = 0.324 curvature mean = 0.021, std = 0.622 curvature mean = 0.024, std = 0.335 curvature mean = 0.007, std = 0.741 MRISregister() return, current seed 0 -01: dt=0.0000, 143 negative triangles 149: dt=0.9900, 143 negative triangles 150: dt=0.9405, 175 negative triangles expanding nbhd size to 1 151: dt=0.9900, 164 negative triangles 152: dt=0.9900, 136 negative triangles 153: dt=0.9900, 116 negative triangles 154: dt=0.9900, 125 negative triangles 155: dt=0.9900, 113 negative triangles 156: dt=0.9900, 108 negative triangles 157: dt=0.9900, 101 negative triangles 158: dt=0.9900, 96 negative triangles 159: dt=0.9900, 86 negative triangles 160: dt=0.9900, 90 negative triangles 161: dt=0.9900, 75 negative triangles 162: dt=0.9900, 70 negative triangles 163: dt=0.9900, 69 negative triangles 164: dt=0.9900, 64 negative triangles 165: dt=0.9900, 61 negative triangles 166: dt=0.9900, 55 negative triangles 167: dt=0.9900, 50 negative triangles 168: dt=0.9900, 62 negative triangles 169: dt=0.9900, 47 negative triangles 170: dt=0.9900, 44 negative triangles 171: dt=0.9900, 43 negative triangles 172: dt=0.9900, 35 negative triangles 173: dt=0.9900, 37 negative triangles 174: dt=0.9900, 34 negative triangles 175: dt=0.9900, 32 negative triangles 176: dt=0.9900, 30 negative triangles 177: dt=0.9900, 30 negative triangles 178: dt=0.9900, 30 negative triangles 179: dt=0.9900, 34 negative triangles 180: dt=0.9900, 30 negative triangles 181: dt=0.9900, 29 negative triangles 182: dt=0.9900, 27 negative triangles 183: dt=0.9900, 28 negative triangles 184: dt=0.9900, 27 negative triangles 185: dt=0.9900, 24 negative triangles 186: dt=0.9900, 29 negative triangles 187: dt=0.9900, 25 negative triangles 188: dt=0.9900, 24 negative triangles 189: dt=0.9900, 22 negative triangles 190: dt=0.9900, 25 negative triangles 191: dt=0.9900, 22 negative triangles 192: dt=0.9900, 21 negative triangles 193: dt=0.9900, 22 negative triangles 194: dt=0.9900, 21 negative triangles 195: dt=0.9900, 21 negative triangles 196: dt=0.9900, 20 negative triangles 197: dt=0.9900, 20 negative triangles 198: dt=0.9900, 21 negative triangles 199: dt=0.9900, 21 negative triangles 200: dt=0.9900, 20 negative triangles 201: dt=0.9900, 20 negative triangles 202: dt=0.9900, 21 negative triangles 203: dt=0.9900, 21 negative triangles 204: dt=0.9900, 20 negative triangles 205: dt=0.9900, 19 negative triangles 206: dt=0.9900, 19 negative triangles 207: dt=0.9900, 20 negative triangles 208: dt=0.9900, 18 negative triangles 209: dt=0.9900, 19 negative triangles 210: dt=0.9900, 18 negative triangles 211: dt=0.9900, 20 negative triangles 212: dt=0.9900, 17 negative triangles 213: dt=0.9900, 19 negative triangles 214: dt=0.9900, 17 negative triangles 215: dt=0.9900, 18 negative triangles 216: dt=0.9900, 18 negative triangles 217: dt=0.9900, 19 negative triangles 218: dt=0.9900, 18 negative triangles 219: dt=0.9900, 18 negative triangles 220: dt=0.9900, 16 negative triangles 221: dt=0.9900, 16 negative triangles 222: dt=0.9900, 14 negative triangles 223: dt=0.9900, 15 negative triangles 224: dt=0.9900, 15 negative triangles 225: dt=0.9900, 15 negative triangles 226: dt=0.9900, 14 negative triangles 227: dt=0.9900, 15 negative triangles 228: dt=0.9900, 14 negative triangles 229: dt=0.9900, 13 negative triangles 230: dt=0.9900, 14 negative triangles 231: dt=0.9900, 14 negative triangles 232: dt=0.9900, 14 negative triangles 233: dt=0.9900, 14 negative triangles 234: dt=0.9900, 14 negative triangles 235: dt=0.9900, 13 negative triangles 236: dt=0.9900, 12 negative triangles 237: dt=0.9900, 13 negative triangles 238: dt=0.9900, 12 negative triangles 239: dt=0.9900, 13 negative triangles 240: dt=0.9900, 11 negative triangles 241: dt=0.9900, 13 negative triangles 242: dt=0.9900, 12 negative triangles 243: dt=0.9900, 11 negative triangles 244: dt=0.9900, 12 negative triangles 245: dt=0.9900, 11 negative triangles 246: dt=0.9900, 12 negative triangles 247: dt=0.9900, 11 negative triangles 248: dt=0.9900, 10 negative triangles 249: dt=0.9900, 11 negative triangles 250: dt=0.9900, 10 negative triangles 251: dt=0.9900, 11 negative triangles 252: dt=0.9900, 10 negative triangles 253: dt=0.9900, 11 negative triangles 254: dt=0.9900, 11 negative triangles 255: dt=0.9900, 9 negative triangles 256: dt=0.9900, 9 negative triangles 257: dt=0.9900, 6 negative triangles 258: dt=0.9900, 7 negative triangles 259: dt=0.9900, 6 negative triangles 260: dt=0.9900, 7 negative triangles 261: dt=0.9900, 6 negative triangles 262: dt=0.9900, 4 negative triangles 263: dt=0.9900, 3 negative triangles 264: dt=0.9900, 2 negative triangles 265: dt=0.9900, 2 negative triangles 266: dt=0.9900, 3 negative triangles 267: dt=0.9900, 1 negative triangles 268: dt=0.9900, 3 negative triangles 269: dt=0.9900, 2 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 0.85 hours mris_register utimesec 9110.075956 mris_register stimesec 15.034768 mris_register ru_maxrss 300476 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 73380 mris_register ru_majflt 10 mris_register ru_nswap 0 mris_register ru_inblock 6912 mris_register ru_oublock 0 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 45478 mris_register ru_nivcsw 1655316 FSRUNTIME@ mris_register 0.8518 hours 1 threads PIDs (32083 32086) completed and logs appended. #-------------------------------------------- #@# Jacobian white lh Thu Oct 3 15:06:10 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white #-------------------------------------------- #@# Jacobian white rh Thu Oct 3 15:06:10 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/scripts mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white Waiting for PID 2842 of (2842 2845) to complete... Waiting for PID 2845 of (2842 2845) 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 (2842 2845) completed and logs appended. #-------------------------------------------- #@# AvgCurv lh Thu Oct 3 15:06:11 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 Thu Oct 3 15:06:11 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 2895 of (2895 2898) to complete... Waiting for PID 2898 of (2895 2898) 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 (2895 2898) completed and logs appended. #----------------------------------------- #@# Cortical Parc lh Thu Oct 3 15:06:13 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 S131032017_Supine 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 Thu Oct 3 15:06:13 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 S131032017_Supine 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 3027 of (3027 3031) to complete... Waiting for PID 3031 of (3027 3031) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 S131032017_Supine 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... 1626 labels changed using aseg relabeling using gibbs priors... 000: 3387 changed, 157621 examined... 001: 801 changed, 14334 examined... 002: 186 changed, 4392 examined... 003: 50 changed, 1157 examined... 004: 12 changed, 314 examined... 005: 8 changed, 77 examined... 006: 4 changed, 49 examined... 007: 4 changed, 20 examined... 008: 3 changed, 24 examined... 009: 0 changed, 13 examined... 224 labels changed using aseg 000: 132 total segments, 84 labels (325 vertices) changed 001: 44 total segments, 5 labels (9 vertices) changed 002: 39 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 9 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1872 vertices marked for relabeling... 1872 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 10 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 S131032017_Supine 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... 1606 labels changed using aseg relabeling using gibbs priors... 000: 3087 changed, 154929 examined... 001: 738 changed, 13133 examined... 002: 163 changed, 4168 examined... 003: 44 changed, 1017 examined... 004: 16 changed, 274 examined... 005: 6 changed, 98 examined... 006: 4 changed, 41 examined... 007: 5 changed, 23 examined... 008: 1 changed, 24 examined... 009: 0 changed, 7 examined... 140 labels changed using aseg 000: 102 total segments, 64 labels (331 vertices) changed 001: 40 total segments, 2 labels (3 vertices) changed 002: 38 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... 1777 vertices marked for relabeling... 1777 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 10 seconds. PIDs (3027 3031) completed and logs appended. #-------------------------------------------- #@# Make Pial Surf lh Thu Oct 3 15:06:23 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs S131032017_Supine lh #-------------------------------------------- #@# Make Pial Surf rh Thu Oct 3 15:06:23 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs S131032017_Supine rh Waiting for PID 3088 of (3088 3091) to complete... Waiting for PID 3091 of (3088 3091) to complete... mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/filled.mgz... reading volume /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/brain.finalsurfs.mgz... reading volume /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/../mri/aseg.presurf.mgz... reading volume /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/wm.mgz... 31356 bright wm thresholded. 6244 bright non-wm voxels segmented. reading original surface position from /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.orig... computing class statistics... border white: 293236 voxels (1.75%) border gray 355995 voxels (2.12%) WM (99.0): 98.4 +- 9.1 [70.0 --> 110.0] GM (72.0) : 70.6 +- 11.2 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 55.8 (was 70) setting MAX_BORDER_WHITE to 114.1 (was 105) setting MIN_BORDER_WHITE to 67.0 (was 85) setting MAX_CSF to 44.6 (was 40) setting MAX_GRAY to 95.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 55.8 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 33.3 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105+-5.2, GM=67+-9.6 mean inside = 94.2, mean outside = 74.6 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 0.88 +- 0.27 (0.02-->7.37) (max @ vno 58377 --> 156261) face area 0.32 +- 0.16 (0.00-->4.13) mean absolute distance = 0.70 +- 0.85 4227 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 1 with 1 points - only 0.00% unknown deleting segment 2 with 5 points - only 0.00% unknown deleting segment 5 with 9 points - only 0.00% unknown deleting segment 6 with 95 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown deleting segment 8 with 39 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown deleting segment 10 with 94 points - only 0.00% unknown deleting segment 11 with 30 points - only 0.00% unknown deleting segment 12 with 12 points - only 0.00% unknown deleting segment 13 with 8 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 14 with 2 points - only 0.00% unknown deleting segment 15 with 6 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 16 with 2 points - only 0.00% unknown deleting segment 17 with 112 points - only 0.00% unknown deleting segment 18 with 7 points - only 0.00% unknown deleting segment 19 with 55 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 20 with 4 points - only 0.00% unknown mean border=79.0, 192 (192) missing vertices, mean dist 0.5 [1.1 (%10.1)->0.7 (%89.9))] %62 local maxima, %34 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=zapps, 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 0.91 +- 0.27 (0.08-->7.72) (max @ vno 156261 --> 58377) face area 0.32 +- 0.16 (0.00-->3.80) mean absolute distance = 0.42 +- 0.64 6384 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3494433.2, rms=9.549 001: dt: 0.5000, sse=1717239.5, rms=5.692 (40.394%) 002: dt: 0.5000, sse=1240361.5, rms=4.102 (27.932%) 003: dt: 0.5000, sse=1151712.9, rms=3.755 (8.452%) 004: dt: 0.5000, sse=1079300.9, rms=3.408 (9.246%) rms = 3.53, time step reduction 1 of 3 to 0.250... 005: dt: 0.2500, sse=924780.7, rms=2.540 (25.478%) 006: dt: 0.2500, sse=871697.8, rms=2.132 (16.058%) 007: dt: 0.2500, sse=848320.5, rms=1.971 (7.538%) 008: dt: 0.2500, sse=842167.1, rms=1.902 (3.513%) rms = 1.86, time step reduction 2 of 3 to 0.125... 009: dt: 0.2500, sse=848454.8, rms=1.857 (2.347%) 010: dt: 0.1250, sse=829430.5, rms=1.789 (3.665%) rms = 1.76, time step reduction 3 of 3 to 0.062... 011: dt: 0.1250, sse=827356.3, rms=1.761 (1.599%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 0 with 2 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 1 with 1 points - only 0.00% unknown deleting segment 2 with 5 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 4 with 7 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 86 points - only 0.00% unknown deleting segment 7 with 49 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 8 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 9 with 4 points - only 0.00% unknown deleting segment 10 with 7 points - only 0.00% unknown deleting segment 11 with 53 points - only 0.00% unknown deleting segment 12 with 34 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 13 with 2 points - only 0.00% unknown deleting segment 14 with 8 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 15 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 16 with 2 points - only 0.00% unknown deleting segment 17 with 95 points - only 0.00% unknown deleting segment 18 with 52 points - only 0.00% unknown deleting segment 19 with 5 points - only 0.00% unknown mean border=83.0, 132 (50) missing vertices, mean dist -0.3 [0.5 (%76.3)->0.2 (%23.7))] %77 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=zapps, 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 0.89 +- 0.26 (0.04-->7.82) (max @ vno 156261 --> 58377) face area 0.34 +- 0.18 (0.00-->4.48) mean absolute distance = 0.28 +- 0.40 4536 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1623799.9, rms=5.245 012: dt: 0.5000, sse=1204806.2, rms=3.670 (30.025%) rms = 3.66, time step reduction 1 of 3 to 0.250... 013: dt: 0.5000, sse=1194184.5, rms=3.658 (0.346%) 014: dt: 0.2500, sse=962720.0, rms=2.291 (37.361%) 015: dt: 0.2500, sse=904649.5, rms=1.906 (16.814%) 016: dt: 0.2500, sse=891604.1, rms=1.726 (9.460%) 017: dt: 0.2500, sse=873661.2, rms=1.594 (7.629%) 018: dt: 0.2500, sse=871497.8, rms=1.541 (3.345%) 019: dt: 0.2500, sse=868762.0, rms=1.484 (3.662%) rms = 1.48, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=869262.5, rms=1.484 (0.024%) 021: dt: 0.1250, sse=859174.6, rms=1.413 (4.789%) rms = 1.41, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=873877.7, rms=1.408 (0.319%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 0 with 2 points - only 0.00% unknown deleting segment 1 with 5 points - only 0.00% unknown deleting segment 2 with 7 points - only 0.00% unknown deleting segment 3 with 85 points - only 0.00% unknown deleting segment 4 with 45 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 5 with 3 points - only 0.00% unknown deleting segment 6 with 72 points - only 0.00% unknown deleting segment 7 with 46 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 8 with 1 points - only 0.00% unknown deleting segment 9 with 5 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 10 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 11 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 12 with 2 points - only 0.00% unknown deleting segment 13 with 95 points - only 0.00% unknown deleting segment 14 with 60 points - only 0.00% unknown deleting segment 15 with 5 points - only 0.00% unknown mean border=86.0, 159 (22) missing vertices, mean dist -0.2 [0.3 (%77.2)->0.3 (%22.8))] %88 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=zapps, 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 0.88 +- 0.27 (0.05-->7.87) (max @ vno 156261 --> 58377) face area 0.33 +- 0.17 (0.00-->4.39) mean absolute distance = 0.20 +- 0.33 3670 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1263245.2, rms=4.025 023: dt: 0.5000, sse=1074201.2, rms=3.098 (23.029%) rms = 3.35, time step reduction 1 of 3 to 0.250... 024: dt: 0.2500, sse=895465.1, rms=2.080 (32.846%) 025: dt: 0.2500, sse=852017.9, rms=1.583 (23.930%) 026: dt: 0.2500, sse=838265.2, rms=1.405 (11.230%) rms = 1.38, time step reduction 2 of 3 to 0.125... 027: dt: 0.2500, sse=826621.9, rms=1.383 (1.530%) 028: dt: 0.1250, sse=813128.8, rms=1.291 (6.662%) rms = 1.28, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=812063.2, rms=1.282 (0.736%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 0 with 2 points - only 0.00% unknown deleting segment 1 with 5 points - only 0.00% unknown deleting segment 2 with 7 points - only 0.00% unknown deleting segment 3 with 90 points - only 0.00% unknown deleting segment 4 with 35 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 5 with 3 points - only 0.00% unknown deleting segment 6 with 79 points - only 0.00% unknown deleting segment 7 with 45 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 8 with 1 points - only 0.00% unknown deleting segment 10 with 5 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 11 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 12 with 2 points - only 0.00% unknown deleting segment 13 with 6 points - only 0.00% unknown deleting segment 14 with 95 points - only 0.00% unknown deleting segment 15 with 65 points - only 0.00% unknown deleting segment 16 with 5 points - only 0.00% unknown mean border=87.0, 213 (15) missing vertices, mean dist -0.0 [0.2 (%60.5)->0.2 (%39.5))] %91 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=zapps, 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/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=843277.6, rms=1.782 rms = 2.09, time step reduction 1 of 3 to 0.250... 030: dt: 0.2500, sse=791797.3, rms=1.241 (30.393%) 031: dt: 0.2500, sse=792537.2, rms=1.015 (18.190%) rms = 1.04, time step reduction 2 of 3 to 0.125... rms = 1.00, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=780168.6, rms=0.998 (1.640%) positioning took 0.3 minutes generating cortex label... 17 non-cortical segments detected only using segment with 7847 vertices erasing segment 1 (vno[0] = 66410) erasing segment 2 (vno[0] = 68766) erasing segment 3 (vno[0] = 69921) erasing segment 4 (vno[0] = 71147) erasing segment 5 (vno[0] = 76132) erasing segment 6 (vno[0] = 77373) erasing segment 7 (vno[0] = 81234) erasing segment 8 (vno[0] = 84043) erasing segment 9 (vno[0] = 88467) erasing segment 10 (vno[0] = 93299) erasing segment 11 (vno[0] = 105194) erasing segment 12 (vno[0] = 107523) erasing segment 13 (vno[0] = 112458) erasing segment 14 (vno[0] = 114480) erasing segment 15 (vno[0] = 118728) erasing segment 16 (vno[0] = 124017) writing cortex label to /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/label/lh.cortex.label... writing curvature file /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.curv writing smoothed area to lh.area writing curvature file /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.area vertex spacing 0.88 +- 0.27 (0.02-->7.78) (max @ vno 58377 --> 156261) face area 0.32 +- 0.17 (0.00-->4.37) 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 13 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 1 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 3 with 4 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 4 with 1 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 5 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 6 with 4 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 7 with 1 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=54.1, 205 (205) missing vertices, mean dist 1.7 [0.5 (%0.0)->2.8 (%100.0))] %10 local maxima, %48 large gradients and %37 min vals, 272 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=zapps, 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=34689340.0, rms=33.552 001: dt: 0.0500, sse=30538200.0, rms=31.434 (6.311%) 002: dt: 0.0500, sse=27628644.0, rms=29.861 (5.007%) 003: dt: 0.0500, sse=25440866.0, rms=28.620 (4.154%) 004: dt: 0.0500, sse=23707464.0, rms=27.598 (3.573%) 005: dt: 0.0500, sse=22275972.0, rms=26.724 (3.167%) 006: dt: 0.0500, sse=21059796.0, rms=25.958 (2.865%) 007: dt: 0.0500, sse=20003008.0, rms=25.274 (2.636%) 008: dt: 0.0500, sse=19068278.0, rms=24.653 (2.457%) 009: dt: 0.0500, sse=18230698.0, rms=24.083 (2.313%) 010: dt: 0.0500, sse=17472086.0, rms=23.555 (2.194%) positioning took 0.7 minutes mean border=53.8, 191 (103) missing vertices, mean dist 1.4 [0.2 (%0.1)->2.2 (%99.9))] %11 local maxima, %50 large gradients and %35 min vals, 257 gradients ignored tol=1.0e-04, sigma=2.0, host=zapps, 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=18656488.0, rms=24.372 011: dt: 0.0500, sse=17951388.0, rms=23.887 (1.988%) 012: dt: 0.0500, sse=17302046.0, rms=23.432 (1.905%) 013: dt: 0.0500, sse=16701125.0, rms=23.003 (1.832%) 014: dt: 0.0500, sse=16142635.0, rms=22.597 (1.766%) 015: dt: 0.0500, sse=15622048.0, rms=22.211 (1.706%) 016: dt: 0.0500, sse=15136095.0, rms=21.845 (1.648%) 017: dt: 0.0500, sse=14681381.0, rms=21.497 (1.594%) 018: dt: 0.0500, sse=14254776.0, rms=21.165 (1.544%) 019: dt: 0.0500, sse=13853342.0, rms=20.848 (1.499%) 020: dt: 0.0500, sse=13475195.0, rms=20.545 (1.455%) positioning took 0.7 minutes mean border=53.7, 218 (82) missing vertices, mean dist 1.2 [0.1 (%0.7)->1.9 (%99.3))] %12 local maxima, %50 large gradients and %34 min vals, 268 gradients ignored tol=1.0e-04, sigma=2.0, host=zapps, 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=13567902.0, rms=20.625 021: dt: 0.0500, sse=13203358.0, rms=20.329 (1.433%) 022: dt: 0.0500, sse=12858965.0, rms=20.046 (1.393%) 023: dt: 0.0500, sse=12530549.0, rms=19.772 (1.367%) 024: dt: 0.0500, sse=12218730.0, rms=19.509 (1.334%) 025: dt: 0.0500, sse=11921357.0, rms=19.254 (1.307%) 026: dt: 0.0500, sse=11636592.0, rms=19.006 (1.285%) 027: dt: 0.0500, sse=11361964.0, rms=18.764 (1.272%) 028: dt: 0.0500, sse=11095285.0, rms=18.527 (1.267%) 029: dt: 0.0500, sse=10836136.0, rms=18.292 (1.264%) 030: dt: 0.0500, sse=10584099.0, rms=18.062 (1.261%) positioning took 0.7 minutes mean border=53.5, 257 (70) missing vertices, mean dist 1.0 [0.1 (%5.9)->1.7 (%94.1))] %12 local maxima, %50 large gradients and %34 min vals, 221 gradients ignored tol=1.0e-04, sigma=2.0, host=zapps, 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=10725179.0, rms=18.192 031: dt: 0.5000, sse=8852564.0, rms=16.393 (9.891%) 032: dt: 0.5000, sse=7339686.5, rms=14.776 (9.866%) 033: dt: 0.5000, sse=6023015.0, rms=13.211 (10.592%) 034: dt: 0.5000, sse=4875930.0, rms=11.672 (11.645%) 035: dt: 0.5000, sse=3944970.8, rms=10.258 (12.117%) 036: dt: 0.5000, sse=3229528.2, rms=9.019 (12.082%) 037: dt: 0.5000, sse=2737351.8, rms=8.059 (10.641%) 038: dt: 0.5000, sse=2423273.2, rms=7.380 (8.429%) 039: dt: 0.5000, sse=2243146.2, rms=6.961 (5.671%) 040: dt: 0.5000, sse=2136680.0, rms=6.697 (3.799%) 041: dt: 0.5000, sse=2076023.0, rms=6.545 (2.269%) 042: dt: 0.5000, sse=2032904.8, rms=6.429 (1.765%) 043: dt: 0.5000, sse=2008572.5, rms=6.365 (0.993%) 044: dt: 0.5000, sse=1990229.9, rms=6.313 (0.821%) rms = 6.29, time step reduction 1 of 3 to 0.250... 045: dt: 0.5000, sse=1982944.0, rms=6.293 (0.313%) 046: dt: 0.2500, sse=1797528.0, rms=5.738 (8.827%) 047: dt: 0.2500, sse=1738087.8, rms=5.562 (3.064%) rms = 5.57, time step reduction 2 of 3 to 0.125... 048: dt: 0.1250, sse=1714551.8, rms=5.488 (1.340%) 049: dt: 0.1250, sse=1683632.2, rms=5.387 (1.833%) rms = 5.37, time step reduction 3 of 3 to 0.062... 050: dt: 0.1250, sse=1679093.1, rms=5.371 (0.294%) positioning took 1.8 minutes mean border=52.9, 4657 (27) missing vertices, mean dist 0.1 [0.2 (%51.9)->0.6 (%48.1))] %21 local maxima, %40 large gradients and %33 min vals, 106 gradients ignored tol=1.0e-04, sigma=1.0, host=zapps, 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=1879489.1, rms=5.361 rms = 5.53, time step reduction 1 of 3 to 0.250... 051: dt: 0.2500, sse=1745627.4, rms=4.912 (8.375%) 052: dt: 0.2500, sse=1684925.4, rms=4.692 (4.468%) rms = 4.67, time step reduction 2 of 3 to 0.125... 053: dt: 0.2500, sse=1677624.1, rms=4.673 (0.408%) 054: dt: 0.1250, sse=1611312.6, rms=4.420 (5.411%) 055: dt: 0.1250, sse=1596435.8, rms=4.366 (1.231%) rms = 4.35, time step reduction 3 of 3 to 0.062... 056: dt: 0.1250, sse=1591600.6, rms=4.349 (0.386%) positioning took 0.7 minutes mean border=52.0, 4868 (22) missing vertices, mean dist 0.1 [0.1 (%48.9)->0.4 (%51.1))] %37 local maxima, %23 large gradients and %32 min vals, 145 gradients ignored tol=1.0e-04, sigma=0.5, host=zapps, 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=1667575.0, rms=4.648 rms = 5.17, time step reduction 1 of 3 to 0.250... 057: dt: 0.2500, sse=1601519.6, rms=4.404 (5.263%) rms = 4.37, time step reduction 2 of 3 to 0.125... 058: dt: 0.2500, sse=1589171.1, rms=4.365 (0.874%) 059: dt: 0.1250, sse=1565446.1, rms=4.270 (2.186%) rms = 4.23, time step reduction 3 of 3 to 0.062... 060: dt: 0.1250, sse=1554728.8, rms=4.231 (0.907%) positioning took 0.5 minutes mean border=51.4, 7202 (20) missing vertices, mean dist 0.1 [0.1 (%48.4)->0.3 (%51.6))] %42 local maxima, %18 large gradients and %31 min vals, 137 gradients ignored tol=1.0e-04, sigma=0.2, host=zapps, 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/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=1593436.8, rms=4.367 rms = 4.84, time step reduction 1 of 3 to 0.250... 061: dt: 0.2500, sse=1552005.4, rms=4.205 (3.705%) 062: dt: 0.2500, sse=1530066.9, rms=4.134 (1.682%) rms = 4.13, time step reduction 2 of 3 to 0.125... rms = 4.09, time step reduction 3 of 3 to 0.062... 063: dt: 0.1250, sse=1518648.2, rms=4.085 (1.175%) positioning took 0.4 minutes writing curvature file /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.area.pial vertex spacing 0.99 +- 0.43 (0.04-->9.64) (max @ vno 156261 --> 58377) face area 0.39 +- 0.31 (0.00-->8.54) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 157621 vertices processed 25000 of 157621 vertices processed 50000 of 157621 vertices processed 75000 of 157621 vertices processed 100000 of 157621 vertices processed 125000 of 157621 vertices processed 150000 of 157621 vertices processed 0 of 157621 vertices processed 25000 of 157621 vertices processed 50000 of 157621 vertices processed 75000 of 157621 vertices processed 100000 of 157621 vertices processed 125000 of 157621 vertices processed 150000 of 157621 vertices processed thickness calculation complete, 316:829 truncations. 38894 vertices at 0 distance 113252 vertices at 1 distance 92293 vertices at 2 distance 38167 vertices at 3 distance 12676 vertices at 4 distance 4105 vertices at 5 distance 1341 vertices at 6 distance 522 vertices at 7 distance 218 vertices at 8 distance 100 vertices at 9 distance 96 vertices at 10 distance 89 vertices at 11 distance 64 vertices at 12 distance 42 vertices at 13 distance 45 vertices at 14 distance 14 vertices at 15 distance 15 vertices at 16 distance 12 vertices at 17 distance 16 vertices at 18 distance 15 vertices at 19 distance 18 vertices at 20 distance writing curvature file /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.thickness positioning took 10.5 minutes mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/filled.mgz... reading volume /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/brain.finalsurfs.mgz... reading volume /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/../mri/aseg.presurf.mgz... reading volume /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/wm.mgz... 31356 bright wm thresholded. 6244 bright non-wm voxels segmented. reading original surface position from /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.orig... computing class statistics... border white: 293236 voxels (1.75%) border gray 355995 voxels (2.12%) WM (99.0): 98.4 +- 9.1 [70.0 --> 110.0] GM (72.0) : 70.6 +- 11.2 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 55.8 (was 70) setting MAX_BORDER_WHITE to 114.1 (was 105) setting MIN_BORDER_WHITE to 67.0 (was 85) setting MAX_CSF to 44.6 (was 40) setting MAX_GRAY to 95.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 55.8 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 33.3 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105+-6.1, GM=67+-10.4 mean inside = 94.2, mean outside = 75.1 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 0.88 +- 0.27 (0.02-->7.50) (max @ vno 131086 --> 143056) face area 0.32 +- 0.17 (0.00-->7.47) mean absolute distance = 0.74 +- 0.92 3343 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 2 with 4 points - only 0.00% unknown deleting segment 3 with 213 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 18 points - only 0.00% unknown deleting segment 6 with 32 points - only 0.00% unknown deleting segment 7 with 19 points - only 0.00% unknown deleting segment 8 with 56 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 9 with 4 points - only 0.00% unknown deleting segment 10 with 160 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 11 with 3 points - only 0.00% unknown deleting segment 12 with 31 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 13 with 1 points - only 0.00% unknown deleting segment 14 with 25 points - only 0.00% unknown deleting segment 15 with 21 points - only 0.00% unknown mean border=79.5, 228 (215) missing vertices, mean dist 0.5 [1.2 (%12.1)->0.7 (%87.9))] %64 local maxima, %32 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=zapps, 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 0.91 +- 0.27 (0.06-->7.38) (max @ vno 131086 --> 143056) face area 0.32 +- 0.17 (0.00-->5.35) mean absolute distance = 0.44 +- 0.68 5329 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3412758.8, rms=9.467 001: dt: 0.5000, sse=1699208.5, rms=5.678 (40.024%) 002: dt: 0.5000, sse=1232943.5, rms=4.032 (28.992%) 003: dt: 0.5000, sse=1124808.1, rms=3.643 (9.647%) 004: dt: 0.5000, sse=1047349.9, rms=3.298 (9.467%) rms = 3.41, time step reduction 1 of 3 to 0.250... 005: dt: 0.2500, sse=912245.9, rms=2.473 (25.020%) 006: dt: 0.2500, sse=864777.6, rms=2.086 (15.627%) 007: dt: 0.2500, sse=845545.9, rms=1.936 (7.196%) 008: dt: 0.2500, sse=840261.2, rms=1.876 (3.117%) rms = 1.83, time step reduction 2 of 3 to 0.125... 009: dt: 0.2500, sse=835717.9, rms=1.834 (2.244%) 010: dt: 0.1250, sse=829466.5, rms=1.778 (3.021%) rms = 1.77, time step reduction 3 of 3 to 0.062... 011: dt: 0.1250, sse=832851.0, rms=1.765 (0.742%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 1 with 119 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 2 points - only 0.00% unknown deleting segment 4 with 32 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 5 with 4 points - only 0.00% unknown deleting segment 7 with 25 points - only 0.00% unknown deleting segment 8 with 46 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 9 with 4 points - only 0.00% unknown deleting segment 10 with 165 points - only 0.00% unknown deleting segment 11 with 5 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 12 with 4 points - only 0.00% unknown deleting segment 13 with 24 points - only 0.00% unknown deleting segment 14 with 5 points - only 0.00% unknown deleting segment 15 with 16 points - only 0.00% unknown mean border=83.4, 162 (71) missing vertices, mean dist -0.3 [0.5 (%75.0)->0.3 (%25.0))] %77 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=zapps, 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 0.89 +- 0.27 (0.05-->7.15) (max @ vno 131086 --> 143056) face area 0.35 +- 0.19 (0.00-->6.85) mean absolute distance = 0.31 +- 0.44 4691 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1614027.0, rms=5.235 012: dt: 0.5000, sse=1188679.2, rms=3.622 (30.815%) 013: dt: 0.5000, sse=1158168.0, rms=3.516 (2.936%) 014: dt: 0.5000, sse=1135923.9, rms=3.409 (3.022%) rms = 3.49, time step reduction 1 of 3 to 0.250... 015: dt: 0.2500, sse=961735.8, rms=2.370 (30.476%) 016: dt: 0.2500, sse=895822.3, rms=1.828 (22.886%) 017: dt: 0.2500, sse=876259.9, rms=1.635 (10.559%) 018: dt: 0.2500, sse=869159.2, rms=1.574 (3.701%) rms = 1.55, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=867832.1, rms=1.546 (1.802%) 020: dt: 0.1250, sse=862568.1, rms=1.484 (4.007%) rms = 1.48, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=860629.5, rms=1.483 (0.089%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 1 with 148 points - only 0.00% unknown deleting segment 2 with 12 points - only 0.00% unknown deleting segment 3 with 30 points - only 0.00% unknown deleting segment 4 with 24 points - only 0.00% unknown deleting segment 5 with 53 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 3 points - only 0.00% unknown deleting segment 7 with 182 points - only 0.00% unknown deleting segment 8 with 5 points - only 0.00% unknown deleting segment 9 with 13 points - only 0.00% unknown deleting segment 10 with 23 points - only 0.00% unknown deleting segment 11 with 21 points - only 0.00% unknown mean border=86.3, 193 (52) missing vertices, mean dist -0.2 [0.3 (%76.5)->0.3 (%23.5))] %88 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=zapps, 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 0.88 +- 0.27 (0.07-->7.01) (max @ vno 131086 --> 143056) face area 0.33 +- 0.18 (0.00-->6.27) mean absolute distance = 0.22 +- 0.36 4682 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1251425.2, rms=4.065 022: dt: 0.5000, sse=1048047.5, rms=3.025 (25.585%) rms = 3.28, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=896296.6, rms=2.083 (31.157%) 024: dt: 0.2500, sse=848238.7, rms=1.609 (22.719%) 025: dt: 0.2500, sse=829069.0, rms=1.449 (9.950%) rms = 1.42, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=830530.9, rms=1.419 (2.117%) 027: dt: 0.1250, sse=817686.9, rms=1.346 (5.124%) rms = 1.34, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=816149.8, rms=1.341 (0.378%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 1 with 175 points - only 0.00% unknown deleting segment 2 with 17 points - only 0.00% unknown deleting segment 3 with 29 points - only 0.00% unknown deleting segment 4 with 24 points - only 0.00% unknown deleting segment 5 with 55 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 6 with 4 points - only 0.00% unknown deleting segment 7 with 177 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 8 with 3 points - only 0.00% unknown deleting segment 9 with 20 points - only 0.00% unknown deleting segment 10 with 22 points - only 0.00% unknown deleting segment 11 with 24 points - only 0.00% unknown mean border=87.2, 239 (41) missing vertices, mean dist -0.0 [0.2 (%60.3)->0.2 (%39.7))] %91 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=zapps, 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/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=850440.5, rms=1.856 rms = 2.06, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=800195.1, rms=1.317 (29.019%) 030: dt: 0.2500, sse=787484.4, rms=1.052 (20.141%) rms = 1.07, time step reduction 2 of 3 to 0.125... rms = 1.04, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=781835.4, rms=1.041 (1.081%) positioning took 0.3 minutes generating cortex label... 22 non-cortical segments detected only using segment with 6603 vertices erasing segment 1 (vno[0] = 60678) erasing segment 2 (vno[0] = 62005) erasing segment 3 (vno[0] = 86711) erasing segment 4 (vno[0] = 90753) erasing segment 5 (vno[0] = 97697) erasing segment 6 (vno[0] = 101057) erasing segment 7 (vno[0] = 106113) erasing segment 8 (vno[0] = 110682) erasing segment 9 (vno[0] = 110703) erasing segment 10 (vno[0] = 111584) erasing segment 11 (vno[0] = 112486) erasing segment 12 (vno[0] = 113927) erasing segment 13 (vno[0] = 114194) erasing segment 14 (vno[0] = 118971) erasing segment 15 (vno[0] = 119844) erasing segment 16 (vno[0] = 121353) erasing segment 17 (vno[0] = 124660) erasing segment 18 (vno[0] = 126249) erasing segment 19 (vno[0] = 126264) erasing segment 20 (vno[0] = 129236) erasing segment 21 (vno[0] = 132367) writing cortex label to /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/label/rh.cortex.label... writing curvature file /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.curv writing smoothed area to rh.area writing curvature file /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.area vertex spacing 0.88 +- 0.28 (0.01-->6.93) (max @ vno 131086 --> 143056) face area 0.33 +- 0.18 (0.00-->6.44) 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 61 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 26 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 3 points - only 0.00% unknown deleting segment 5 with 27 points - only 0.00% unknown deleting segment 6 with 7 points - only 0.00% unknown deleting segment 7 with 10 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=54.7, 227 (227) missing vertices, mean dist 1.6 [0.7 (%0.0)->2.9 (%100.0))] %10 local maxima, %43 large gradients and %43 min vals, 185 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=zapps, 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=33906148.0, rms=33.356 001: dt: 0.0500, sse=30011192.0, rms=31.337 (6.055%) 002: dt: 0.0500, sse=27247234.0, rms=29.821 (4.838%) 003: dt: 0.0500, sse=25149814.0, rms=28.616 (4.038%) 004: dt: 0.0500, sse=23476726.0, rms=27.618 (3.489%) 005: dt: 0.0500, sse=22088086.0, rms=26.761 (3.103%) 006: dt: 0.0500, sse=20900370.0, rms=26.006 (2.823%) 007: dt: 0.0500, sse=19863254.0, rms=25.328 (2.607%) 008: dt: 0.0500, sse=18941238.0, rms=24.709 (2.442%) 009: dt: 0.0500, sse=18110380.0, rms=24.138 (2.311%) 010: dt: 0.0500, sse=17355320.0, rms=23.607 (2.199%) positioning took 0.7 minutes mean border=54.2, 189 (123) missing vertices, mean dist 1.4 [0.3 (%0.1)->2.4 (%99.9))] %12 local maxima, %45 large gradients and %39 min vals, 157 gradients ignored tol=1.0e-04, sigma=2.0, host=zapps, 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=18812594.0, rms=24.619 011: dt: 0.0500, sse=18102808.0, rms=24.131 (1.984%) 012: dt: 0.0500, sse=17446914.0, rms=23.670 (1.908%) 013: dt: 0.0500, sse=16837654.0, rms=23.234 (1.842%) 014: dt: 0.0500, sse=16269856.0, rms=22.821 (1.781%) 015: dt: 0.0500, sse=15739414.0, rms=22.427 (1.724%) 016: dt: 0.0500, sse=15242773.0, rms=22.052 (1.671%) 017: dt: 0.0500, sse=14776045.0, rms=21.694 (1.625%) 018: dt: 0.0500, sse=14336447.0, rms=21.351 (1.581%) 019: dt: 0.0500, sse=13921195.0, rms=21.022 (1.542%) 020: dt: 0.0500, sse=13528926.0, rms=20.706 (1.502%) positioning took 0.7 minutes mean border=54.0, 210 (92) missing vertices, mean dist 1.2 [0.1 (%0.6)->2.0 (%99.4))] %12 local maxima, %45 large gradients and %39 min vals, 137 gradients ignored tol=1.0e-04, sigma=2.0, host=zapps, 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=13680357.0, rms=20.834 021: dt: 0.0500, sse=13299820.0, rms=20.525 (1.484%) 022: dt: 0.0500, sse=12939310.0, rms=20.228 (1.448%) 023: dt: 0.0500, sse=12595351.0, rms=19.940 (1.423%) 024: dt: 0.0500, sse=12267721.0, rms=19.662 (1.395%) 025: dt: 0.0500, sse=11954754.0, rms=19.392 (1.370%) 026: dt: 0.0500, sse=11656185.0, rms=19.132 (1.344%) 027: dt: 0.0500, sse=11369152.0, rms=18.877 (1.328%) 028: dt: 0.0500, sse=11091579.0, rms=18.628 (1.319%) 029: dt: 0.0500, sse=10822190.0, rms=18.383 (1.315%) 030: dt: 0.0500, sse=10561334.0, rms=18.143 (1.308%) positioning took 0.7 minutes mean border=53.9, 239 (79) missing vertices, mean dist 1.0 [0.1 (%5.1)->1.8 (%94.9))] %12 local maxima, %45 large gradients and %39 min vals, 149 gradients ignored tol=1.0e-04, sigma=2.0, host=zapps, 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=10663740.0, rms=18.240 031: dt: 0.5000, sse=8777529.0, rms=16.410 (10.035%) 032: dt: 0.5000, sse=7285074.5, rms=14.797 (9.831%) 033: dt: 0.5000, sse=6015946.0, rms=13.275 (10.282%) 034: dt: 0.5000, sse=4932419.0, rms=11.817 (10.987%) 035: dt: 0.5000, sse=4039999.5, rms=10.468 (11.415%) 036: dt: 0.5000, sse=3357854.8, rms=9.301 (11.147%) 037: dt: 0.5000, sse=2854732.2, rms=8.340 (10.329%) 038: dt: 0.5000, sse=2528040.8, rms=7.648 (8.298%) 039: dt: 0.5000, sse=2326480.5, rms=7.191 (5.979%) 040: dt: 0.5000, sse=2200231.5, rms=6.885 (4.248%) 041: dt: 0.5000, sse=2120026.8, rms=6.686 (2.892%) 042: dt: 0.5000, sse=2073140.4, rms=6.563 (1.841%) 043: dt: 0.5000, sse=2036049.2, rms=6.466 (1.479%) rms = 6.43, time step reduction 1 of 3 to 0.250... 044: dt: 0.5000, sse=2021751.9, rms=6.426 (0.617%) 045: dt: 0.2500, sse=1823209.2, rms=5.842 (9.098%) 046: dt: 0.2500, sse=1770688.5, rms=5.687 (2.643%) rms = 5.69, time step reduction 2 of 3 to 0.125... 047: dt: 0.2500, sse=1771223.1, rms=5.685 (0.038%) 048: dt: 0.1250, sse=1714420.5, rms=5.506 (3.149%) rms = 5.47, time step reduction 3 of 3 to 0.062... 049: dt: 0.1250, sse=1702401.4, rms=5.469 (0.680%) positioning took 1.7 minutes mean border=53.5, 6106 (23) missing vertices, mean dist 0.1 [0.2 (%51.8)->0.6 (%48.2))] %20 local maxima, %36 large gradients and %37 min vals, 102 gradients ignored tol=1.0e-04, sigma=1.0, host=zapps, 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=1875164.9, rms=5.407 rms = 5.56, time step reduction 1 of 3 to 0.250... 050: dt: 0.2500, sse=1739444.9, rms=4.951 (8.441%) 051: dt: 0.2500, sse=1678261.4, rms=4.731 (4.447%) rms = 4.71, time step reduction 2 of 3 to 0.125... 052: dt: 0.2500, sse=1671936.5, rms=4.715 (0.337%) 053: dt: 0.1250, sse=1600690.0, rms=4.442 (5.785%) 054: dt: 0.1250, sse=1583781.8, rms=4.380 (1.401%) rms = 4.37, time step reduction 3 of 3 to 0.062... 055: dt: 0.1250, sse=1581175.0, rms=4.372 (0.190%) positioning took 0.7 minutes mean border=52.8, 6155 (20) missing vertices, mean dist 0.1 [0.1 (%49.6)->0.4 (%50.4))] %34 local maxima, %22 large gradients and %36 min vals, 91 gradients ignored tol=1.0e-04, sigma=0.5, host=zapps, 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=1641316.4, rms=4.621 rms = 5.16, time step reduction 1 of 3 to 0.250... 056: dt: 0.2500, sse=1581269.1, rms=4.395 (4.872%) rms = 4.37, time step reduction 2 of 3 to 0.125... 057: dt: 0.2500, sse=1571775.9, rms=4.369 (0.592%) 058: dt: 0.1250, sse=1549271.5, rms=4.278 (2.099%) rms = 4.24, time step reduction 3 of 3 to 0.062... 059: dt: 0.1250, sse=1539207.9, rms=4.241 (0.853%) positioning took 0.5 minutes mean border=52.2, 8832 (16) missing vertices, mean dist 0.1 [0.1 (%48.7)->0.3 (%51.3))] %38 local maxima, %18 large gradients and %35 min vals, 98 gradients ignored tol=1.0e-04, sigma=0.2, host=zapps, 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/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=1575625.6, rms=4.370 rms = 4.82, time step reduction 1 of 3 to 0.250... 060: dt: 0.2500, sse=1534442.2, rms=4.208 (3.701%) 061: dt: 0.2500, sse=1510401.6, rms=4.129 (1.870%) rms = 4.14, time step reduction 2 of 3 to 0.125... 062: dt: 0.1250, sse=1498480.1, rms=4.078 (1.248%) 063: dt: 0.1250, sse=1479369.6, rms=3.999 (1.943%) rms = 3.95, time step reduction 3 of 3 to 0.062... 064: dt: 0.1250, sse=1466909.2, rms=3.950 (1.222%) positioning took 0.7 minutes writing curvature file /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.area.pial vertex spacing 0.99 +- 0.43 (0.07-->7.86) (max @ vno 131086 --> 143056) face area 0.39 +- 0.30 (0.00-->8.39) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 154929 vertices processed 25000 of 154929 vertices processed 50000 of 154929 vertices processed 75000 of 154929 vertices processed 100000 of 154929 vertices processed 125000 of 154929 vertices processed 150000 of 154929 vertices processed 0 of 154929 vertices processed 25000 of 154929 vertices processed 50000 of 154929 vertices processed 75000 of 154929 vertices processed 100000 of 154929 vertices processed 125000 of 154929 vertices processed 150000 of 154929 vertices processed thickness calculation complete, 567:1013 truncations. 36863 vertices at 0 distance 111988 vertices at 1 distance 92452 vertices at 2 distance 38405 vertices at 3 distance 12644 vertices at 4 distance 3752 vertices at 5 distance 1268 vertices at 6 distance 462 vertices at 7 distance 200 vertices at 8 distance 118 vertices at 9 distance 89 vertices at 10 distance 56 vertices at 11 distance 48 vertices at 12 distance 43 vertices at 13 distance 31 vertices at 14 distance 34 vertices at 15 distance 23 vertices at 16 distance 14 vertices at 17 distance 8 vertices at 18 distance 11 vertices at 19 distance 19 vertices at 20 distance writing curvature file /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.thickness positioning took 10.5 minutes PIDs (3088 3091) completed and logs appended. #-------------------------------------------- #@# Surf Volume lh Thu Oct 3 15:16:54 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 S131032017_Supine lh /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.volume masking with /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/label/lh.cortex.label Total face volume 267976 Total vertex volume 265335 (mask=0) #@# S131032017_Supine lh 265335 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Thu Oct 3 15:16:57 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 S131032017_Supine rh /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.volume masking with /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/label/rh.cortex.label Total face volume 266235 Total vertex volume 263821 (mask=0) #@# S131032017_Supine rh 263821 vertexvol Done #-------------------------------------------- #@# Cortical ribbon mask Thu Oct 3 15:16:59 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 S131032017_Supine SUBJECTS_DIR is /mnt/8E74B1C874B1B377/FreeSurfer/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 = 178 writing volume /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/ribbon.mgz mris_volmask took 12.04 minutes writing ribbon files #----------------------------------------- #@# Parcellation Stats lh Thu Oct 3 15:29:02 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 S131032017_Supine 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 S131032017_Supine lh pial #----------------------------------------- #@# Parcellation Stats rh Thu Oct 3 15:29:02 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 S131032017_Supine 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 S131032017_Supine rh pial Waiting for PID 4277 of (4277 4280 4283 4286) to complete... Waiting for PID 4280 of (4277 4280 4283 4286) to complete... Waiting for PID 4283 of (4277 4280 4283 4286) to complete... Waiting for PID 4286 of (4277 4280 4283 4286) 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 S131032017_Supine lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/wm.mgz... reading input surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.white... reading input pial surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.pial... reading input white surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 267976 Total vertex volume 265335 (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) = 1261180 mm^3 (det: 1.544669 ) lhCtxGM: 264546.501 264183.000 diff= 363.5 pctdiff= 0.137 rhCtxGM: 261758.298 261428.000 diff= 330.3 pctdiff= 0.126 lhCtxWM: 218582.612 219657.500 diff=-1074.9 pctdiff=-0.492 rhCtxWM: 229425.186 230659.500 diff=-1234.3 pctdiff=-0.538 SubCortGMVol 54769.000 SupraTentVol 1042140.598 (1040097.000) diff=2043.598 pctdiff=0.196 SupraTentVolNotVent 1032745.598 (1030702.000) diff=2043.598 pctdiff=0.198 BrainSegVol 1207065.000 (1204153.000) diff=2912.000 pctdiff=0.241 BrainSegVolNotVent 1193598.000 (1191872.598) diff=1725.402 pctdiff=0.145 BrainSegVolNotVent 1193598.000 CerebellumVol 162786.000 VentChorVol 9395.000 3rd4th5thCSF 4072.000 CSFVol 1160.000, OptChiasmVol 110.000 MaskVol 1697541.000 1279 904 2480 2.406 0.603 0.104 0.017 10 0.8 bankssts 997 647 1782 2.638 0.521 0.131 0.026 20 0.9 caudalanteriorcingulate 5290 3276 9246 2.508 0.436 0.112 0.024 62 5.1 caudalmiddlefrontal 2727 1785 3954 2.074 0.507 0.154 0.037 48 4.0 cuneus 634 402 1997 3.696 0.778 0.114 0.029 6 0.7 entorhinal 5043 3535 9885 2.473 0.678 0.138 0.041 116 9.9 fusiform 6913 4375 11584 2.407 0.509 0.124 0.029 90 8.3 inferiorparietal 5870 3976 11294 2.504 0.824 0.144 0.045 96 10.6 inferiortemporal 1903 1196 3191 2.456 0.820 0.136 0.037 36 2.6 isthmuscingulate 9455 5859 14597 2.225 0.459 0.137 0.035 149 13.1 lateraloccipital 4124 2790 7906 2.659 0.624 0.145 0.045 69 8.1 lateralorbitofrontal 5760 3853 8218 2.078 0.611 0.150 0.045 102 11.0 lingual 2180 1471 3750 2.327 0.557 0.140 0.039 45 3.1 medialorbitofrontal 6212 3723 11425 2.662 0.709 0.129 0.048 102 12.4 middletemporal 1101 674 2278 2.765 0.984 0.102 0.035 15 1.5 parahippocampal 2560 1553 4315 2.595 0.562 0.107 0.027 27 2.5 paracentral 2465 1677 4404 2.377 0.530 0.123 0.027 31 2.7 parsopercularis 1267 830 2967 2.697 0.565 0.138 0.040 21 1.8 parsorbitalis 2501 1675 4935 2.445 0.523 0.135 0.036 47 3.9 parstriangularis 2388 1595 2310 1.637 0.385 0.140 0.034 29 3.5 pericalcarine 8077 4857 12049 2.183 0.640 0.108 0.029 91 8.9 postcentral 1857 1210 3294 2.625 0.911 0.140 0.028 29 2.2 posteriorcingulate 9149 5481 16652 2.713 0.597 0.106 0.022 86 8.1 precentral 5977 3939 10664 2.506 0.449 0.120 0.026 67 6.3 precuneus 1143 757 2399 2.793 0.500 0.120 0.031 16 1.4 rostralanteriorcingulate 10316 6826 18177 2.351 0.512 0.140 0.034 158 14.6 rostralmiddlefrontal 12901 7941 26332 2.893 0.548 0.116 0.027 160 13.3 superiorfrontal 8737 5350 13468 2.264 0.482 0.116 0.027 117 9.7 superiorparietal 7353 4843 14032 2.627 0.706 0.122 0.033 88 9.9 superiortemporal 6952 4412 12377 2.529 0.590 0.137 0.043 118 12.5 supramarginal 432 290 857 2.218 0.493 0.154 0.040 10 0.8 frontalpole 636 472 2266 3.255 1.132 0.165 0.061 10 2.1 temporalpole 940 553 1493 2.326 0.417 0.114 0.029 14 0.9 transversetemporal 4223 2891 8693 3.002 0.902 0.120 0.033 51 5.3 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 S131032017_Supine lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/wm.mgz... reading input surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.pial... reading input pial surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.pial... reading input white surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 267976 Total vertex volume 265335 (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) = 1261180 mm^3 (det: 1.544669 ) lhCtxGM: 264546.501 264183.000 diff= 363.5 pctdiff= 0.137 rhCtxGM: 261758.298 261428.000 diff= 330.3 pctdiff= 0.126 lhCtxWM: 218582.612 219657.500 diff=-1074.9 pctdiff=-0.492 rhCtxWM: 229425.186 230659.500 diff=-1234.3 pctdiff=-0.538 SubCortGMVol 54769.000 SupraTentVol 1042140.598 (1040097.000) diff=2043.598 pctdiff=0.196 SupraTentVolNotVent 1032745.598 (1030702.000) diff=2043.598 pctdiff=0.198 BrainSegVol 1207065.000 (1204153.000) diff=2912.000 pctdiff=0.241 BrainSegVolNotVent 1193598.000 (1191872.598) diff=1725.402 pctdiff=0.145 BrainSegVolNotVent 1193598.000 CerebellumVol 162786.000 VentChorVol 9395.000 3rd4th5thCSF 4072.000 CSFVol 1160.000, OptChiasmVol 110.000 MaskVol 1697541.000 1279 1070 2480 2.406 0.603 0.130 0.026 14 1.5 bankssts 997 775 1782 2.638 0.521 0.157 0.044 29 1.7 caudalanteriorcingulate 5290 4054 9246 2.508 0.436 0.129 0.028 61 6.6 caudalmiddlefrontal 2727 2166 3954 2.074 0.507 0.151 0.041 50 4.8 cuneus 634 708 1997 3.696 0.778 0.161 0.037 6 1.0 entorhinal 5043 4396 9885 2.473 0.678 0.166 0.045 104 10.5 fusiform 6913 5216 11584 2.407 0.509 0.137 0.033 89 10.4 inferiorparietal 5870 4757 11294 2.504 0.824 0.156 0.045 133 12.5 inferiortemporal 1903 1450 3191 2.456 0.820 0.161 0.054 49 4.6 isthmuscingulate 9455 7419 14597 2.225 0.459 0.146 0.053 711 27.6 lateraloccipital 4124 3263 7906 2.659 0.624 0.157 0.048 83 8.2 lateralorbitofrontal 5760 4353 8218 2.078 0.611 0.144 0.040 95 10.2 lingual 2180 1840 3750 2.327 0.557 0.169 0.051 91 5.4 medialorbitofrontal 6212 4893 11425 2.662 0.709 0.130 0.039 211 11.1 middletemporal 1101 987 2278 2.765 0.984 0.146 0.039 11 2.1 parahippocampal 2560 1795 4315 2.595 0.562 0.125 0.033 38 3.5 paracentral 2465 2013 4404 2.377 0.530 0.153 0.039 40 4.1 parsopercularis 1267 1291 2967 2.697 0.565 0.170 0.034 19 2.0 parsorbitalis 2501 2308 4935 2.445 0.523 0.174 0.044 39 5.0 parstriangularis 2388 1319 2310 1.637 0.385 0.116 0.034 35 3.5 pericalcarine 8077 6188 12049 2.183 0.640 0.125 0.031 86 11.2 postcentral 1857 1456 3294 2.625 0.911 0.179 0.058 72 5.1 posteriorcingulate 9149 6756 16652 2.713 0.597 0.121 0.029 105 11.6 precentral 5977 4501 10664 2.506 0.449 0.136 0.033 81 8.9 precuneus 1143 1007 2399 2.793 0.500 0.173 0.049 21 2.4 rostralanteriorcingulate 10316 8501 18177 2.351 0.512 0.161 0.038 167 18.5 rostralmiddlefrontal 12901 10225 26332 2.893 0.548 0.145 0.036 194 20.9 superiorfrontal 8737 6479 13468 2.264 0.482 0.127 0.029 109 10.7 superiorparietal 7353 5747 14032 2.627 0.706 0.145 0.039 117 12.8 superiortemporal 6952 5176 12377 2.529 0.590 0.139 0.037 105 11.5 supramarginal 432 493 857 2.218 0.493 0.219 0.037 8 0.8 frontalpole 636 843 2266 3.255 1.132 0.184 0.036 6 1.0 temporalpole 940 800 1493 2.326 0.417 0.143 0.037 8 1.4 transversetemporal 4223 2932 8693 3.002 0.902 0.173 0.060 107 11.3 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 S131032017_Supine rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/wm.mgz... reading input surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.white... reading input pial surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.pial... reading input white surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 266235 Total vertex volume 263821 (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) = 1261180 mm^3 (det: 1.544669 ) lhCtxGM: 264546.501 264183.000 diff= 363.5 pctdiff= 0.137 rhCtxGM: 261758.298 261428.000 diff= 330.3 pctdiff= 0.126 lhCtxWM: 218582.612 219657.500 diff=-1074.9 pctdiff=-0.492 rhCtxWM: 229425.186 230659.500 diff=-1234.3 pctdiff=-0.538 SubCortGMVol 54769.000 SupraTentVol 1042140.598 (1040097.000) diff=2043.598 pctdiff=0.196 SupraTentVolNotVent 1032745.598 (1030702.000) diff=2043.598 pctdiff=0.198 BrainSegVol 1207065.000 (1204153.000) diff=2912.000 pctdiff=0.241 BrainSegVolNotVent 1193598.000 (1191872.598) diff=1725.402 pctdiff=0.145 BrainSegVolNotVent 1193598.000 CerebellumVol 162786.000 VentChorVol 9395.000 3rd4th5thCSF 4072.000 CSFVol 1160.000, OptChiasmVol 110.000 MaskVol 1697541.000 1366 938 2297 2.719 0.468 0.124 0.025 12 1.5 bankssts 1587 1021 3023 2.587 0.631 0.134 0.021 29 1.2 caudalanteriorcingulate 4408 2739 8117 2.579 0.501 0.116 0.032 63 6.4 caudalmiddlefrontal 3091 1992 4501 2.079 0.486 0.145 0.036 51 4.2 cuneus 432 298 1767 3.593 0.827 0.125 0.033 5 0.6 entorhinal 4348 2981 8012 2.571 0.606 0.132 0.028 68 4.7 fusiform 7877 5161 14113 2.447 0.469 0.126 0.026 107 8.4 inferiorparietal 5703 3931 9668 2.420 0.786 0.153 0.054 97 13.4 inferiortemporal 1805 1121 2747 2.340 0.791 0.143 0.049 34 3.3 isthmuscingulate 9671 6359 15408 2.178 0.452 0.143 0.032 153 12.2 lateraloccipital 4203 2830 7404 2.412 0.642 0.144 0.048 80 8.5 lateralorbitofrontal 5813 3887 8772 2.148 0.638 0.145 0.036 94 8.6 lingual 2323 1614 4530 2.513 0.672 0.134 0.035 44 3.1 medialorbitofrontal 7082 4619 10519 2.147 0.832 0.150 0.057 129 17.8 middletemporal 1119 691 2506 3.019 0.690 0.092 0.017 9 0.6 parahippocampal 2674 1674 4677 2.629 0.466 0.109 0.022 21 2.3 paracentral 2228 1500 4612 2.663 0.466 0.116 0.024 27 2.1 parsopercularis 1330 900 3017 2.724 0.592 0.152 0.040 28 2.1 parsorbitalis 2647 1733 5243 2.599 0.548 0.122 0.027 40 2.7 parstriangularis 2602 1711 2659 1.721 0.434 0.129 0.029 27 2.9 pericalcarine 6498 4088 9576 2.088 0.564 0.109 0.025 80 5.9 postcentral 2200 1462 4051 2.565 0.604 0.151 0.038 40 3.4 posteriorcingulate 10410 6355 17798 2.573 0.521 0.107 0.025 100 10.2 precentral 6455 4138 10835 2.467 0.407 0.122 0.027 81 6.7 precuneus 1242 836 2925 3.010 0.680 0.142 0.037 22 1.9 rostralanteriorcingulate 9483 6291 17532 2.495 0.550 0.136 0.032 147 11.9 rostralmiddlefrontal 13729 8612 28154 2.855 0.582 0.120 0.031 167 17.1 superiorfrontal 8473 5356 13954 2.298 0.498 0.116 0.024 110 7.8 superiorparietal 6206 4316 12256 2.714 0.776 0.133 0.037 70 9.4 superiortemporal 5830 3749 10459 2.501 0.522 0.130 0.036 88 8.4 supramarginal 409 306 1096 2.920 0.651 0.209 0.087 11 1.6 frontalpole 596 437 2846 4.240 0.728 0.157 0.049 10 1.1 temporalpole 626 392 1200 2.517 0.483 0.137 0.037 10 0.9 transversetemporal 3545 2451 7536 3.012 0.831 0.128 0.033 41 4.6 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 S131032017_Supine rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/wm.mgz... reading input surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.pial... reading input pial surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.pial... reading input white surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 266235 Total vertex volume 263821 (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) = 1261180 mm^3 (det: 1.544669 ) lhCtxGM: 264546.501 264183.000 diff= 363.5 pctdiff= 0.137 rhCtxGM: 261758.298 261428.000 diff= 330.3 pctdiff= 0.126 lhCtxWM: 218582.612 219657.500 diff=-1074.9 pctdiff=-0.492 rhCtxWM: 229425.186 230659.500 diff=-1234.3 pctdiff=-0.538 SubCortGMVol 54769.000 SupraTentVol 1042140.598 (1040097.000) diff=2043.598 pctdiff=0.196 SupraTentVolNotVent 1032745.598 (1030702.000) diff=2043.598 pctdiff=0.198 BrainSegVol 1207065.000 (1204153.000) diff=2912.000 pctdiff=0.241 BrainSegVolNotVent 1193598.000 (1191872.598) diff=1725.402 pctdiff=0.145 BrainSegVolNotVent 1193598.000 CerebellumVol 162786.000 VentChorVol 9395.000 3rd4th5thCSF 4072.000 CSFVol 1160.000, OptChiasmVol 110.000 MaskVol 1697541.000 1366 775 2297 2.719 0.468 0.136 0.042 24 2.6 bankssts 1587 1301 3023 2.587 0.631 0.163 0.038 49 2.7 caudalanteriorcingulate 4408 3453 8117 2.579 0.501 0.133 0.033 60 6.6 caudalmiddlefrontal 3091 2426 4501 2.079 0.486 0.145 0.035 49 4.7 cuneus 432 646 1767 3.593 0.827 0.194 0.039 3 0.9 entorhinal 4348 3262 8012 2.571 0.606 0.155 0.167 230 8.5 fusiform 7877 6245 14113 2.447 0.469 0.144 0.032 114 11.4 inferiorparietal 5703 4066 9668 2.420 0.786 0.133 0.050 136 14.3 inferiortemporal 1805 1241 2747 2.340 0.791 0.154 0.054 45 4.7 isthmuscingulate 9671 7824 15408 2.178 0.452 0.150 0.035 157 15.0 lateraloccipital 4203 3389 7404 2.412 0.642 0.175 0.055 79 10.5 lateralorbitofrontal 5813 4521 8772 2.148 0.638 0.159 0.048 116 12.7 lingual 2323 2061 4530 2.513 0.672 0.174 0.052 47 5.2 medialorbitofrontal 7082 5385 10519 2.147 0.832 0.127 0.036 162 11.7 middletemporal 1119 979 2506 3.019 0.690 0.161 0.040 16 2.3 parahippocampal 2674 1887 4677 2.629 0.466 0.124 0.031 30 3.8 paracentral 2228 1943 4612 2.663 0.466 0.159 0.040 29 4.4 parsopercularis 1330 1330 3017 2.724 0.592 0.174 0.042 23 2.5 parsorbitalis 2647 2335 5243 2.599 0.548 0.162 0.037 41 4.6 parstriangularis 2602 1503 2659 1.721 0.434 0.121 0.033 37 3.9 pericalcarine 6498 5212 9576 2.088 0.564 0.127 0.028 71 8.0 postcentral 2200 1688 4051 2.565 0.604 0.167 0.049 67 4.6 posteriorcingulate 10410 7376 17798 2.573 0.521 0.116 0.028 129 12.4 precentral 6455 4637 10835 2.467 0.407 0.131 0.030 83 8.6 precuneus 1242 1267 2925 3.010 0.680 0.184 0.049 19 2.6 rostralanteriorcingulate 9483 7775 17532 2.495 0.550 0.157 0.038 146 16.3 rostralmiddlefrontal 13729 10879 28154 2.855 0.582 0.143 0.035 212 21.5 superiorfrontal 8473 6642 13954 2.298 0.498 0.132 0.027 95 10.0 superiorparietal 6206 4868 12256 2.714 0.776 0.143 0.040 117 11.1 superiortemporal 5830 4436 10459 2.501 0.522 0.143 0.041 89 10.8 supramarginal 409 443 1096 2.920 0.651 0.204 0.048 7 0.9 frontalpole 596 873 2846 4.240 0.728 0.223 0.042 7 1.3 temporalpole 626 556 1200 2.517 0.483 0.155 0.040 6 1.2 transversetemporal 3545 2385 7536 3.012 0.831 0.167 0.056 79 8.5 insula PIDs (4277 4280 4283 4286) completed and logs appended. #----------------------------------------- #@# Cortical Parc 2 lh Thu Oct 3 15:30:07 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 S131032017_Supine 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 Thu Oct 3 15:30:07 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 S131032017_Supine 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 4378 of (4378 4381) to complete... Waiting for PID 4381 of (4378 4381) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 S131032017_Supine 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... 40 labels changed using aseg relabeling using gibbs priors... 000: 10048 changed, 157621 examined... 001: 2347 changed, 39456 examined... 002: 718 changed, 12227 examined... 003: 303 changed, 4005 examined... 004: 149 changed, 1761 examined... 005: 68 changed, 831 examined... 006: 37 changed, 373 examined... 007: 15 changed, 203 examined... 008: 8 changed, 88 examined... 009: 3 changed, 42 examined... 010: 2 changed, 22 examined... 011: 0 changed, 13 examined... 3 labels changed using aseg 000: 304 total segments, 221 labels (2393 vertices) changed 001: 98 total segments, 15 labels (63 vertices) changed 002: 83 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 39 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1296 vertices marked for relabeling... 1296 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 12 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 S131032017_Supine 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... 17 labels changed using aseg relabeling using gibbs priors... 000: 9866 changed, 154929 examined... 001: 2209 changed, 39135 examined... 002: 620 changed, 11651 examined... 003: 237 changed, 3479 examined... 004: 96 changed, 1354 examined... 005: 46 changed, 547 examined... 006: 30 changed, 278 examined... 007: 21 changed, 141 examined... 008: 7 changed, 103 examined... 009: 2 changed, 35 examined... 010: 0 changed, 9 examined... 0 labels changed using aseg 000: 282 total segments, 193 labels (2460 vertices) changed 001: 101 total segments, 12 labels (21 vertices) changed 002: 89 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 58 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1381 vertices marked for relabeling... 1381 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 12 seconds. PIDs (4378 4381) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 2 lh Thu Oct 3 15:30:19 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 S131032017_Supine lh white #----------------------------------------- #@# Parcellation Stats 2 rh Thu Oct 3 15:30:19 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 S131032017_Supine rh white Waiting for PID 4440 of (4440 4443) to complete... Waiting for PID 4443 of (4440 4443) 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 S131032017_Supine lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/wm.mgz... reading input surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.white... reading input pial surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.pial... reading input white surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 267976 Total vertex volume 265335 (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) = 1261180 mm^3 (det: 1.544669 ) lhCtxGM: 264546.501 264183.000 diff= 363.5 pctdiff= 0.137 rhCtxGM: 261758.298 261428.000 diff= 330.3 pctdiff= 0.126 lhCtxWM: 218582.612 219657.500 diff=-1074.9 pctdiff=-0.492 rhCtxWM: 229425.186 230659.500 diff=-1234.3 pctdiff=-0.538 SubCortGMVol 54769.000 SupraTentVol 1042140.598 (1040097.000) diff=2043.598 pctdiff=0.196 SupraTentVolNotVent 1032745.598 (1030702.000) diff=2043.598 pctdiff=0.198 BrainSegVol 1207065.000 (1204153.000) diff=2912.000 pctdiff=0.241 BrainSegVolNotVent 1193598.000 (1191872.598) diff=1725.402 pctdiff=0.145 BrainSegVolNotVent 1193598.000 CerebellumVol 162786.000 VentChorVol 9395.000 3rd4th5thCSF 4072.000 CSFVol 1160.000, OptChiasmVol 110.000 MaskVol 1697541.000 1559 1056 2503 2.195 0.600 0.154 0.045 23 3.3 G&S_frontomargin 2026 1264 3416 2.376 0.482 0.148 0.062 46 6.2 G&S_occipital_inf 1961 1073 3233 2.485 0.591 0.104 0.023 19 2.0 G&S_paracentral 2039 1336 4102 2.566 0.567 0.137 0.043 37 3.4 G&S_subcentral 966 658 2119 2.512 0.523 0.162 0.039 23 1.6 G&S_transv_frontopol 2501 1758 4991 2.734 0.449 0.122 0.030 33 3.0 G&S_cingul-Ant 1499 1019 2676 2.750 0.507 0.110 0.019 17 1.1 G&S_cingul-Mid-Ant 1379 948 2632 2.898 0.645 0.136 0.030 17 1.6 G&S_cingul-Mid-Post 757 483 1951 2.921 0.590 0.152 0.035 15 1.1 G_cingul-Post-dorsal 395 219 712 2.731 0.803 0.138 0.051 13 0.6 G_cingul-Post-ventral 2617 1647 3974 2.033 0.553 0.150 0.038 46 4.1 G_cuneus 1385 930 3163 2.495 0.535 0.136 0.038 26 2.0 G_front_inf-Opercular 509 328 1322 2.746 0.574 0.165 0.045 12 0.9 G_front_inf-Orbital 1403 931 3133 2.506 0.530 0.153 0.045 36 3.1 G_front_inf-Triangul 6313 3818 12622 2.550 0.483 0.128 0.032 109 8.0 G_front_middle 9131 5283 20420 3.007 0.559 0.121 0.032 140 10.9 G_front_sup 790 509 1870 3.454 0.814 0.136 0.049 17 1.2 G_Ins_lg&S_cent_ins 793 512 2623 3.630 0.628 0.123 0.032 11 1.0 G_insular_short 3046 1703 5571 2.455 0.498 0.133 0.037 60 4.3 G_occipital_middle 1622 1028 2575 2.142 0.422 0.142 0.035 26 2.1 G_occipital_sup 2092 1432 4744 2.597 0.593 0.152 0.042 73 3.6 G_oc-temp_lat-fusifor 4056 2613 5696 1.956 0.641 0.163 0.054 87 9.3 G_oc-temp_med-Lingual 1246 765 3455 3.354 0.786 0.102 0.028 12 1.2 G_oc-temp_med-Parahip 2788 1809 6382 2.676 0.640 0.152 0.055 62 6.3 G_orbital 2793 1606 5709 2.611 0.555 0.131 0.043 48 5.0 G_pariet_inf-Angular 3924 2383 8094 2.667 0.641 0.148 0.054 91 8.4 G_pariet_inf-Supramar 3121 1755 5308 2.437 0.547 0.105 0.032 48 4.5 G_parietal_sup 3277 1695 4853 2.236 0.685 0.108 0.034 42 3.8 G_postcentral 3734 1901 8133 3.097 0.554 0.100 0.025 44 3.4 G_precentral 2946 1786 6397 2.605 0.464 0.133 0.035 54 4.0 G_precuneus 811 519 1436 2.123 0.492 0.150 0.056 27 1.6 G_rectus 763 561 1106 2.141 0.979 0.128 0.052 12 1.3 G_subcallosal 821 475 1392 2.303 0.387 0.115 0.028 12 0.8 G_temp_sup-G_T_transv 2632 1699 5854 2.631 0.725 0.148 0.051 51 5.6 G_temp_sup-Lateral 984 650 2777 3.519 0.784 0.106 0.034 9 1.4 G_temp_sup-Plan_polar 1123 759 2020 2.366 0.432 0.094 0.017 7 0.8 G_temp_sup-Plan_tempo 2841 1922 6504 2.638 0.878 0.150 0.052 57 5.7 G_temporal_inf 3658 1996 7330 2.764 0.790 0.141 0.060 80 8.9 G_temporal_middle 438 288 592 2.167 0.365 0.100 0.017 3 0.3 Lat_Fis-ant-Horizont 370 252 553 2.391 0.548 0.122 0.021 3 0.3 Lat_Fis-ant-Vertical 1341 860 1618 2.352 0.469 0.114 0.023 11 1.3 Lat_Fis-post 2728 1668 3973 2.051 0.454 0.145 0.034 47 3.7 Pole_occipital 1972 1305 4768 2.579 1.011 0.163 0.067 38 5.8 Pole_temporal 3130 2152 3605 1.927 0.590 0.131 0.033 35 4.6 S_calcarine 3474 2358 4559 2.157 0.557 0.102 0.019 19 2.7 S_central 1377 935 1998 2.481 0.516 0.101 0.018 8 0.9 S_cingul-Marginalis 744 516 1179 2.868 0.592 0.115 0.022 4 0.8 S_circular_insula_ant 1512 1030 2497 2.890 0.791 0.095 0.016 7 1.1 S_circular_insula_inf 2059 1388 3056 2.726 0.535 0.105 0.018 11 1.7 S_circular_insula_sup 905 654 1990 3.131 0.842 0.137 0.031 11 1.1 S_collat_transv_ant 628 434 718 1.967 0.299 0.122 0.027 4 0.7 S_collat_transv_post 2676 1843 4300 2.231 0.480 0.139 0.031 31 3.6 S_front_inf 2251 1535 3444 2.308 0.421 0.124 0.022 23 2.2 S_front_middle 3037 2041 4480 2.394 0.366 0.106 0.020 25 2.2 S_front_sup 195 128 317 2.981 0.546 0.148 0.042 1 0.5 S_interm_prim-Jensen 3006 2006 3943 2.190 0.390 0.134 0.025 35 3.3 S_intrapariet&P_trans 1393 943 1700 2.083 0.384 0.117 0.025 10 1.4 S_oc_middle&Lunatus 1555 1042 1997 2.112 0.316 0.120 0.024 13 1.5 S_oc_sup&transversal 807 557 1035 2.120 0.280 0.110 0.021 5 0.7 S_occipital_ant 1036 734 1570 2.102 0.479 0.121 0.026 11 1.0 S_oc-temp_lat 2382 1735 3693 2.295 0.616 0.120 0.021 21 2.2 S_oc-temp_med&Lingual 514 345 764 2.223 0.555 0.131 0.030 5 0.6 S_orbital_lateral 585 412 1002 2.740 0.725 0.132 0.027 5 0.6 S_orbital_med-olfact 1342 947 2344 2.508 0.492 0.139 0.035 18 1.9 S_orbital-H_Shaped 2162 1461 3193 2.388 0.447 0.116 0.020 19 1.8 S_parieto_occipital 1367 810 1239 1.866 0.782 0.128 0.020 22 0.9 S_pericallosal 3396 2384 4744 2.103 0.359 0.109 0.019 28 2.7 S_postcentral 2452 1660 3606 2.366 0.373 0.100 0.017 19 1.6 S_precentral-inf-part 1467 981 2042 2.317 0.386 0.101 0.017 7 1.0 S_precentral-sup-part 619 427 857 2.315 0.447 0.128 0.024 5 0.6 S_suborbital 1295 894 1822 2.433 0.353 0.119 0.025 9 1.3 S_subparietal 2299 1618 3330 2.375 0.488 0.119 0.023 20 2.2 S_temporal_inf 6088 4137 9430 2.444 0.522 0.115 0.023 55 5.9 S_temporal_sup 488 327 585 2.110 0.407 0.099 0.014 2 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 S131032017_Supine rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/wm.mgz... reading input surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.white... reading input pial surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.pial... reading input white surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 266235 Total vertex volume 263821 (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) = 1261180 mm^3 (det: 1.544669 ) lhCtxGM: 264546.501 264183.000 diff= 363.5 pctdiff= 0.137 rhCtxGM: 261758.298 261428.000 diff= 330.3 pctdiff= 0.126 lhCtxWM: 218582.612 219657.500 diff=-1074.9 pctdiff=-0.492 rhCtxWM: 229425.186 230659.500 diff=-1234.3 pctdiff=-0.538 SubCortGMVol 54769.000 SupraTentVol 1042140.598 (1040097.000) diff=2043.598 pctdiff=0.196 SupraTentVolNotVent 1032745.598 (1030702.000) diff=2043.598 pctdiff=0.198 BrainSegVol 1207065.000 (1204153.000) diff=2912.000 pctdiff=0.241 BrainSegVolNotVent 1193598.000 (1191872.598) diff=1725.402 pctdiff=0.145 BrainSegVolNotVent 1193598.000 CerebellumVol 162786.000 VentChorVol 9395.000 3rd4th5thCSF 4072.000 CSFVol 1160.000, OptChiasmVol 110.000 MaskVol 1697541.000 974 653 1938 2.617 0.669 0.163 0.051 19 2.4 G&S_frontomargin 1666 1118 2738 2.268 0.495 0.140 0.029 27 1.8 G&S_occipital_inf 1603 891 2614 2.406 0.494 0.106 0.024 17 1.4 G&S_paracentral 1690 1148 3500 2.600 0.527 0.142 0.040 28 2.3 G&S_subcentral 1053 734 2428 2.741 0.428 0.180 0.052 27 2.3 G&S_transv_frontopol 3187 2137 5950 2.701 0.463 0.126 0.030 38 3.7 G&S_cingul-Ant 1893 1291 3892 2.919 0.461 0.115 0.019 20 1.6 G&S_cingul-Mid-Ant 1855 1251 3439 2.777 0.419 0.130 0.029 22 2.1 G&S_cingul-Mid-Post 683 443 1492 2.615 0.623 0.183 0.069 20 1.7 G_cingul-Post-dorsal 609 358 990 2.384 0.847 0.151 0.060 10 1.5 G_cingul-Post-ventral 2874 1837 4133 2.037 0.529 0.145 0.036 46 4.0 G_cuneus 1458 935 3721 2.811 0.480 0.128 0.029 25 1.6 G_front_inf-Opercular 602 364 1416 2.813 0.541 0.148 0.038 14 0.8 G_front_inf-Orbital 1080 703 2622 2.707 0.590 0.146 0.039 26 1.6 G_front_inf-Triangul 5233 3105 11514 2.715 0.551 0.134 0.038 109 7.4 G_front_middle 8874 5210 20551 2.984 0.609 0.124 0.036 133 12.8 G_front_sup 813 589 1962 3.166 1.032 0.152 0.055 20 1.8 G_Ins_lg&S_cent_ins 691 464 2095 3.198 0.845 0.141 0.043 14 1.1 G_insular_short 2770 1754 5551 2.478 0.458 0.140 0.030 55 3.3 G_occipital_middle 2009 1288 3526 2.258 0.435 0.135 0.027 30 2.4 G_occipital_sup 2319 1505 4936 2.566 0.697 0.151 0.035 49 3.1 G_oc-temp_lat-fusifor 3698 2364 5765 2.109 0.693 0.154 0.044 70 6.4 G_oc-temp_med-Lingual 1066 680 3532 3.443 0.810 0.098 0.022 9 0.8 G_oc-temp_med-Parahip 2975 1964 6822 2.678 0.693 0.159 0.057 73 7.0 G_orbital 2971 1825 6862 2.725 0.502 0.141 0.039 60 4.9 G_pariet_inf-Angular 2578 1632 5435 2.660 0.551 0.138 0.042 50 4.2 G_pariet_inf-Supramar 2362 1416 5099 2.637 0.545 0.121 0.030 41 2.6 G_parietal_sup 2484 1409 3866 2.146 0.527 0.107 0.026 40 2.4 G_postcentral 4305 2250 8349 2.779 0.554 0.103 0.030 53 4.6 G_precentral 2894 1681 5602 2.549 0.426 0.124 0.033 53 3.3 G_precuneus 706 494 1664 2.475 0.619 0.157 0.051 25 1.2 G_rectus 469 317 726 2.409 0.879 0.109 0.039 6 0.6 G_subcallosal 423 268 984 2.668 0.424 0.144 0.036 7 0.7 G_temp_sup-G_T_transv 2115 1435 4988 2.769 0.805 0.149 0.047 33 4.0 G_temp_sup-Lateral 1092 697 2905 3.598 0.871 0.115 0.039 13 1.5 G_temp_sup-Plan_polar 861 581 1596 2.516 0.451 0.104 0.020 7 0.6 G_temp_sup-Plan_tempo 3084 2014 5342 2.334 0.809 0.155 0.063 65 8.4 G_temporal_inf 4352 2702 7213 2.246 0.780 0.152 0.057 84 10.8 G_temporal_middle 476 325 615 2.260 0.370 0.090 0.013 2 0.2 Lat_Fis-ant-Horizont 409 293 619 2.455 0.320 0.106 0.018 2 0.3 Lat_Fis-ant-Vertical 1568 1048 2170 2.466 0.445 0.110 0.025 11 1.4 Lat_Fis-post 4242 2734 6585 2.105 0.446 0.149 0.036 71 5.8 Pole_occipital 1998 1359 5065 2.769 1.093 0.160 0.066 35 5.7 Pole_temporal 2810 1946 3468 2.055 0.611 0.136 0.029 31 3.3 S_calcarine 3660 2464 4539 2.041 0.572 0.099 0.021 24 3.1 S_central 1542 1044 2296 2.401 0.396 0.097 0.016 8 1.0 S_cingul-Marginalis 713 498 1227 2.873 0.524 0.118 0.023 5 0.8 S_circular_insula_ant 1237 813 1937 2.801 0.676 0.095 0.017 7 0.9 S_circular_insula_inf 1479 1018 2210 2.623 0.441 0.110 0.021 8 1.3 S_circular_insula_sup 740 507 1459 2.925 0.653 0.115 0.036 11 0.9 S_collat_transv_ant 664 455 849 2.128 0.382 0.135 0.028 7 0.7 S_collat_transv_post 2076 1430 3059 2.265 0.393 0.110 0.024 19 2.5 S_front_inf 2523 1760 3763 2.252 0.450 0.126 0.024 22 2.5 S_front_middle 4015 2757 6293 2.447 0.376 0.113 0.023 34 3.9 S_front_sup 428 293 598 2.195 0.374 0.113 0.019 3 0.4 S_interm_prim-Jensen 3755 2514 4960 2.139 0.338 0.110 0.018 36 2.8 S_intrapariet&P_trans 984 675 1133 1.867 0.413 0.117 0.022 7 0.9 S_oc_middle&Lunatus 1735 1163 2156 2.051 0.349 0.120 0.022 17 1.6 S_oc_sup&transversal 672 516 882 2.083 0.393 0.131 0.023 5 0.8 S_occipital_ant 1535 1124 2082 2.303 0.371 0.132 0.026 16 2.0 S_oc-temp_lat 2232 1546 3164 2.409 0.546 0.109 0.017 18 1.4 S_oc-temp_med&Lingual 434 306 590 2.412 0.482 0.127 0.023 3 0.5 S_orbital_lateral 600 431 900 2.172 0.614 0.132 0.025 8 0.7 S_orbital_med-olfact 1312 913 2056 2.254 0.441 0.142 0.034 15 2.0 S_orbital-H_Shaped 2545 1689 3649 2.327 0.407 0.117 0.022 25 2.2 S_parieto_occipital 1915 1210 2350 2.248 0.941 0.138 0.027 34 1.9 S_pericallosal 2546 1711 3260 2.102 0.348 0.111 0.019 21 2.0 S_postcentral 1945 1311 2969 2.451 0.379 0.113 0.021 18 1.6 S_precentral-inf-part 2351 1637 3720 2.482 0.405 0.105 0.017 15 1.8 S_precentral-sup-part 297 230 647 2.614 0.907 0.165 0.027 4 0.4 S_suborbital 1423 985 2208 2.436 0.397 0.134 0.031 15 1.9 S_subparietal 1586 1115 2326 2.539 1.024 0.140 0.046 22 3.3 S_temporal_inf 6845 4931 9783 2.273 0.609 0.136 0.034 77 9.9 S_temporal_sup 359 242 478 2.701 0.596 0.109 0.018 2 0.2 S_temporal_transverse PIDs (4440 4443) completed and logs appended. #----------------------------------------- #@# Cortical Parc 3 lh Thu Oct 3 15:30:55 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 S131032017_Supine 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 Thu Oct 3 15:30:55 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 S131032017_Supine 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 4505 of (4505 4508) to complete... Waiting for PID 4508 of (4505 4508) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 S131032017_Supine 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... 1646 labels changed using aseg relabeling using gibbs priors... 000: 2168 changed, 157621 examined... 001: 499 changed, 10152 examined... 002: 156 changed, 2849 examined... 003: 65 changed, 871 examined... 004: 23 changed, 373 examined... 005: 13 changed, 133 examined... 006: 9 changed, 78 examined... 007: 9 changed, 50 examined... 008: 7 changed, 45 examined... 009: 6 changed, 40 examined... 010: 1 changed, 30 examined... 011: 0 changed, 7 examined... 216 labels changed using aseg 000: 54 total segments, 21 labels (206 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 12 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 896 vertices marked for relabeling... 896 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 10 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 S131032017_Supine 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... 1567 labels changed using aseg relabeling using gibbs priors... 000: 2169 changed, 154929 examined... 001: 493 changed, 9949 examined... 002: 144 changed, 2862 examined... 003: 65 changed, 854 examined... 004: 23 changed, 371 examined... 005: 12 changed, 141 examined... 006: 11 changed, 66 examined... 007: 7 changed, 53 examined... 008: 6 changed, 40 examined... 009: 5 changed, 34 examined... 010: 2 changed, 25 examined... 011: 3 changed, 12 examined... 012: 1 changed, 13 examined... 013: 2 changed, 7 examined... 014: 2 changed, 12 examined... 015: 0 changed, 10 examined... 140 labels changed using aseg 000: 61 total segments, 28 labels (208 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 6 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1187 vertices marked for relabeling... 1187 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 10 seconds. PIDs (4505 4508) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 3 lh Thu Oct 3 15:31:05 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 S131032017_Supine lh white #----------------------------------------- #@# Parcellation Stats 3 rh Thu Oct 3 15:31:05 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 S131032017_Supine rh white Waiting for PID 4555 of (4555 4558) to complete... Waiting for PID 4558 of (4555 4558) 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 S131032017_Supine lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/wm.mgz... reading input surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.white... reading input pial surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.pial... reading input white surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 267976 Total vertex volume 265335 (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) = 1261180 mm^3 (det: 1.544669 ) lhCtxGM: 264546.501 264183.000 diff= 363.5 pctdiff= 0.137 rhCtxGM: 261758.298 261428.000 diff= 330.3 pctdiff= 0.126 lhCtxWM: 218582.612 219657.500 diff=-1074.9 pctdiff=-0.492 rhCtxWM: 229425.186 230659.500 diff=-1234.3 pctdiff=-0.538 SubCortGMVol 54769.000 SupraTentVol 1042140.598 (1040097.000) diff=2043.598 pctdiff=0.196 SupraTentVolNotVent 1032745.598 (1030702.000) diff=2043.598 pctdiff=0.198 BrainSegVol 1207065.000 (1204153.000) diff=2912.000 pctdiff=0.241 BrainSegVolNotVent 1193598.000 (1191872.598) diff=1725.402 pctdiff=0.145 BrainSegVolNotVent 1193598.000 CerebellumVol 162786.000 VentChorVol 9395.000 3rd4th5thCSF 4072.000 CSFVol 1160.000, OptChiasmVol 110.000 MaskVol 1697541.000 1853 1184 3247 2.693 0.480 0.120 0.024 30 1.6 caudalanteriorcingulate 5755 3546 10045 2.517 0.445 0.112 0.024 66 5.6 caudalmiddlefrontal 3550 2306 5303 2.123 0.518 0.141 0.032 54 4.6 cuneus 561 357 1772 3.651 0.808 0.110 0.028 5 0.6 entorhinal 4606 3234 8898 2.397 0.645 0.138 0.042 110 9.1 fusiform 6991 4412 11649 2.405 0.508 0.125 0.030 92 8.6 inferiorparietal 5678 3866 11640 2.608 0.845 0.146 0.047 96 11.0 inferiortemporal 1935 1225 3268 2.474 0.797 0.136 0.037 35 2.6 isthmuscingulate 9528 5900 14757 2.230 0.460 0.137 0.035 150 13.1 lateraloccipital 4503 3042 8766 2.606 0.713 0.154 0.054 90 10.5 lateralorbitofrontal 5896 3932 8408 2.069 0.600 0.149 0.044 104 11.0 lingual 2255 1525 3733 2.217 0.642 0.141 0.044 47 3.5 medialorbitofrontal 7726 4784 13871 2.576 0.710 0.128 0.045 117 14.2 middletemporal 1166 723 2420 2.784 0.973 0.107 0.037 16 1.8 parahippocampal 3071 1868 5355 2.616 0.546 0.102 0.025 29 2.8 paracentral 2254 1529 4134 2.428 0.525 0.125 0.028 30 2.5 parsopercularis 1384 904 2970 2.628 0.571 0.136 0.033 20 1.8 parsorbitalis 2946 1966 5501 2.387 0.543 0.135 0.034 50 4.5 parstriangularis 2416 1610 2336 1.637 0.393 0.142 0.034 30 3.5 pericalcarine 9036 5476 13518 2.206 0.633 0.109 0.028 101 9.9 postcentral 2100 1358 3721 2.648 0.887 0.140 0.029 34 2.4 posteriorcingulate 8958 5378 16292 2.714 0.590 0.106 0.023 86 7.8 precentral 5892 3833 10675 2.507 0.438 0.120 0.026 70 6.2 precuneus 1781 1195 3475 2.731 0.515 0.116 0.029 22 1.9 rostralanteriorcingulate 7643 5050 13814 2.360 0.504 0.138 0.034 118 10.4 rostralmiddlefrontal 13537 8461 27210 2.813 0.589 0.122 0.028 178 14.7 superiorfrontal 6871 4219 10383 2.263 0.485 0.117 0.029 94 8.1 superiorparietal 8917 5937 17925 2.668 0.760 0.122 0.033 103 11.9 superiortemporal 6446 4076 11539 2.548 0.599 0.138 0.043 112 11.8 supramarginal 945 557 1501 2.328 0.416 0.115 0.028 14 0.9 transversetemporal 3191 2183 7206 3.197 0.768 0.115 0.025 32 3.3 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 S131032017_Supine rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/wm.mgz... reading input surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.white... reading input pial surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.pial... reading input white surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 266235 Total vertex volume 263821 (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) = 1261180 mm^3 (det: 1.544669 ) lhCtxGM: 264546.501 264183.000 diff= 363.5 pctdiff= 0.137 rhCtxGM: 261758.298 261428.000 diff= 330.3 pctdiff= 0.126 lhCtxWM: 218582.612 219657.500 diff=-1074.9 pctdiff=-0.492 rhCtxWM: 229425.186 230659.500 diff=-1234.3 pctdiff=-0.538 SubCortGMVol 54769.000 SupraTentVol 1042140.598 (1040097.000) diff=2043.598 pctdiff=0.196 SupraTentVolNotVent 1032745.598 (1030702.000) diff=2043.598 pctdiff=0.198 BrainSegVol 1207065.000 (1204153.000) diff=2912.000 pctdiff=0.241 BrainSegVolNotVent 1193598.000 (1191872.598) diff=1725.402 pctdiff=0.145 BrainSegVolNotVent 1193598.000 CerebellumVol 162786.000 VentChorVol 9395.000 3rd4th5thCSF 4072.000 CSFVol 1160.000, OptChiasmVol 110.000 MaskVol 1697541.000 1757 1120 3338 2.606 0.642 0.134 0.024 32 1.4 caudalanteriorcingulate 4577 2874 8380 2.577 0.495 0.117 0.032 64 6.6 caudalmiddlefrontal 3670 2372 5425 2.098 0.482 0.139 0.033 56 4.6 cuneus 402 275 1726 3.680 0.835 0.123 0.035 5 0.6 entorhinal 4286 2918 7824 2.538 0.613 0.134 0.029 67 4.6 fusiform 7973 5216 14318 2.454 0.484 0.127 0.026 108 8.8 inferiorparietal 5930 4106 10377 2.461 0.776 0.151 0.052 100 13.5 inferiortemporal 1807 1130 2708 2.339 0.781 0.143 0.048 33 3.4 isthmuscingulate 9611 6304 15316 2.173 0.449 0.144 0.032 152 12.4 lateraloccipital 4408 2924 8276 2.493 0.711 0.152 0.052 95 10.0 lateralorbitofrontal 5722 3798 8565 2.140 0.638 0.144 0.036 94 8.4 lingual 1895 1344 3760 2.424 0.722 0.140 0.041 38 2.9 medialorbitofrontal 8152 5350 12129 2.187 0.813 0.147 0.053 140 19.1 middletemporal 1132 702 2535 3.016 0.682 0.090 0.017 9 0.6 parahippocampal 2909 1811 5087 2.613 0.471 0.109 0.022 24 2.5 paracentral 2596 1741 5277 2.666 0.462 0.115 0.024 30 2.4 parsopercularis 1228 824 2753 2.656 0.601 0.144 0.041 25 1.9 parsorbitalis 2497 1650 4849 2.555 0.559 0.122 0.027 38 2.5 parstriangularis 2503 1656 2547 1.711 0.420 0.130 0.029 26 2.9 pericalcarine 7202 4528 10577 2.116 0.564 0.111 0.025 89 6.7 postcentral 2296 1525 4182 2.581 0.600 0.150 0.039 41 3.4 posteriorcingulate 9832 5936 16903 2.578 0.527 0.106 0.026 97 9.7 precentral 6583 4247 11360 2.475 0.412 0.123 0.028 86 6.9 precuneus 1508 1011 3276 2.917 0.708 0.137 0.036 25 2.1 rostralanteriorcingulate 6819 4521 12308 2.494 0.561 0.135 0.031 98 8.2 rostralmiddlefrontal 16743 10692 34105 2.800 0.577 0.124 0.031 220 21.1 superiorfrontal 7024 4462 11579 2.302 0.496 0.115 0.024 94 6.3 superiorparietal 7862 5446 16711 2.829 0.853 0.133 0.037 89 11.7 superiortemporal 5348 3426 9583 2.498 0.517 0.127 0.036 79 7.6 supramarginal 604 375 1189 2.549 0.489 0.137 0.037 10 0.9 transversetemporal 3146 2216 6858 3.008 0.778 0.126 0.031 37 3.9 insula PIDs (4555 4558) completed and logs appended. #----------------------------------------- #@# WM/GM Contrast lh Thu Oct 3 15:31:39 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/scripts pctsurfcon --s S131032017_Supine --lh-only #----------------------------------------- #@# WM/GM Contrast rh Thu Oct 3 15:31:39 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/scripts pctsurfcon --s S131032017_Supine --rh-only Waiting for PID 4629 of (4629 4632) to complete... Waiting for PID 4632 of (4629 4632) to complete... pctsurfcon --s S131032017_Supine --lh-only Log file is /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/scripts/pctsurfcon.log Thu Oct 3 15:31:39 BST 2019 setenv SUBJECTS_DIR /mnt/8E74B1C874B1B377/FreeSurfer/subjects cd /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/scripts /usr/local/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux zappst-Q170M-C 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/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/tmp.pctsurfcon.4629/lh.wm.mgh --regheader S131032017_Supine --cortex srcvol = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 Done loading volume Computing registration from header. Using /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 -0.00001; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/label/lh.cortex.label Reading surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 = 106090 Masking with /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/label/lh.cortex.label Writing to /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/tmp.pctsurfcon.4629/lh.wm.mgh Dim: 157621 1 1 mri_vol2surf --mov /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/tmp.pctsurfcon.4629/lh.gm.mgh --projfrac 0.3 --regheader S131032017_Supine --cortex srcvol = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 Done loading volume Computing registration from header. Using /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 -0.00001; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/label/lh.cortex.label Reading surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.white Done reading source surface Reading thickness /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 = 128263 Masking with /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/label/lh.cortex.label Writing to /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/tmp.pctsurfcon.4629/lh.gm.mgh Dim: 157621 1 1 mri_concat /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/tmp.pctsurfcon.4629/lh.wm.mgh /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/tmp.pctsurfcon.4629/lh.gm.mgh --paired-diff-norm --mul 100 --o /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.w-g.pct.mgh mri_segstats --in /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.w-g.pct.mgh --annot S131032017_Supine lh aparc --sum /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.w-g.pct.mgh --annot S131032017_Supine lh aparc --sum /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/stats/lh.w-g.pct.stats --snr sysname Linux hostname zappst-Q170M-C machine x86_64 user zappst UseRobust 0 Constructing seg from annotation Reading annotation /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.w-g.pct.mgh Vertex Area is 0.6399 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 S131032017_Supine --rh-only Log file is /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/scripts/pctsurfcon.log Thu Oct 3 15:31:39 BST 2019 setenv SUBJECTS_DIR /mnt/8E74B1C874B1B377/FreeSurfer/subjects cd /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/scripts /usr/local/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux zappst-Q170M-C 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/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/tmp.pctsurfcon.4632/rh.wm.mgh --regheader S131032017_Supine --cortex srcvol = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 Done loading volume Computing registration from header. Using /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 -0.00001; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/label/rh.cortex.label Reading surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 = 105633 Masking with /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/label/rh.cortex.label Writing to /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/tmp.pctsurfcon.4632/rh.wm.mgh Dim: 154929 1 1 mri_vol2surf --mov /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/tmp.pctsurfcon.4632/rh.gm.mgh --projfrac 0.3 --regheader S131032017_Supine --cortex srcvol = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 Done loading volume Computing registration from header. Using /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 -0.00001; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/label/rh.cortex.label Reading surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.white Done reading source surface Reading thickness /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 = 126177 Masking with /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/label/rh.cortex.label Writing to /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/tmp.pctsurfcon.4632/rh.gm.mgh Dim: 154929 1 1 mri_concat /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/tmp.pctsurfcon.4632/rh.wm.mgh /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/tmp.pctsurfcon.4632/rh.gm.mgh --paired-diff-norm --mul 100 --o /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.w-g.pct.mgh mri_segstats --in /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.w-g.pct.mgh --annot S131032017_Supine rh aparc --sum /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.w-g.pct.mgh --annot S131032017_Supine rh aparc --sum /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/stats/rh.w-g.pct.stats --snr sysname Linux hostname zappst-Q170M-C machine x86_64 user zappst UseRobust 0 Constructing seg from annotation Reading annotation /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.w-g.pct.mgh Vertex Area is 0.652621 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 (4629 4632) completed and logs appended. #----------------------------------------- #@# Relabel Hypointensities Thu Oct 3 15:31:45 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 1769 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 6965 voxels changed to hypointensity... 7388 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg aparc Thu Oct 3 15:32:00 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine mri_aparc2aseg --s S131032017_Supine --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 Thu Oct 3 15:32:00 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine mri_aparc2aseg --s S131032017_Supine --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 Thu Oct 3 15:32:00 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine mri_aparc2aseg --s S131032017_Supine --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 4850 of (4850 4853 4856) to complete... Waiting for PID 4853 of (4850 4853 4856) to complete... Waiting for PID 4856 of (4850 4853 4856) to complete... mri_aparc2aseg --s S131032017_Supine --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/8E74B1C874B1B377/FreeSurfer/subjects subject S131032017_Supine outvol /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.white Reading lh pial surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.pial Loading lh annotations from /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.white Reading rh pial surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.pial Loading rh annotations from /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 7.48 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 103 rescaling Left_Cerebral_Cortex from 61 --> 68 rescaling Left_Lateral_Ventricle from 13 --> 23 rescaling Left_Inf_Lat_Vent from 34 --> 30 rescaling Left_Cerebellum_White_Matter from 86 --> 86 rescaling Left_Cerebellum_Cortex from 60 --> 75 rescaling Left_Thalamus from 94 --> 98 rescaling Left_Thalamus_Proper from 84 --> 91 rescaling Left_Caudate from 75 --> 75 rescaling Left_Putamen from 80 --> 91 rescaling Left_Pallidum from 98 --> 99 rescaling Third_Ventricle from 25 --> 35 rescaling Fourth_Ventricle from 22 --> 16 rescaling Brain_Stem from 81 --> 88 rescaling Left_Hippocampus from 57 --> 66 rescaling Left_Amygdala from 56 --> 73 rescaling CSF from 32 --> 50 rescaling Left_Accumbens_area from 62 --> 68 rescaling Left_VentralDC from 87 --> 99 rescaling Right_Cerebral_White_Matter from 105 --> 101 rescaling Right_Cerebral_Cortex from 58 --> 74 rescaling Right_Lateral_Ventricle from 13 --> 23 rescaling Right_Inf_Lat_Vent from 25 --> 26 rescaling Right_Cerebellum_White_Matter from 87 --> 87 rescaling Right_Cerebellum_Cortex from 59 --> 78 rescaling Right_Thalamus_Proper from 85 --> 91 rescaling Right_Caudate from 62 --> 77 rescaling Right_Putamen from 80 --> 83 rescaling Right_Pallidum from 97 --> 99 rescaling Right_Hippocampus from 53 --> 62 rescaling Right_Amygdala from 55 --> 59 rescaling Right_Accumbens_area from 65 --> 75 rescaling Right_VentralDC from 86 --> 105 rescaling Fifth_Ventricle from 40 --> 43 rescaling WM_hypointensities from 78 --> 76 rescaling non_WM_hypointensities from 40 --> 54 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 = 524704 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 282 changed. pass 2: 47 changed. pass 3: 7 changed. pass 4: 5 changed. pass 5: 2 changed. pass 6: 0 changed. nchanged = 0 Writing output aseg to /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/aparc+aseg.mgz mri_aparc2aseg --s S131032017_Supine --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/8E74B1C874B1B377/FreeSurfer/subjects subject S131032017_Supine outvol /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.white Reading lh pial surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.pial Loading lh annotations from /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.white Reading rh pial surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.pial Loading rh annotations from /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 7.48 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 103 rescaling Left_Cerebral_Cortex from 61 --> 68 rescaling Left_Lateral_Ventricle from 13 --> 23 rescaling Left_Inf_Lat_Vent from 34 --> 30 rescaling Left_Cerebellum_White_Matter from 86 --> 86 rescaling Left_Cerebellum_Cortex from 60 --> 75 rescaling Left_Thalamus from 94 --> 98 rescaling Left_Thalamus_Proper from 84 --> 91 rescaling Left_Caudate from 75 --> 75 rescaling Left_Putamen from 80 --> 91 rescaling Left_Pallidum from 98 --> 99 rescaling Third_Ventricle from 25 --> 35 rescaling Fourth_Ventricle from 22 --> 16 rescaling Brain_Stem from 81 --> 88 rescaling Left_Hippocampus from 57 --> 66 rescaling Left_Amygdala from 56 --> 73 rescaling CSF from 32 --> 50 rescaling Left_Accumbens_area from 62 --> 68 rescaling Left_VentralDC from 87 --> 99 rescaling Right_Cerebral_White_Matter from 105 --> 101 rescaling Right_Cerebral_Cortex from 58 --> 74 rescaling Right_Lateral_Ventricle from 13 --> 23 rescaling Right_Inf_Lat_Vent from 25 --> 26 rescaling Right_Cerebellum_White_Matter from 87 --> 87 rescaling Right_Cerebellum_Cortex from 59 --> 78 rescaling Right_Thalamus_Proper from 85 --> 91 rescaling Right_Caudate from 62 --> 77 rescaling Right_Putamen from 80 --> 83 rescaling Right_Pallidum from 97 --> 99 rescaling Right_Hippocampus from 53 --> 62 rescaling Right_Amygdala from 55 --> 59 rescaling Right_Accumbens_area from 65 --> 75 rescaling Right_VentralDC from 86 --> 105 rescaling Fifth_Ventricle from 40 --> 43 rescaling WM_hypointensities from 78 --> 76 rescaling non_WM_hypointensities from 40 --> 54 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 = 524711 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 282 changed. pass 2: 47 changed. pass 3: 7 changed. pass 4: 5 changed. pass 5: 2 changed. pass 6: 0 changed. nchanged = 0 Writing output aseg to /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/aparc.a2009s+aseg.mgz mri_aparc2aseg --s S131032017_Supine --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/8E74B1C874B1B377/FreeSurfer/subjects subject S131032017_Supine outvol mri/aparc.DKTatlas+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.white Reading lh pial surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.pial Loading lh annotations from /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.white Reading rh pial surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.pial Loading rh annotations from /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 7.48 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 103 rescaling Left_Cerebral_Cortex from 61 --> 68 rescaling Left_Lateral_Ventricle from 13 --> 23 rescaling Left_Inf_Lat_Vent from 34 --> 30 rescaling Left_Cerebellum_White_Matter from 86 --> 86 rescaling Left_Cerebellum_Cortex from 60 --> 75 rescaling Left_Thalamus from 94 --> 98 rescaling Left_Thalamus_Proper from 84 --> 91 rescaling Left_Caudate from 75 --> 75 rescaling Left_Putamen from 80 --> 91 rescaling Left_Pallidum from 98 --> 99 rescaling Third_Ventricle from 25 --> 35 rescaling Fourth_Ventricle from 22 --> 16 rescaling Brain_Stem from 81 --> 88 rescaling Left_Hippocampus from 57 --> 66 rescaling Left_Amygdala from 56 --> 73 rescaling CSF from 32 --> 50 rescaling Left_Accumbens_area from 62 --> 68 rescaling Left_VentralDC from 87 --> 99 rescaling Right_Cerebral_White_Matter from 105 --> 101 rescaling Right_Cerebral_Cortex from 58 --> 74 rescaling Right_Lateral_Ventricle from 13 --> 23 rescaling Right_Inf_Lat_Vent from 25 --> 26 rescaling Right_Cerebellum_White_Matter from 87 --> 87 rescaling Right_Cerebellum_Cortex from 59 --> 78 rescaling Right_Thalamus_Proper from 85 --> 91 rescaling Right_Caudate from 62 --> 77 rescaling Right_Putamen from 80 --> 83 rescaling Right_Pallidum from 97 --> 99 rescaling Right_Hippocampus from 53 --> 62 rescaling Right_Amygdala from 55 --> 59 rescaling Right_Accumbens_area from 65 --> 75 rescaling Right_VentralDC from 86 --> 105 rescaling Fifth_Ventricle from 40 --> 43 rescaling WM_hypointensities from 78 --> 76 rescaling non_WM_hypointensities from 40 --> 54 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 = 524711 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 282 changed. pass 2: 47 changed. pass 3: 7 changed. pass 4: 5 changed. pass 5: 2 changed. pass 6: 0 changed. nchanged = 0 Writing output aseg to mri/aparc.DKTatlas+aseg.mgz PIDs (4850 4853 4856) completed and logs appended. #----------------------------------------- #@# APas-to-ASeg Thu Oct 3 15:36:59 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri apas2aseg --i aparc+aseg.mgz --o aseg.mgz Thu Oct 3 15:37:00 BST 2019 setenv SUBJECTS_DIR /mnt/8E74B1C874B1B377/FreeSurfer/subjects cd /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 zappst-Q170M-C 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/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 zappst-Q170M-C machine x86_64 user zappst input aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output aseg.mgz Binarizing based on threshold min -infinity max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Replacing 72 1: 1000 3 2: 2000 42 3: 1001 3 4: 2001 42 5: 1002 3 6: 2002 42 7: 1003 3 8: 2003 42 9: 1004 3 10: 2004 42 11: 1005 3 12: 2005 42 13: 1006 3 14: 2006 42 15: 1007 3 16: 2007 42 17: 1008 3 18: 2008 42 19: 1009 3 20: 2009 42 21: 1010 3 22: 2010 42 23: 1011 3 24: 2011 42 25: 1012 3 26: 2012 42 27: 1013 3 28: 2013 42 29: 1014 3 30: 2014 42 31: 1015 3 32: 2015 42 33: 1016 3 34: 2016 42 35: 1017 3 36: 2017 42 37: 1018 3 38: 2018 42 39: 1019 3 40: 2019 42 41: 1020 3 42: 2020 42 43: 1021 3 44: 2021 42 45: 1022 3 46: 2022 42 47: 1023 3 48: 2023 42 49: 1024 3 50: 2024 42 51: 1025 3 52: 2025 42 53: 1026 3 54: 2026 42 55: 1027 3 56: 2027 42 57: 1028 3 58: 2028 42 59: 1029 3 60: 2029 42 61: 1030 3 62: 2030 42 63: 1031 3 64: 2031 42 65: 1032 3 66: 2032 42 67: 1033 3 68: 2033 42 69: 1034 3 70: 2034 42 71: 1035 3 72: 2035 42 Found 0 values in range Counting number of voxels in first frame Found 0 voxels in final mask Count: 0 0.000000 16777216 0.000000 mri_binarize done Started at Thu Oct 3 15:37:00 BST 2019 Ended at Thu Oct 3 15:37:03 BST 2019 Apas2aseg-Run-Time-Sec 3 apas2aseg Done #-------------------------------------------- #@# ASeg Stats Thu Oct 3 15:37:03 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine 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 S131032017_Supine $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 S131032017_Supine sysname Linux hostname zappst-Q170M-C machine x86_64 user zappst UseRobust 0 atlas_icv (eTIV) = 1261180 mm^3 (det: 1.544669 ) Computing euler number orig.nofix lheno = -160, rheno = -164 orig.nofix lhholes = 81, rhholes = 83 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 264546.501 264183.000 diff= 363.5 pctdiff= 0.137 rhCtxGM: 261758.298 261428.000 diff= 330.3 pctdiff= 0.126 lhCtxWM: 218582.612 219657.500 diff=-1074.9 pctdiff=-0.492 rhCtxWM: 229425.186 230659.500 diff=-1234.3 pctdiff=-0.538 SubCortGMVol 54769.000 SupraTentVol 1042140.598 (1040097.000) diff=2043.598 pctdiff=0.196 SupraTentVolNotVent 1032745.598 (1030702.000) diff=2043.598 pctdiff=0.198 BrainSegVol 1207065.000 (1204153.000) diff=2912.000 pctdiff=0.241 BrainSegVolNotVent 1193598.000 (1191872.598) diff=1725.402 pctdiff=0.145 BrainSegVolNotVent 1193598.000 CerebellumVol 162786.000 VentChorVol 9395.000 3rd4th5thCSF 4072.000 CSFVol 1160.000, OptChiasmVol 110.000 MaskVol 1697541.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation Reporting on 45 segmentations Using PrintSegStat mri_segstats done #----------------------------------------- #@# WMParc Thu Oct 3 15:38:03 BST 2019 /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine mri_aparc2aseg --s S131032017_Supine --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /mnt/8E74B1C874B1B377/FreeSurfer/subjects subject S131032017_Supine outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/aparc+aseg.mgz Reading lh white surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.white Reading lh pial surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.pial Loading lh annotations from /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.white Reading rh pial surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.pial Loading rh annotations from /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/ribbon.mgz Loading filled from /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/ribbon.mgz Ripping vertices labeled as unkown Ripped 8259 vertices from left hemi Ripped 6918 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/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/aseg.mgz Loading Ctx Seg File /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 = 970686 Used brute-force search on 2 voxels Fixing Parahip LH WM Found 20 clusters 0 k 1.000000 1 k 2.000000 2 k 2.000000 3 k 2.000000 4 k 2.000000 5 k 1.000000 6 k 1.000000 7 k 1.000000 8 k 1.000000 9 k 2.000000 10 k 2.000000 11 k 1.000000 12 k 1.000000 13 k 12.000000 14 k 1.000000 15 k 1.000000 16 k 1.000000 17 k 1285.000000 18 k 1.000000 19 k 2.000000 Fixing Parahip RH WM Found 11 clusters 0 k 1.000000 1 k 1652.000000 2 k 1.000000 3 k 1.000000 4 k 1.000000 5 k 1.000000 6 k 2.000000 7 k 1.000000 8 k 19.000000 9 k 3.000000 10 k 1.000000 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 S131032017_Supine --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 S131032017_Supine --surf-wm-vol --ctab /usr/local/freesurfer/WMParcStatsLUT.txt --etiv sysname Linux hostname zappst-Q170M-C machine x86_64 user zappst UseRobust 0 atlas_icv (eTIV) = 1261180 mm^3 (det: 1.544669 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 264546.501 264183.000 diff= 363.5 pctdiff= 0.137 rhCtxGM: 261758.298 261428.000 diff= 330.3 pctdiff= 0.126 lhCtxWM: 218582.612 219657.500 diff=-1074.9 pctdiff=-0.492 rhCtxWM: 229425.186 230659.500 diff=-1234.3 pctdiff=-0.538 SubCortGMVol 54769.000 SupraTentVol 1042140.598 (1040097.000) diff=2043.598 pctdiff=0.196 SupraTentVolNotVent 1032745.598 (1030702.000) diff=2043.598 pctdiff=0.198 BrainSegVol 1207065.000 (1204153.000) diff=2912.000 pctdiff=0.241 BrainSegVolNotVent 1193598.000 (1191872.598) diff=1725.402 pctdiff=0.145 BrainSegVolNotVent 1193598.000 CerebellumVol 162786.000 VentChorVol 9395.000 3rd4th5thCSF 4072.000 CSFVol 1160.000, OptChiasmVol 110.000 MaskVol 1697541.000 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/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/label #-------------------------------------------- #@# BA_exvivo Labels lh Thu Oct 3 15:43:04 BST 2019 mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA1_exvivo.label --trgsubject S131032017_Supine --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA2_exvivo.label --trgsubject S131032017_Supine --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA3a_exvivo.label --trgsubject S131032017_Supine --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA3b_exvivo.label --trgsubject S131032017_Supine --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA4a_exvivo.label --trgsubject S131032017_Supine --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface Waiting for PID 5752 of (5752 5755 5764 5769 5775) to complete... Waiting for PID 5755 of (5752 5755 5764 5769 5775) to complete... Waiting for PID 5764 of (5752 5755 5764 5769 5775) to complete... Waiting for PID 5769 of (5752 5755 5764 5769 5775) to complete... Waiting for PID 5775 of (5752 5755 5764 5769 5775) to complete... mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA1_exvivo.label --trgsubject S131032017_Supine --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 157621 Number of reverse mapping hits = 737 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4866 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA2_exvivo.label --trgsubject S131032017_Supine --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA2_exvivo.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 157621 Number of reverse mapping hits = 1173 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 9082 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA3a_exvivo.label --trgsubject S131032017_Supine --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 157621 Number of reverse mapping hits = 213 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4290 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA3b_exvivo.label --trgsubject S131032017_Supine --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 157621 Number of reverse mapping hits = 733 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6716 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA4a_exvivo.label --trgsubject S131032017_Supine --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 157621 Number of reverse mapping hits = 700 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 6484 mri_label2label: Done PIDs (5752 5755 5764 5769 5775) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA4p_exvivo.label --trgsubject S131032017_Supine --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA6_exvivo.label --trgsubject S131032017_Supine --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA44_exvivo.label --trgsubject S131032017_Supine --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA45_exvivo.label --trgsubject S131032017_Supine --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface Waiting for PID 5824 of (5824 5829 5834 5840) to complete... Waiting for PID 5829 of (5824 5829 5834 5840) to complete... Waiting for PID 5834 of (5824 5829 5834 5840) to complete... Waiting for PID 5840 of (5824 5829 5834 5840) to complete... mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA4p_exvivo.label --trgsubject S131032017_Supine --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 157621 Number of reverse mapping hits = 295 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4365 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA6_exvivo.label --trgsubject S131032017_Supine --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA6_exvivo.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 157621 Number of reverse mapping hits = 3045 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 16634 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA44_exvivo.label --trgsubject S131032017_Supine --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA44_exvivo.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 157621 Number of reverse mapping hits = 487 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4668 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA45_exvivo.label --trgsubject S131032017_Supine --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA45_exvivo.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 157621 Number of reverse mapping hits = 1107 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 4529 mri_label2label: Done PIDs (5824 5829 5834 5840) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.V1_exvivo.label --trgsubject S131032017_Supine --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.V2_exvivo.label --trgsubject S131032017_Supine --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.MT_exvivo.label --trgsubject S131032017_Supine --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject S131032017_Supine --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject S131032017_Supine --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface Waiting for PID 5891 of (5891 5896 5902 5908 5914) to complete... Waiting for PID 5896 of (5891 5896 5902 5908 5914) to complete... Waiting for PID 5902 of (5891 5896 5902 5908 5914) to complete... Waiting for PID 5908 of (5891 5896 5902 5908 5914) to complete... Waiting for PID 5914 of (5891 5896 5902 5908 5914) to complete... mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.V1_exvivo.label --trgsubject S131032017_Supine --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.V1_exvivo.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 157621 Number of reverse mapping hits = 2173 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 6814 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.V2_exvivo.label --trgsubject S131032017_Supine --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.V2_exvivo.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 157621 Number of reverse mapping hits = 4354 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 12468 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.MT_exvivo.label --trgsubject S131032017_Supine --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.MT_exvivo.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 157621 Number of reverse mapping hits = 724 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2742 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject S131032017_Supine --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1290 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 157621 Number of reverse mapping hits = 77 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1367 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject S131032017_Supine --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 157621 Number of reverse mapping hits = 56 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1255 mri_label2label: Done PIDs (5891 5896 5902 5908 5914) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 5972 of (5972 5977 5983 5989 5994) to complete... Waiting for PID 5977 of (5972 5977 5983 5989 5994) to complete... Waiting for PID 5983 of (5972 5977 5983 5989 5994) to complete... Waiting for PID 5989 of (5972 5977 5983 5989 5994) to complete... Waiting for PID 5994 of (5972 5977 5983 5989 5994) to complete... mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 157621 Number of reverse mapping hits = 213 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1227 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 157621 Number of reverse mapping hits = 429 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2521 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 157621 Number of reverse mapping hits = 51 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1555 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 157621 Number of reverse mapping hits = 166 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2162 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 157621 Number of reverse mapping hits = 326 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2645 mri_label2label: Done PIDs (5972 5977 5983 5989 5994) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 6044 of (6044 6049 6055 6062) to complete... Waiting for PID 6049 of (6044 6049 6055 6062) to complete... Waiting for PID 6055 of (6044 6049 6055 6062) to complete... Waiting for PID 6062 of (6044 6049 6055 6062) to complete... mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 157621 Number of reverse mapping hits = 101 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1650 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 157621 Number of reverse mapping hits = 1190 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 8225 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 157621 Number of reverse mapping hits = 154 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 2066 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 157621 Number of reverse mapping hits = 398 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1549 mri_label2label: Done PIDs (6044 6049 6055 6062) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 6110 of (6110 6115 6121 6127 6134) to complete... Waiting for PID 6115 of (6110 6115 6121 6127 6134) to complete... Waiting for PID 6121 of (6110 6115 6121 6127 6134) to complete... Waiting for PID 6127 of (6110 6115 6121 6127 6134) to complete... Waiting for PID 6134 of (6110 6115 6121 6127 6134) to complete... mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 157621 Number of reverse mapping hits = 1607 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 5012 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 157621 Number of reverse mapping hits = 1906 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 5240 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 157621 Number of reverse mapping hits = 149 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 662 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 470 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 157621 Number of reverse mapping hits = 24 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 494 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/lh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 450 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 157621 Number of reverse mapping hits = 14 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 464 mri_label2label: Done PIDs (6110 6115 6121 6127 6134) completed and logs appended. mris_label2annot --s S131032017_Supine --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/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/label cmdline mris_label2annot --s S131032017_Supine --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 zappst-Q170M-C machine x86_64 user zappst subject S131032017_Supine hemi lh SUBJECTS_DIR /mnt/8E74B1C874B1B377/FreeSurfer/subjects ColorTable /usr/local/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 107901 unhit vertices Writing annot to /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/label/lh.BA_exvivo.annot mris_label2annot --s S131032017_Supine --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/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/label cmdline mris_label2annot --s S131032017_Supine --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 zappst-Q170M-C machine x86_64 user zappst subject S131032017_Supine hemi lh SUBJECTS_DIR /mnt/8E74B1C874B1B377/FreeSurfer/subjects ColorTable /usr/local/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 129027 unhit vertices Writing annot to /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 S131032017_Supine lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/wm.mgz... reading input surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.white... reading input pial surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.pial... reading input white surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 267976 Total vertex volume 265335 (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) = 1261180 mm^3 (det: 1.544669 ) lhCtxGM: 264546.501 264183.000 diff= 363.5 pctdiff= 0.137 rhCtxGM: 261758.298 261428.000 diff= 330.3 pctdiff= 0.126 lhCtxWM: 218582.612 219657.500 diff=-1074.9 pctdiff=-0.492 rhCtxWM: 229425.186 230659.500 diff=-1234.3 pctdiff=-0.538 SubCortGMVol 54769.000 SupraTentVol 1042140.598 (1040097.000) diff=2043.598 pctdiff=0.196 SupraTentVolNotVent 1032745.598 (1030702.000) diff=2043.598 pctdiff=0.198 BrainSegVol 1207065.000 (1204153.000) diff=2912.000 pctdiff=0.241 BrainSegVolNotVent 1193598.000 (1191872.598) diff=1725.402 pctdiff=0.145 BrainSegVolNotVent 1193598.000 CerebellumVol 162786.000 VentChorVol 9395.000 3rd4th5thCSF 4072.000 CSFVol 1160.000, OptChiasmVol 110.000 MaskVol 1697541.000 1510 716 2426 2.447 0.699 0.111 0.030 20 1.9 BA1_exvivo 4858 3159 7506 2.257 0.509 0.109 0.026 47 4.6 BA2_exvivo 1130 758 1275 2.074 0.459 0.127 0.026 9 1.1 BA3a_exvivo 2867 1798 4062 1.939 0.605 0.109 0.033 36 3.8 BA3b_exvivo 1942 1100 3845 2.905 0.506 0.102 0.026 22 1.9 BA4a_exvivo 1348 905 2239 2.611 0.382 0.098 0.018 7 1.0 BA4p_exvivo 11996 6903 22872 2.816 0.615 0.103 0.023 121 11.0 BA6_exvivo 2369 1589 4551 2.453 0.489 0.122 0.030 33 2.8 BA44_exvivo 3665 2448 6994 2.367 0.536 0.137 0.036 61 5.8 BA45_exvivo 4375 2885 4995 1.710 0.435 0.140 0.035 59 6.3 V1_exvivo 10037 6468 14768 2.124 0.499 0.151 0.041 179 16.9 V2_exvivo 2441 1492 4051 2.309 0.475 0.119 0.034 33 3.3 MT_exvivo 579 355 1902 3.702 0.750 0.114 0.028 6 0.7 perirhinal_exvivo 603 420 1304 2.860 0.919 0.102 0.023 4 0.5 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 S131032017_Supine lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/wm.mgz... reading input surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.white... reading input pial surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.pial... reading input white surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 267976 Total vertex volume 265335 (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) = 1261180 mm^3 (det: 1.544669 ) lhCtxGM: 264546.501 264183.000 diff= 363.5 pctdiff= 0.137 rhCtxGM: 261758.298 261428.000 diff= 330.3 pctdiff= 0.126 lhCtxWM: 218582.612 219657.500 diff=-1074.9 pctdiff=-0.492 rhCtxWM: 229425.186 230659.500 diff=-1234.3 pctdiff=-0.538 SubCortGMVol 54769.000 SupraTentVol 1042140.598 (1040097.000) diff=2043.598 pctdiff=0.196 SupraTentVolNotVent 1032745.598 (1030702.000) diff=2043.598 pctdiff=0.198 BrainSegVol 1207065.000 (1204153.000) diff=2912.000 pctdiff=0.241 BrainSegVolNotVent 1193598.000 (1191872.598) diff=1725.402 pctdiff=0.145 BrainSegVolNotVent 1193598.000 CerebellumVol 162786.000 VentChorVol 9395.000 3rd4th5thCSF 4072.000 CSFVol 1160.000, OptChiasmVol 110.000 MaskVol 1697541.000 1006 446 1481 2.318 0.685 0.113 0.033 15 1.3 BA1_exvivo 2104 1289 3318 2.290 0.520 0.094 0.024 17 1.6 BA2_exvivo 914 613 1004 2.056 0.435 0.128 0.028 7 0.9 BA3a_exvivo 1588 1043 1744 1.622 0.385 0.092 0.018 11 1.2 BA3b_exvivo 1927 1109 3745 2.934 0.495 0.096 0.022 18 1.8 BA4a_exvivo 1149 752 1801 2.550 0.386 0.103 0.019 7 1.0 BA4p_exvivo 6232 3450 12038 2.852 0.635 0.102 0.024 67 6.1 BA6_exvivo 1449 996 2988 2.520 0.470 0.122 0.030 21 1.5 BA44_exvivo 1403 970 2908 2.411 0.548 0.140 0.032 25 1.7 BA45_exvivo 4661 3078 5381 1.707 0.438 0.139 0.036 64 7.0 V1_exvivo 4963 3274 6846 2.013 0.477 0.162 0.044 91 9.0 V2_exvivo 602 377 905 2.260 0.393 0.123 0.033 8 0.6 MT_exvivo 290 183 1017 3.770 0.603 0.126 0.028 3 0.4 perirhinal_exvivo 306 209 711 2.935 0.644 0.074 0.019 1 0.2 entorhinal_exvivo #-------------------------------------------- #@# BA_exvivo Labels rh Thu Oct 3 15:44:44 BST 2019 mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA1_exvivo.label --trgsubject S131032017_Supine --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA2_exvivo.label --trgsubject S131032017_Supine --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA3a_exvivo.label --trgsubject S131032017_Supine --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA3b_exvivo.label --trgsubject S131032017_Supine --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA4a_exvivo.label --trgsubject S131032017_Supine --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface Waiting for PID 6255 of (6255 6260 6266 6283 6288) to complete... Waiting for PID 6260 of (6255 6260 6266 6283 6288) to complete... Waiting for PID 6266 of (6255 6260 6266 6283 6288) to complete... Waiting for PID 6283 of (6255 6260 6266 6283 6288) to complete... Waiting for PID 6288 of (6255 6260 6266 6283 6288) to complete... mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA1_exvivo.label --trgsubject S131032017_Supine --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA1_exvivo.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 154929 Number of reverse mapping hits = 355 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4317 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA2_exvivo.label --trgsubject S131032017_Supine --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA2_exvivo.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 154929 Number of reverse mapping hits = 429 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 7116 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA3a_exvivo.label --trgsubject S131032017_Supine --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 154929 Number of reverse mapping hits = 265 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4245 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA3b_exvivo.label --trgsubject S131032017_Supine --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 154929 Number of reverse mapping hits = 291 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 4813 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA4a_exvivo.label --trgsubject S131032017_Supine --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 154929 Number of reverse mapping hits = 1286 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 7033 mri_label2label: Done PIDs (6255 6260 6266 6283 6288) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA4p_exvivo.label --trgsubject S131032017_Supine --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA6_exvivo.label --trgsubject S131032017_Supine --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA44_exvivo.label --trgsubject S131032017_Supine --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA45_exvivo.label --trgsubject S131032017_Supine --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface Waiting for PID 6337 of (6337 6342 6348 6354) to complete... Waiting for PID 6342 of (6337 6342 6348 6354) to complete... Waiting for PID 6348 of (6337 6342 6348 6354) to complete... Waiting for PID 6354 of (6337 6342 6348 6354) to complete... mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA4p_exvivo.label --trgsubject S131032017_Supine --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 154929 Number of reverse mapping hits = 681 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 5154 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA6_exvivo.label --trgsubject S131032017_Supine --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA6_exvivo.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 154929 Number of reverse mapping hits = 4121 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 16377 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA44_exvivo.label --trgsubject S131032017_Supine --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA44_exvivo.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 154929 Number of reverse mapping hits = 970 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 7882 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA45_exvivo.label --trgsubject S131032017_Supine --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA45_exvivo.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 154929 Number of reverse mapping hits = 1186 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 6541 mri_label2label: Done PIDs (6337 6342 6348 6354) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.V1_exvivo.label --trgsubject S131032017_Supine --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.V2_exvivo.label --trgsubject S131032017_Supine --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.MT_exvivo.label --trgsubject S131032017_Supine --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject S131032017_Supine --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject S131032017_Supine --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface Waiting for PID 6408 of (6408 6413 6418 6425 6430) to complete... Waiting for PID 6413 of (6408 6413 6418 6425 6430) to complete... Waiting for PID 6418 of (6408 6413 6418 6425 6430) to complete... Waiting for PID 6425 of (6408 6413 6418 6425 6430) to complete... Waiting for PID 6430 of (6408 6413 6418 6425 6430) to complete... mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.V1_exvivo.label --trgsubject S131032017_Supine --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.V1_exvivo.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 154929 Number of reverse mapping hits = 2155 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 6882 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.V2_exvivo.label --trgsubject S131032017_Supine --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.V2_exvivo.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 154929 Number of reverse mapping hits = 4765 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 12781 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.MT_exvivo.label --trgsubject S131032017_Supine --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.MT_exvivo.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 154929 Number of reverse mapping hits = 802 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2734 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject S131032017_Supine --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1038 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 154929 Number of reverse mapping hits = 29 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1067 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject S131032017_Supine --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 154929 Number of reverse mapping hits = 22 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 774 mri_label2label: Done PIDs (6408 6413 6418 6425 6430) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 6487 of (6487 6492 6498 6504 6511) to complete... Waiting for PID 6492 of (6487 6492 6498 6504 6511) to complete... Waiting for PID 6498 of (6487 6492 6498 6504 6511) to complete... Waiting for PID 6504 of (6487 6492 6498 6504 6511) to complete... Waiting for PID 6511 of (6487 6492 6498 6504 6511) to complete... mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 154929 Number of reverse mapping hits = 89 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 965 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 154929 Number of reverse mapping hits = 135 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2823 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 154929 Number of reverse mapping hits = 47 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1745 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 154929 Number of reverse mapping hits = 112 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2295 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 154929 Number of reverse mapping hits = 182 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1570 mri_label2label: Done PIDs (6487 6492 6498 6504 6511) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 6568 of (6568 6573 6579 6585) to complete... Waiting for PID 6573 of (6568 6573 6579 6585) to complete... Waiting for PID 6579 of (6568 6573 6579 6585) to complete... Waiting for PID 6585 of (6568 6573 6579 6585) to complete... mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 154929 Number of reverse mapping hits = 206 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1695 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 154929 Number of reverse mapping hits = 2638 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 9597 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 154929 Number of reverse mapping hits = 188 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1200 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 154929 Number of reverse mapping hits = 285 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1463 mri_label2label: Done PIDs (6568 6573 6579 6585) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 6635 of (6635 6640 6646 6652 6658) to complete... Waiting for PID 6640 of (6635 6640 6646 6652 6658) to complete... Waiting for PID 6646 of (6635 6640 6646 6652 6658) to complete... Waiting for PID 6652 of (6635 6640 6646 6652 6658) to complete... Waiting for PID 6658 of (6635 6640 6646 6652 6658) to complete... mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 154929 Number of reverse mapping hits = 1311 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 4543 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 154929 Number of reverse mapping hits = 2219 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 5656 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 154929 Number of reverse mapping hits = 124 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 392 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 694 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 154929 Number of reverse mapping hits = 16 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 710 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject S131032017_Supine --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/label/rh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = S131032017_Supine 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/8E74B1C874B1B377/FreeSurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 291 points in source label. Starting surface-based mapping Reading source registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.white Reading target registration /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 154929 Number of reverse mapping hits = 4 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 295 mri_label2label: Done PIDs (6635 6640 6646 6652 6658) completed and logs appended. mris_label2annot --s S131032017_Supine --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/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/label cmdline mris_label2annot --s S131032017_Supine --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 zappst-Q170M-C machine x86_64 user zappst subject S131032017_Supine hemi rh SUBJECTS_DIR /mnt/8E74B1C874B1B377/FreeSurfer/subjects ColorTable /usr/local/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 104049 unhit vertices Writing annot to /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/label/rh.BA_exvivo.annot mris_label2annot --s S131032017_Supine --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/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/label cmdline mris_label2annot --s S131032017_Supine --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 zappst-Q170M-C machine x86_64 user zappst subject S131032017_Supine hemi rh SUBJECTS_DIR /mnt/8E74B1C874B1B377/FreeSurfer/subjects ColorTable /usr/local/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 125853 unhit vertices Writing annot to /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/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 S131032017_Supine rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/wm.mgz... reading input surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.white... reading input pial surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.pial... reading input white surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 266235 Total vertex volume 263821 (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) = 1261180 mm^3 (det: 1.544669 ) lhCtxGM: 264546.501 264183.000 diff= 363.5 pctdiff= 0.137 rhCtxGM: 261758.298 261428.000 diff= 330.3 pctdiff= 0.126 lhCtxWM: 218582.612 219657.500 diff=-1074.9 pctdiff=-0.492 rhCtxWM: 229425.186 230659.500 diff=-1234.3 pctdiff=-0.538 SubCortGMVol 54769.000 SupraTentVol 1042140.598 (1040097.000) diff=2043.598 pctdiff=0.196 SupraTentVolNotVent 1032745.598 (1030702.000) diff=2043.598 pctdiff=0.198 BrainSegVol 1207065.000 (1204153.000) diff=2912.000 pctdiff=0.241 BrainSegVolNotVent 1193598.000 (1191872.598) diff=1725.402 pctdiff=0.145 BrainSegVolNotVent 1193598.000 CerebellumVol 162786.000 VentChorVol 9395.000 3rd4th5thCSF 4072.000 CSFVol 1160.000, OptChiasmVol 110.000 MaskVol 1697541.000 1083 550 1777 2.253 0.579 0.125 0.033 17 1.4 BA1_exvivo 3292 2086 4720 2.231 0.444 0.110 0.022 42 2.7 BA2_exvivo 1263 857 1253 1.849 0.400 0.127 0.027 10 1.3 BA3a_exvivo 2056 1361 2709 1.795 0.524 0.095 0.020 17 1.5 BA3b_exvivo 2092 1121 3898 2.767 0.425 0.094 0.024 19 2.0 BA4a_exvivo 1640 1059 2630 2.501 0.413 0.092 0.020 9 1.3 BA4p_exvivo 12845 7781 24903 2.780 0.597 0.113 0.030 143 15.3 BA6_exvivo 3897 2614 7517 2.589 0.439 0.120 0.025 45 3.8 BA44_exvivo 4643 3090 9364 2.569 0.568 0.130 0.030 75 5.3 BA45_exvivo 4412 2922 5664 1.819 0.503 0.136 0.031 58 5.7 V1_exvivo 10478 6835 15800 2.170 0.536 0.150 0.037 170 14.8 V2_exvivo 2458 1690 3888 2.198 0.446 0.143 0.032 36 3.4 MT_exvivo 439 297 1858 3.789 0.699 0.116 0.029 5 0.6 perirhinal_exvivo 282 195 675 3.147 0.559 0.079 0.014 1 0.2 entorhinal_exvivo mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab S131032017_Supine rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/mri/wm.mgz... reading input surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.white... reading input pial surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.pial... reading input white surface /mnt/8E74B1C874B1B377/FreeSurfer/subjects/S131032017_Supine/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 266235 Total vertex volume 263821 (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) = 1261180 mm^3 (det: 1.544669 ) lhCtxGM: 264546.501 264183.000 diff= 363.5 pctdiff= 0.137 rhCtxGM: 261758.298 261428.000 diff= 330.3 pctdiff= 0.126 lhCtxWM: 218582.612 219657.500 diff=-1074.9 pctdiff=-0.492 rhCtxWM: 229425.186 230659.500 diff=-1234.3 pctdiff=-0.538 SubCortGMVol 54769.000 SupraTentVol 1042140.598 (1040097.000) diff=2043.598 pctdiff=0.196 SupraTentVolNotVent 1032745.598 (1030702.000) diff=2043.598 pctdiff=0.198 BrainSegVol 1207065.000 (1204153.000) diff=2912.000 pctdiff=0.241 BrainSegVolNotVent 1193598.000 (1191872.598) diff=1725.402 pctdiff=0.145 BrainSegVolNotVent 1193598.000 CerebellumVol 162786.000 VentChorVol 9395.000 3rd4th5thCSF 4072.000 CSFVol 1160.000, OptChiasmVol 110.000 MaskVol 1697541.000 714 375 1067 2.045 0.536 0.123 0.032 10 0.8 BA1_exvivo 1842 1156 2733 2.181 0.440 0.094 0.016 15 1.1 BA2_exvivo 1072 735 1011 1.815 0.391 0.125 0.028 8 1.1 BA3a_exvivo 1577 1098 1854 1.636 0.392 0.090 0.016 11 0.9 BA3b_exvivo 1164 609 2211 2.879 0.406 0.098 0.022 11 0.9 BA4a_exvivo 1333 874 2186 2.557 0.377 0.083 0.019 5 1.0 BA4p_exvivo 8610 5085 16341 2.753 0.583 0.112 0.032 99 10.9 BA6_exvivo 1032 684 2314 2.708 0.398 0.125 0.028 16 1.1 BA44_exvivo 1273 836 3055 2.764 0.588 0.135 0.035 21 1.7 BA45_exvivo 4199 2794 5352 1.829 0.505 0.135 0.031 53 5.3 V1_exvivo 5442 3558 7741 2.051 0.539 0.159 0.041 95 8.8 V2_exvivo 367 258 754 2.280 0.421 0.172 0.036 9 0.6 MT_exvivo 265 183 1168 3.890 0.584 0.120 0.029 3 0.4 perirhinal_exvivo 186 131 544 3.022 0.496 0.076 0.012 1 0.1 entorhinal_exvivo Started at Thu Oct 3 10:12:00 BST 2019 Ended at Thu Oct 3 15:46:24 BST 2019 #@#%# recon-all-run-time-hours 5.573 recon-all -s S131032017_Supine finished without error at Thu Oct 3 15:46:24 BST 2019