Thu Mar 7 06:55:10 UTC 2019 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030 /opt/freesurfer/bin/recon-all -autorecon1 -i /home/mc2835/scratch60/RVLdata/BIDS/sub-030/ses-1/anat/sub-030_ses-1_T1w.nii.gz -noskullstrip -openmp 7 -subjid sub-030 -sd /home/mc2835/scratch60/RVLdata/fmriprep_output/freesurfer subjid sub-030 setenv SUBJECTS_DIR /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /opt/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a Linux c14n09.farnam.hpc.yale.internal 3.10.0-693.37.4.el7.x86_64 #1 SMP Fri Aug 10 12:34:55 EDT 2018 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize unlimited memoryuse 65536000 kbytes vmemoryuse unlimited descriptors 51200 memorylocked unlimited maxproc 512036 maxlocks unlimited maxsignal 512036 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 131317832 17679672 79611676 654424 34026484 112234632 Swap: 16777212 151228 16625984 ######################################## 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: 2019/03/07-06:55:10-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-06:55:10-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-06:55:10-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-06:55:10-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-06:55:10-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-06:55:10-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-06:55:10-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-06:55:11-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-06:55:11-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-06:55:11-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-06:55:11-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-06:55:11-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-06:55:11-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-06:55:11-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-06:55:11-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-06:55:11-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-06:55:11-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-06:55:11-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-06:55:11-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-06:55:11-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-06:55:11-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-06:55:11-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-06:55:11-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-06:55:11-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-06:55:11-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-06:55:12-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-06:55:12-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-06:55:12-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-06:55:12-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-06:55:12-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-06:55:12-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-06:55:12-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-06:55:12-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-06:55:12-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-06:55:12-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-06:55:12-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-06:55:12-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-06:55:12-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-06:55:12-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /opt/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /opt/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030 mri_convert /gpfs/ysm/scratch60/mc2835/RVLdata/BIDS/sub-030/ses-1/anat/sub-030_ses-1_T1w.nii.gz /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/orig/001.mgz mri_convert.bin /gpfs/ysm/scratch60/mc2835/RVLdata/BIDS/sub-030/ses-1/anat/sub-030_ses-1_T1w.nii.gz /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /gpfs/ysm/scratch60/mc2835/RVLdata/BIDS/sub-030/ses-1/anat/sub-030_ses-1_T1w.nii.gz... TR=2530.00, 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Thu Mar 7 06:55:19 UTC 2019 Found 1 runs /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/orig/001.mgz /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/rawavg.mgz /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030 mri_convert /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/rawavg.mgz /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/orig.mgz --conform mri_convert.bin /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/rawavg.mgz /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/rawavg.mgz... TR=2530.00, 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/orig.mgz... mri_add_xform_to_header -c /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/transforms/talairach.xfm /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/orig.mgz /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Mar 7 06:55:26 UTC 2019 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri /opt/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux c14n09.farnam.hpc.yale.internal 3.10.0-693.37.4.el7.x86_64 #1 SMP Fri Aug 10 12:34:55 EDT 2018 x86_64 x86_64 x86_64 GNU/Linux Thu Mar 7 06:55:26 UTC 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.26831 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.26831/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.26831/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=2530.00, 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.26831/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Mar 7 06:55:27 UTC 2019 nu_correct -clobber ./tmp.mri_nu_correct.mni.26831/nu0.mnc ./tmp.mri_nu_correct.mni.26831/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.26831/0/ -iterations 1000 -distance 50 [mc2835@c14n09.farnam.hpc.yale.internal:/gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/] [2019-03-07 06:55:28] running: /opt/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.26831/0/ ./tmp.mri_nu_correct.mni.26831/nu0.mnc ./tmp.mri_nu_correct.mni.26831/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done 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Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 53 CV of field change: 0.000993044 mri_convert ./tmp.mri_nu_correct.mni.26831/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.26831/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.26831/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 Mar 7 06:56:32 UTC 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 Mar 7 06:56:32 UTC 2019 Ended at Thu Mar 7 06:56:56 UTC 2019 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Thu Mar 7 06:56:58 UTC 2019 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7560, pval=0.6675 >= threshold=0.0050) awk -f /opt/freesurfer/bin/extract_talairach_avi_QA.awk /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/transforms/talairach_avi.log tal_QC_AZS /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/transforms/talairach_avi.log TalAviQA: 0.97447 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Thu Mar 7 06:56:58 UTC 2019 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri /opt/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux c14n09.farnam.hpc.yale.internal 3.10.0-693.37.4.el7.x86_64 #1 SMP Fri Aug 10 12:34:55 EDT 2018 x86_64 x86_64 x86_64 GNU/Linux Thu Mar 7 06:56:58 UTC 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.27823 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.27823/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.27823/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=2530.00, 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.27823/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Mar 7 06:56:59 UTC 2019 nu_correct -clobber ./tmp.mri_nu_correct.mni.27823/nu0.mnc ./tmp.mri_nu_correct.mni.27823/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.27823/0/ [mc2835@c14n09.farnam.hpc.yale.internal:/gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/] [2019-03-07 06:56:59] running: /opt/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.27823/0/ ./tmp.mri_nu_correct.mni.27823/nu0.mnc ./tmp.mri_nu_correct.mni.27823/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done 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Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 50 CV of field change: 0.00103135 -------------------------------------------------------- Iteration 2 Thu Mar 7 06:57:49 UTC 2019 nu_correct -clobber ./tmp.mri_nu_correct.mni.27823/nu1.mnc ./tmp.mri_nu_correct.mni.27823/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.27823/1/ [mc2835@c14n09.farnam.hpc.yale.internal:/gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/] [2019-03-07 06:57:49] running: /opt/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.27823/1/ ./tmp.mri_nu_correct.mni.27823/nu1.mnc ./tmp.mri_nu_correct.mni.27823/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 42 CV of field change: 0.000971428 mri_binarize --i ./tmp.mri_nu_correct.mni.27823/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.27823/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.27823/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.27823/ones.mgz sysname Linux hostname c14n09.farnam.hpc.yale.internal machine x86_64 user mc2835 input ./tmp.mri_nu_correct.mni.27823/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.27823/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.27823/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.27823/sum.junk --avgwf ./tmp.mri_nu_correct.mni.27823/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.27823/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.27823/sum.junk --avgwf ./tmp.mri_nu_correct.mni.27823/input.mean.dat sysname Linux hostname c14n09.farnam.hpc.yale.internal machine x86_64 user mc2835 UseRobust 0 Loading ./tmp.mri_nu_correct.mni.27823/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.27823/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.27823/ones.mgz --i ./tmp.mri_nu_correct.mni.27823/nu2.mnc --sum ./tmp.mri_nu_correct.mni.27823/sum.junk --avgwf ./tmp.mri_nu_correct.mni.27823/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.27823/ones.mgz --i ./tmp.mri_nu_correct.mni.27823/nu2.mnc --sum ./tmp.mri_nu_correct.mni.27823/sum.junk --avgwf ./tmp.mri_nu_correct.mni.27823/output.mean.dat sysname Linux hostname c14n09.farnam.hpc.yale.internal machine x86_64 user mc2835 UseRobust 0 Loading ./tmp.mri_nu_correct.mni.27823/ones.mgz Loading ./tmp.mri_nu_correct.mni.27823/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.27823/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.27823/nu2.mnc ./tmp.mri_nu_correct.mni.27823/nu2.mnc mul 1.02261072023037568801 Saving result to './tmp.mri_nu_correct.mni.27823/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.27823/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.27823/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.27823/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 7 seconds. mapping ( 2, 137) to ( 3, 110) Thu Mar 7 06:58:58 UTC 2019 mri_nu_correct.mni done mri_add_xform_to_header -c /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Thu Mar 7 06:58:59 UTC 2019 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 1.14627 0.03529 0.00314 -9.99066; -0.07145 1.00491 0.21176 -35.18166; -0.01190 -0.17305 1.06080 -13.43111; 0.00000 0.00000 0.00000 1.00000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 16 Starting OpenSpline(): npoints = 16 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 66 (65), valley at 24 (23) csf peak at 33, setting threshold to 55 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 65 (64), valley at 24 (23) csf peak at 33, setting threshold to 54 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 26 seconds. Started at Thu Mar 7 06:55:10 UTC 2019 Ended at Thu Mar 7 07:00:26 UTC 2019 #@#%# recon-all-run-time-hours 0.088 recon-all -s sub-030 finished without error at Thu Mar 7 07:00:26 UTC 2019 New invocation of recon-all Thu Mar 7 07:00:29 UTC 2019 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030 /opt/freesurfer/bin/recon-all -autorecon2-volonly -openmp 7 -subjid sub-030 -sd /home/mc2835/scratch60/RVLdata/fmriprep_output/freesurfer subjid sub-030 setenv SUBJECTS_DIR /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /opt/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a Linux c14n09.farnam.hpc.yale.internal 3.10.0-693.37.4.el7.x86_64 #1 SMP Fri Aug 10 12:34:55 EDT 2018 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize unlimited memoryuse 65536000 kbytes vmemoryuse unlimited descriptors 51200 memorylocked unlimited maxproc 512036 maxlocks unlimited maxsignal 512036 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 131317832 18016176 78671800 654424 34629856 111897372 Swap: 16777212 151228 16625984 ######################################## 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: 2019/03/07-07:00:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-07:00:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-07:00:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-07:00:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-07:00:30-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-07:00:30-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-07:00:30-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-07:00:30-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-07:00:30-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-07:00:30-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-07:00:30-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-07:00:30-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-07:00:30-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-07:00:30-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-07:00:30-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-07:00:30-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-07:00:30-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-07:00:30-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-07:00:30-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-07:00:30-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-07:00:30-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-07:00:30-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-07:00:30-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-07:00:30-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-07:00:30-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-07:00:30-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-07:00:30-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-07:00:30-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-07:00:30-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-07:00:30-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-07:00:30-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-07:00:30-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-07:00:30-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-07:00:30-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-07:00:30-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-07:00:30-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-07:00:30-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-07:00:30-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-07:00:30-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /opt/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /opt/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #------------------------------------- #@# EM Registration Thu Mar 7 07:00:30 UTC 2019 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri mri_em_register -rusage /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 7 == reading 1 input volumes... logging results to talairach.log reading '/opt/freesurfer/average/RB_all_2016-05-10.vc700.gca'... average std = 7.3 using min determinant for regularization = 5.3 0 singular and 841 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 6.3 or > 503.7 total sample mean = 78.8 (1011 zeros) ************************************************ spacing=8, using 2830 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2830, passno 0, spacing 8 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=14.0 skull bounding box = (66, 40, 36) --> (187, 165, 202) using (106, 82, 119) as brain centroid... mean wm in atlas = 107, using box (91,67,99) --> (120, 97,139) to find MRI wm before smoothing, mri peak at 107 robust fit to distribution - 107 +- 4.6 after smoothing, mri peak at 107, scaling input intensities by 1.000 scaling channel 0 by 1 initial log_p = -4.328 ************************************************ First Search limited to translation only. ************************************************ max log p = -3.969694 @ (-9.091, 9.091, -9.091) max log p = -3.772211 @ (4.545, 4.545, 4.545) max log p = -3.688235 @ (2.273, 2.273, -6.818) max log p = -3.666120 @ (-1.136, 1.136, 1.136) max log p = -3.660756 @ (0.568, -1.705, 2.841) max log p = -3.660756 @ (0.000, 0.000, 0.000) Found translation: (-2.8, 15.3, -7.4): log p = -3.661 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.360, old_max_log_p =-3.661 (thresh=-3.7) 1.15000 0.00000 0.00000 -22.27761; 0.00000 1.13509 0.16902 -17.77232; 0.00000 -0.11161 0.99651 4.60938; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.360, old_max_log_p =-3.360 (thresh=-3.4) 1.15000 0.00000 0.00000 -22.27761; 0.00000 1.13509 0.16902 -17.77232; 0.00000 -0.11161 0.99651 4.60938; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.222, old_max_log_p =-3.360 (thresh=-3.4) 1.12703 0.00505 -0.03427 -14.08007; 0.00000 1.10856 0.20010 -14.70291; 0.03622 -0.15140 1.02745 2.31372; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.222, old_max_log_p =-3.222 (thresh=-3.2) 1.12703 0.00505 -0.03427 -14.08007; 0.00000 1.10856 0.20010 -14.70291; 0.03622 -0.15140 1.02745 2.31372; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.186, old_max_log_p =-3.222 (thresh=-3.2) 1.12725 -0.00519 -0.02741 -14.77138; 0.00850 1.11322 0.17495 -14.39772; 0.02713 -0.12434 1.03227 -1.21064; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.185, old_max_log_p =-3.186 (thresh=-3.2) 1.12725 -0.00519 -0.02741 -14.77138; 0.00851 1.11452 0.17515 -14.55438; 0.02707 -0.12405 1.02986 -0.96067; 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 1.12725 -0.00519 -0.02741 -14.77138; 0.00851 1.11452 0.17515 -14.55438; 0.02707 -0.12405 1.02986 -0.96067; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.12725 -0.00519 -0.02741 -14.77138; 0.00851 1.11452 0.17515 -14.55438; 0.02707 -0.12405 1.02986 -0.96067; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.12725 -0.00519 -0.02741 -14.77138; 0.00851 1.11452 0.17515 -14.55438; 0.02707 -0.12405 1.02986 -0.96067; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.185 (old=-4.328) transform before final EM align: 1.12725 -0.00519 -0.02741 -14.77138; 0.00851 1.11452 0.17515 -14.55438; 0.02707 -0.12405 1.02986 -0.96067; 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 1.12725 -0.00519 -0.02741 -14.77138; 0.00851 1.11452 0.17515 -14.55438; 0.02707 -0.12405 1.02986 -0.96067; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 1.12725 -0.00519 -0.02741 -14.77138; 0.00851 1.11452 0.17515 -14.55438; 0.02707 -0.12405 1.02986 -0.96067; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = 3.8 tol 0.000000 final transform: 1.12725 -0.00519 -0.02741 -14.77138; 0.00851 1.11452 0.17515 -14.55438; 0.02707 -0.12405 1.02986 -0.96067; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 1148.845492 mri_em_register stimesec 2.103114 mri_em_register ru_maxrss 596256 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 735856 mri_em_register ru_majflt 4 mri_em_register ru_nswap 0 mri_em_register ru_inblock 26824 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 1043 mri_em_register ru_nivcsw 390 registration took 3 minutes and 12 seconds. #-------------------------------------- #@# CA Normalize Thu Mar 7 07:03:42 UTC 2019 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/opt/freesurfer/average/RB_all_2016-05-10.vc700.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=14.0 skull bounding box = (66, 40, 36) --> (187, 165, 202) using (106, 82, 119) as brain centroid... mean wm in atlas = 107, using box (91,67,99) --> (120, 97,139) to find MRI wm before smoothing, mri peak at 107 robust fit to distribution - 107 +- 4.6 after smoothing, mri peak at 107, scaling input intensities by 1.000 scaling channel 0 by 1 using 246344 sample points... INFO: compute sample coordinates transform 1.12725 -0.00519 -0.02741 -14.77138; 0.00851 1.11452 0.17515 -14.55438; 0.02707 -0.12405 1.02986 -0.96067; 0.00000 0.00000 0.00000 1.00000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (126, 41, 37) --> (187, 145, 197) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0 0 of 3239 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (71, 43, 37) --> (130, 146, 198) Right_Cerebral_White_Matter: limiting intensities to 94.0 --> 132.0 1 of 3258 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (129, 123, 61) --> (172, 161, 113) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 50 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (89, 123, 60) --> (128, 159, 115) Right_Cerebellum_White_Matter: limiting intensities to 89.0 --> 132.0 0 of 63 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (114, 111, 96) --> (144, 175, 125) Brain_Stem: limiting intensities to 88.0 --> 132.0 3 of 110 (2.7%) samples deleted using 6720 total control points for intensity normalization... bias field = 0.962 +- 0.038 14 of 6716 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (126, 41, 37) --> (187, 145, 197) Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 132.0 0 of 4293 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (71, 43, 37) --> (130, 146, 198) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 1 of 4078 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (129, 123, 61) --> (172, 161, 113) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 76 of 136 (55.9%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (89, 123, 60) --> (128, 159, 115) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 33 of 125 (26.4%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (114, 111, 96) --> (144, 175, 125) Brain_Stem: limiting intensities to 88.0 --> 132.0 190 of 213 (89.2%) samples deleted using 8845 total control points for intensity normalization... bias field = 1.023 +- 0.035 4 of 8473 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (126, 41, 37) --> (187, 145, 197) Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 132.0 0 of 4328 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (71, 43, 37) --> (130, 146, 198) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 1 of 4033 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (129, 123, 61) --> (172, 161, 113) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 145 of 202 (71.8%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (89, 123, 60) --> (128, 159, 115) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 100 of 184 (54.3%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (114, 111, 96) --> (144, 175, 125) Brain_Stem: limiting intensities to 88.0 --> 132.0 248 of 262 (94.7%) samples deleted using 9009 total control points for intensity normalization... bias field = 1.019 +- 0.033 6 of 8366 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 16 seconds. #-------------------------------------- #@# CA Reg Thu Mar 7 07:04:57 UTC 2019 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri mri_ca_register -rusage /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_ca_register for OpenMP = 7 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/opt/freesurfer/average/RB_all_2016-05-10.vc700.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.32 (predicted orig area = 6.1) 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=0.824, neg=0, invalid=762 0001: dt=196.256709, rms=0.763 (7.407%), neg=0, invalid=762 0002: dt=160.362812, rms=0.743 (2.703%), neg=0, invalid=762 0003: dt=200.648649, rms=0.731 (1.596%), neg=0, invalid=762 0004: dt=160.507937, rms=0.724 (0.995%), neg=0, invalid=762 0005: dt=221.952000, rms=0.718 (0.779%), neg=0, invalid=762 0006: dt=149.333333, rms=0.714 (0.614%), neg=0, invalid=762 0007: dt=295.936000, rms=0.710 (0.538%), neg=0, invalid=762 0008: dt=129.472000, rms=0.706 (0.493%), neg=0, invalid=762 0009: dt=295.936000, rms=0.703 (0.406%), neg=0, invalid=762 0010: dt=129.472000, rms=0.701 (0.332%), neg=0, invalid=762 0011: dt=369.920000, rms=0.699 (0.320%), neg=0, invalid=762 0012: dt=129.472000, rms=0.697 (0.310%), neg=0, invalid=762 0013: dt=221.952000, rms=0.695 (0.195%), neg=0, invalid=762 0014: dt=221.952000, rms=0.694 (0.193%), neg=0, invalid=762 0015: dt=221.952000, rms=0.691 (0.479%), neg=0, invalid=762 0016: dt=221.952000, rms=0.688 (0.392%), neg=0, invalid=762 0017: dt=221.952000, rms=0.684 (0.632%), neg=0, invalid=762 0018: dt=221.952000, rms=0.680 (0.498%), neg=0, invalid=762 0019: dt=221.952000, rms=0.677 (0.413%), neg=0, invalid=762 0020: dt=221.952000, rms=0.675 (0.409%), neg=0, invalid=762 0021: dt=221.952000, rms=0.673 (0.296%), neg=0, invalid=762 0022: dt=221.952000, rms=0.670 (0.315%), neg=0, invalid=762 0023: dt=221.952000, rms=0.669 (0.256%), neg=0, invalid=762 0024: dt=221.952000, rms=0.667 (0.243%), neg=0, invalid=762 0025: dt=221.952000, rms=0.665 (0.256%), neg=0, invalid=762 0026: dt=221.952000, rms=0.664 (0.204%), neg=0, invalid=762 0027: dt=221.952000, rms=0.663 (0.209%), neg=0, invalid=762 0028: dt=221.952000, rms=0.661 (0.178%), neg=0, invalid=762 0029: dt=221.952000, rms=0.660 (0.192%), neg=0, invalid=762 0030: dt=221.952000, rms=0.659 (0.195%), neg=0, invalid=762 0031: dt=221.952000, rms=0.658 (0.139%), neg=0, invalid=762 0032: dt=221.952000, rms=0.657 (0.148%), neg=0, invalid=762 0033: dt=221.952000, rms=0.656 (0.153%), neg=0, invalid=762 0034: dt=221.952000, rms=0.655 (0.123%), neg=0, invalid=762 0035: dt=221.952000, rms=0.654 (0.129%), neg=0, invalid=762 0036: dt=221.952000, rms=0.654 (0.087%), neg=0, invalid=762 0037: dt=221.952000, rms=0.653 (0.097%), neg=0, invalid=762 0038: dt=221.952000, rms=0.653 (0.086%), neg=0, invalid=762 0039: dt=517.888000, rms=0.652 (0.037%), neg=0, invalid=762 0040: dt=517.888000, rms=0.652 (-0.242%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.653, neg=0, invalid=762 0041: dt=129.472000, rms=0.652 (0.122%), neg=0, invalid=762 0042: dt=295.936000, rms=0.652 (0.031%), neg=0, invalid=762 0043: dt=295.936000, rms=0.652 (0.015%), neg=0, invalid=762 0044: dt=295.936000, rms=0.652 (0.031%), neg=0, invalid=762 0045: dt=295.936000, rms=0.651 (0.023%), neg=0, invalid=762 0046: dt=295.936000, rms=0.651 (0.026%), neg=0, invalid=762 0047: dt=295.936000, rms=0.651 (0.038%), neg=0, invalid=762 0048: dt=295.936000, rms=0.651 (0.016%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.657, neg=0, invalid=762 0049: dt=170.470046, rms=0.651 (0.983%), neg=0, invalid=762 0050: dt=194.258824, rms=0.642 (1.351%), neg=0, invalid=762 0051: dt=73.230769, rms=0.638 (0.547%), neg=0, invalid=762 0052: dt=145.152000, rms=0.635 (0.564%), neg=0, invalid=762 0053: dt=76.964630, rms=0.633 (0.333%), neg=0, invalid=762 0054: dt=145.152000, rms=0.630 (0.380%), neg=0, invalid=762 0055: dt=63.621302, rms=0.628 (0.290%), neg=0, invalid=762 0056: dt=145.152000, rms=0.626 (0.311%), neg=0, invalid=762 0057: dt=81.377483, rms=0.625 (0.203%), neg=0, invalid=762 0058: dt=81.377483, rms=0.624 (0.194%), neg=0, invalid=762 0059: dt=81.377483, rms=0.622 (0.303%), neg=0, invalid=762 0060: dt=81.377483, rms=0.619 (0.419%), neg=0, invalid=762 0061: dt=81.377483, rms=0.617 (0.398%), neg=0, invalid=762 0062: dt=81.377483, rms=0.614 (0.522%), neg=0, invalid=762 0063: dt=81.377483, rms=0.611 (0.446%), neg=0, invalid=762 0064: dt=81.377483, rms=0.608 (0.478%), neg=0, invalid=762 0065: dt=81.377483, rms=0.606 (0.348%), neg=0, invalid=762 0066: dt=81.377483, rms=0.604 (0.365%), neg=0, invalid=762 0067: dt=81.377483, rms=0.602 (0.313%), neg=0, invalid=762 0068: dt=81.377483, rms=0.600 (0.292%), neg=0, invalid=762 0069: dt=81.377483, rms=0.599 (0.208%), neg=0, invalid=762 0070: dt=81.377483, rms=0.597 (0.232%), neg=0, invalid=762 0071: dt=81.377483, rms=0.596 (0.173%), neg=0, invalid=762 0072: dt=81.377483, rms=0.596 (0.159%), neg=0, invalid=762 0073: dt=81.377483, rms=0.595 (0.144%), neg=0, invalid=762 0074: dt=81.377483, rms=0.594 (0.155%), neg=0, invalid=762 0075: dt=81.377483, rms=0.593 (0.102%), neg=0, invalid=762 0076: dt=81.377483, rms=0.593 (0.089%), neg=0, invalid=762 0077: dt=103.680000, rms=0.592 (0.027%), neg=0, invalid=762 0078: dt=103.680000, rms=0.592 (-0.025%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.593, neg=0, invalid=762 0079: dt=82.944000, rms=0.592 (0.217%), neg=0, invalid=762 0080: dt=145.152000, rms=0.591 (0.081%), neg=0, invalid=762 0081: dt=145.152000, rms=0.591 (0.030%), neg=0, invalid=762 0082: dt=145.152000, rms=0.590 (0.164%), neg=0, invalid=762 0083: dt=145.152000, rms=0.590 (0.066%), neg=0, invalid=762 0084: dt=145.152000, rms=0.590 (0.033%), neg=0, invalid=762 0085: dt=62.208000, rms=0.589 (0.044%), neg=0, invalid=762 0086: dt=145.152000, rms=0.589 (0.023%), neg=0, invalid=762 0087: dt=145.152000, rms=0.589 (-0.016%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.611, neg=0, invalid=762 0088: dt=0.000000, rms=0.610 (0.099%), neg=0, invalid=762 0089: dt=0.000000, rms=0.610 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.611, neg=0, invalid=762 0090: dt=0.000000, rms=0.610 (0.099%), neg=0, invalid=762 0091: dt=0.000000, rms=0.610 (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=0.674, neg=0, invalid=762 0092: dt=4.543210, rms=0.657 (2.442%), neg=0, invalid=762 0093: dt=1.083333, rms=0.657 (0.038%), neg=0, invalid=762 0094: dt=1.083333, rms=0.657 (-0.020%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.657, neg=0, invalid=762 0095: dt=0.000000, rms=0.657 (0.082%), neg=0, invalid=762 0096: dt=0.000000, rms=0.657 (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=0.727, neg=0, invalid=762 0097: dt=1.536000, rms=0.719 (1.046%), neg=0, invalid=762 0098: dt=1.536000, rms=0.716 (0.477%), neg=0, invalid=762 0099: dt=0.448000, rms=0.715 (0.057%), neg=0, invalid=762 0100: dt=0.448000, rms=0.715 (0.027%), neg=0, invalid=762 0101: dt=0.448000, rms=0.715 (0.003%), neg=0, invalid=762 0102: dt=0.448000, rms=0.715 (-0.088%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.715, neg=0, invalid=762 0103: dt=1.024000, rms=0.714 (0.168%), neg=0, invalid=762 0104: dt=0.000000, rms=0.714 (0.000%), neg=0, invalid=762 0105: dt=0.100000, rms=0.714 (-0.001%), 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=0.662, neg=0, invalid=762 0106: dt=0.925166, rms=0.642 (3.152%), neg=0, invalid=762 0107: dt=0.080000, rms=0.640 (0.171%), neg=0, invalid=762 0108: dt=0.080000, rms=0.640 (-0.071%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.641, neg=0, invalid=762 0109: dt=0.028000, rms=0.640 (0.101%), neg=0, invalid=762 0110: dt=0.007000, rms=0.640 (0.001%), neg=0, invalid=762 0111: dt=0.007000, rms=0.640 (0.001%), neg=0, invalid=762 0112: dt=0.007000, rms=0.640 (-0.005%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.16318 (14) Left_Lateral_Ventricle (4): linear fit = 0.67 x + 0.0 (1594 voxels, overlap=0.357) Left_Lateral_Ventricle (4): linear fit = 0.67 x + 0.0 (1594 voxels, peak = 13), gca=13.3 gca peak = 0.15565 (16) mri peak = 0.15011 (14) Right_Lateral_Ventricle (43): linear fit = 0.80 x + 0.0 (1660 voxels, overlap=0.662) Right_Lateral_Ventricle (43): linear fit = 0.80 x + 0.0 (1660 voxels, peak = 13), gca=12.7 gca peak = 0.26829 (96) mri peak = 0.10839 (96) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (791 voxels, overlap=1.000) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (791 voxels, peak = 95), gca=94.6 gca peak = 0.20183 (93) mri peak = 0.07275 (98) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (705 voxels, overlap=0.980) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (705 voxels, peak = 97), gca=97.2 gca peak = 0.21683 (55) mri peak = 0.13308 (63) Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (796 voxels, overlap=0.355) Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (796 voxels, peak = 62), gca=62.4 gca peak = 0.30730 (58) mri peak = 0.08710 (63) Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (974 voxels, overlap=0.868) Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (974 voxels, peak = 64), gca=63.5 gca peak = 0.11430 (101) mri peak = 0.08332 (104) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (54055 voxels, overlap=0.687) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (54055 voxels, peak = 106), gca=105.5 gca peak = 0.12076 (102) mri peak = 0.11032 (107) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (56935 voxels, overlap=0.587) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (56935 voxels, peak = 108), gca=107.6 gca peak = 0.14995 (59) mri peak = 0.03189 (58) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (19814 voxels, overlap=0.968) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (19814 voxels, peak = 60), gca=60.5 gca peak = 0.15082 (58) mri peak = 0.03118 (63) Right_Cerebral_Cortex (42): linear fit = 1.10 x + 0.0 (20399 voxels, overlap=0.862) Right_Cerebral_Cortex (42): linear fit = 1.10 x + 0.0 (20399 voxels, peak = 64), gca=63.5 gca peak = 0.14161 (67) mri peak = 0.11558 (72) Right_Caudate (50): linear fit = 1.09 x + 0.0 (493 voxels, overlap=0.420) Right_Caudate (50): linear fit = 1.09 x + 0.0 (493 voxels, peak = 73), gca=72.7 gca peak = 0.15243 (71) mri peak = 0.12266 (79) Left_Caudate (11): linear fit = 1.03 x + 0.0 (856 voxels, overlap=0.803) Left_Caudate (11): linear fit = 1.03 x + 0.0 (856 voxels, peak = 73), gca=73.5 gca peak = 0.13336 (57) mri peak = 0.05726 (63) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (24414 voxels, overlap=0.745) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (24414 voxels, peak = 64), gca=63.6 gca peak = 0.13252 (56) mri peak = 0.05279 (64) Right_Cerebellum_Cortex (47): linear fit = 1.16 x + 0.0 (29285 voxels, overlap=0.670) Right_Cerebellum_Cortex (47): linear fit = 1.16 x + 0.0 (29285 voxels, peak = 65), gca=65.2 gca peak = 0.18181 (84) mri peak = 0.09715 (86) Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (8780 voxels, overlap=0.730) Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (8780 voxels, peak = 87), gca=86.9 gca peak = 0.20573 (83) mri peak = 0.10633 (87) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (7612 voxels, overlap=0.749) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (7612 voxels, peak = 86), gca=85.9 gca peak = 0.21969 (57) mri peak = 0.08605 (66) Left_Amygdala (18): linear fit = 1.13 x + 0.0 (426 voxels, overlap=0.516) Left_Amygdala (18): linear fit = 1.13 x + 0.0 (426 voxels, peak = 65), gca=64.7 gca peak = 0.39313 (56) mri peak = 0.11512 (63) Right_Amygdala (54): linear fit = 1.04 x + 0.0 (509 voxels, overlap=0.954) Right_Amygdala (54): linear fit = 1.04 x + 0.0 (509 voxels, peak = 59), gca=58.5 gca peak = 0.14181 (85) mri peak = 0.05927 (87) Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (5029 voxels, overlap=0.911) Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (5029 voxels, peak = 87), gca=87.1 gca peak = 0.11978 (83) mri peak = 0.07619 (84) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (3825 voxels, overlap=0.926) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (3825 voxels, peak = 84), gca=84.2 gca peak = 0.13399 (79) mri peak = 0.06958 (85) Left_Putamen (12): linear fit = 1.10 x + 0.0 (2129 voxels, overlap=0.491) Left_Putamen (12): linear fit = 1.10 x + 0.0 (2129 voxels, peak = 87), gca=86.5 gca peak = 0.14159 (79) mri peak = 0.06030 (82) Right_Putamen (51): linear fit = 1.04 x + 0.0 (2158 voxels, overlap=0.973) Right_Putamen (51): linear fit = 1.04 x + 0.0 (2158 voxels, peak = 83), gca=82.6 gca peak = 0.10025 (80) mri peak = 0.12526 (83) Brain_Stem (16): linear fit = 1.07 x + 0.0 (11067 voxels, overlap=0.401) Brain_Stem (16): linear fit = 1.07 x + 0.0 (11067 voxels, peak = 85), gca=85.2 gca peak = 0.13281 (86) mri peak = 0.08394 (94) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1048 voxels, overlap=0.554) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1048 voxels, peak = 93), gca=93.3 gca peak = 0.12801 (89) mri peak = 0.08132 (93) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (1245 voxels, overlap=0.536) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (1245 voxels, peak = 97), gca=96.6 gca peak = 0.20494 (23) mri peak = 1.00000 (26) gca peak = 0.15061 (21) mri peak = 0.12431 (16) Fourth_Ventricle (15): linear fit = 0.86 x + 0.0 (441 voxels, overlap=0.783) Fourth_Ventricle (15): linear fit = 0.86 x + 0.0 (441 voxels, peak = 18), gca=18.0 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 1.09 x + 0.0 estimating mean wm scale to be 1.05 x + 0.0 estimating mean csf scale to be 0.77 x + 0.0 saving intensity scales to talairach.label_intensities.txt **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.654, neg=0, invalid=762 0113: dt=110.976000, rms=0.649 (0.758%), neg=0, invalid=762 0114: dt=369.920000, rms=0.644 (0.778%), neg=0, invalid=762 0115: dt=129.472000, rms=0.642 (0.309%), neg=0, invalid=762 0116: dt=295.936000, rms=0.640 (0.296%), neg=0, invalid=762 0117: dt=129.472000, rms=0.638 (0.276%), neg=0, invalid=762 0118: dt=92.480000, rms=0.638 (0.052%), neg=0, invalid=762 0119: dt=1183.744000, rms=0.634 (0.592%), neg=0, invalid=762 0120: dt=56.765217, rms=0.633 (0.187%), neg=0, invalid=762 0121: dt=55.488000, rms=0.633 (0.012%), neg=0, invalid=762 0122: dt=55.488000, rms=0.633 (0.015%), neg=0, invalid=762 0123: dt=55.488000, rms=0.633 (0.030%), neg=0, invalid=762 0124: dt=55.488000, rms=0.632 (0.055%), neg=0, invalid=762 0125: dt=55.488000, rms=0.632 (0.079%), neg=0, invalid=762 0126: dt=55.488000, rms=0.631 (0.094%), neg=0, invalid=762 0127: dt=55.488000, rms=0.630 (0.099%), neg=0, invalid=762 0128: dt=55.488000, rms=0.630 (0.097%), neg=0, invalid=762 0129: dt=55.488000, rms=0.629 (0.090%), neg=0, invalid=762 0130: dt=55.488000, rms=0.629 (0.085%), neg=0, invalid=762 0131: dt=55.488000, rms=0.628 (0.083%), neg=0, invalid=762 0132: dt=55.488000, rms=0.628 (0.086%), neg=0, invalid=762 0133: dt=55.488000, rms=0.627 (0.090%), neg=0, invalid=762 0134: dt=55.488000, rms=0.627 (0.089%), neg=0, invalid=762 0135: dt=55.488000, rms=0.626 (0.083%), neg=0, invalid=762 0136: dt=55.488000, rms=0.626 (0.075%), neg=0, invalid=762 0137: dt=55.488000, rms=0.625 (0.067%), neg=0, invalid=762 0138: dt=55.488000, rms=0.625 (0.062%), neg=0, invalid=762 0139: dt=55.488000, rms=0.624 (0.061%), neg=0, invalid=762 0140: dt=55.488000, rms=0.624 (0.059%), neg=0, invalid=762 0141: dt=55.488000, rms=0.624 (0.059%), neg=0, invalid=762 0142: dt=55.488000, rms=0.623 (0.057%), neg=0, invalid=762 0143: dt=55.488000, rms=0.623 (0.052%), neg=0, invalid=762 0144: dt=55.488000, rms=0.623 (0.047%), neg=0, invalid=762 0145: dt=55.488000, rms=0.622 (0.044%), neg=0, invalid=762 0146: dt=55.488000, rms=0.622 (0.044%), neg=0, invalid=762 0147: dt=55.488000, rms=0.622 (0.044%), neg=0, invalid=762 0148: dt=55.488000, rms=0.622 (0.045%), neg=0, invalid=762 0149: dt=55.488000, rms=0.621 (0.043%), neg=0, invalid=762 0150: dt=55.488000, rms=0.621 (0.039%), neg=0, invalid=762 0151: dt=55.488000, rms=0.621 (0.038%), neg=0, invalid=762 0152: dt=55.488000, rms=0.621 (0.036%), neg=0, invalid=762 0153: dt=55.488000, rms=0.620 (0.036%), neg=0, invalid=762 0154: dt=55.488000, rms=0.620 (0.034%), neg=0, invalid=762 0155: dt=55.488000, rms=0.620 (0.034%), neg=0, invalid=762 0156: dt=55.488000, rms=0.620 (0.032%), neg=0, invalid=762 0157: dt=55.488000, rms=0.620 (0.030%), neg=0, invalid=762 0158: dt=55.488000, rms=0.619 (0.029%), neg=0, invalid=762 0159: dt=55.488000, rms=0.619 (0.028%), neg=0, invalid=762 0160: dt=55.488000, rms=0.619 (0.030%), neg=0, invalid=762 0161: dt=55.488000, rms=0.619 (0.026%), neg=0, invalid=762 0162: dt=55.488000, rms=0.619 (0.024%), neg=0, invalid=762 0163: dt=55.488000, rms=0.619 (0.025%), neg=0, invalid=762 0164: dt=55.488000, rms=0.618 (0.023%), neg=0, invalid=762 0165: dt=887.808000, rms=0.618 (0.010%), neg=0, invalid=762 0166: dt=887.808000, rms=0.618 (-0.280%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.619, neg=0, invalid=762 0167: dt=369.920000, rms=0.617 (0.290%), neg=0, invalid=762 0168: dt=55.488000, rms=0.617 (0.011%), neg=0, invalid=762 0169: dt=55.488000, rms=0.617 (0.006%), neg=0, invalid=762 0170: dt=55.488000, rms=0.617 (0.002%), neg=0, invalid=762 0171: dt=55.488000, rms=0.617 (-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=0.618, neg=0, invalid=762 0172: dt=226.232558, rms=0.609 (1.381%), neg=0, invalid=762 0173: dt=127.788779, rms=0.600 (1.496%), neg=0, invalid=762 0174: dt=65.088435, rms=0.598 (0.400%), neg=0, invalid=762 0175: dt=414.720000, rms=0.591 (1.165%), neg=0, invalid=762 0176: dt=67.310345, rms=0.588 (0.578%), neg=0, invalid=762 0177: dt=124.416000, rms=0.586 (0.347%), neg=0, invalid=762 0178: dt=36.288000, rms=0.585 (0.156%), neg=0, invalid=762 0179: dt=145.152000, rms=0.583 (0.225%), neg=0, invalid=762 0180: dt=145.152000, rms=0.582 (0.266%), neg=0, invalid=762 0181: dt=36.288000, rms=0.581 (0.145%), neg=0, invalid=762 0182: dt=145.152000, rms=0.580 (0.162%), neg=0, invalid=762 0183: dt=103.680000, rms=0.579 (0.212%), neg=0, invalid=762 0184: dt=36.288000, rms=0.578 (0.072%), neg=0, invalid=762 0185: dt=414.720000, rms=0.577 (0.252%), neg=0, invalid=762 0186: dt=36.288000, rms=0.575 (0.287%), neg=0, invalid=762 0187: dt=145.152000, rms=0.574 (0.188%), neg=0, invalid=762 0188: dt=36.288000, rms=0.574 (0.058%), neg=0, invalid=762 0189: dt=145.152000, rms=0.573 (0.081%), neg=0, invalid=762 0190: dt=124.416000, rms=0.572 (0.157%), neg=0, invalid=762 0191: dt=36.288000, rms=0.572 (0.046%), neg=0, invalid=762 0192: dt=36.288000, rms=0.572 (0.032%), neg=0, invalid=762 0193: dt=36.288000, rms=0.572 (0.046%), neg=0, invalid=762 0194: dt=36.288000, rms=0.571 (0.078%), neg=0, invalid=762 0195: dt=36.288000, rms=0.571 (0.113%), neg=0, invalid=762 0196: dt=36.288000, rms=0.570 (0.130%), neg=0, invalid=762 0197: dt=36.288000, rms=0.569 (0.137%), neg=0, invalid=762 0198: dt=36.288000, rms=0.568 (0.139%), neg=0, invalid=762 0199: dt=36.288000, rms=0.567 (0.139%), neg=0, invalid=762 0200: dt=36.288000, rms=0.567 (0.141%), neg=0, invalid=762 0201: dt=36.288000, rms=0.566 (0.147%), neg=0, invalid=762 0202: dt=36.288000, rms=0.565 (0.150%), neg=0, invalid=762 0203: dt=36.288000, rms=0.564 (0.147%), neg=0, invalid=762 0204: dt=36.288000, rms=0.563 (0.139%), neg=0, invalid=762 0205: dt=36.288000, rms=0.563 (0.135%), neg=0, invalid=762 0206: dt=36.288000, rms=0.562 (0.130%), neg=0, invalid=762 0207: dt=36.288000, rms=0.561 (0.127%), neg=0, invalid=762 0208: dt=36.288000, rms=0.560 (0.125%), neg=0, invalid=762 0209: dt=36.288000, rms=0.560 (0.016%), neg=0, invalid=762 0210: dt=36.288000, rms=0.560 (0.029%), neg=0, invalid=762 0211: dt=36.288000, rms=0.560 (0.038%), neg=0, invalid=762 0212: dt=36.288000, rms=0.560 (0.042%), neg=0, invalid=762 0213: dt=36.288000, rms=0.560 (0.047%), neg=0, invalid=762 0214: dt=36.288000, rms=0.559 (0.008%), neg=0, invalid=762 0215: dt=9.072000, rms=0.559 (0.003%), neg=0, invalid=762 0216: dt=2.268000, rms=0.559 (0.001%), neg=0, invalid=762 0217: dt=1.134000, rms=0.559 (0.000%), neg=0, invalid=762 0218: dt=0.283500, rms=0.559 (0.000%), neg=0, invalid=762 0219: dt=0.035437, rms=0.559 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.560, neg=0, invalid=762 0220: dt=124.416000, rms=0.558 (0.459%), neg=0, invalid=762 0221: dt=124.416000, rms=0.557 (0.136%), neg=0, invalid=762 0222: dt=103.680000, rms=0.556 (0.104%), neg=0, invalid=762 0223: dt=103.680000, rms=0.556 (0.081%), neg=0, invalid=762 0224: dt=103.680000, rms=0.555 (0.076%), neg=0, invalid=762 0225: dt=62.208000, rms=0.555 (0.052%), neg=0, invalid=762 0226: dt=145.152000, rms=0.555 (0.082%), neg=0, invalid=762 0227: dt=36.288000, rms=0.554 (0.037%), neg=0, invalid=762 0228: dt=36.288000, rms=0.554 (0.021%), neg=0, invalid=762 0229: dt=36.288000, rms=0.554 (0.039%), neg=0, invalid=762 0230: dt=36.288000, rms=0.554 (0.054%), neg=0, invalid=762 0231: dt=36.288000, rms=0.553 (0.069%), neg=0, invalid=762 0232: dt=36.288000, rms=0.553 (0.076%), neg=0, invalid=762 0233: dt=36.288000, rms=0.553 (0.075%), neg=0, invalid=762 0234: dt=36.288000, rms=0.552 (0.082%), neg=0, invalid=762 0235: dt=36.288000, rms=0.552 (0.091%), neg=0, invalid=762 0236: dt=36.288000, rms=0.551 (0.090%), neg=0, invalid=762 0237: dt=36.288000, rms=0.551 (0.087%), neg=0, invalid=762 0238: dt=36.288000, rms=0.550 (0.092%), neg=0, invalid=762 0239: dt=36.288000, rms=0.550 (0.083%), neg=0, invalid=762 0240: dt=36.288000, rms=0.549 (0.083%), neg=0, invalid=762 0241: dt=36.288000, rms=0.549 (0.082%), neg=0, invalid=762 0242: dt=36.288000, rms=0.548 (0.088%), neg=0, invalid=762 0243: dt=36.288000, rms=0.548 (0.083%), neg=0, invalid=762 0244: dt=36.288000, rms=0.547 (0.081%), neg=0, invalid=762 0245: dt=36.288000, rms=0.547 (0.079%), neg=0, invalid=762 0246: dt=36.288000, rms=0.547 (0.077%), neg=0, invalid=762 0247: dt=36.288000, rms=0.546 (0.074%), neg=0, invalid=762 0248: dt=36.288000, rms=0.546 (0.077%), neg=0, invalid=762 0249: dt=36.288000, rms=0.545 (0.076%), neg=0, invalid=762 0250: dt=36.288000, rms=0.545 (0.076%), neg=0, invalid=762 0251: dt=36.288000, rms=0.544 (0.075%), neg=0, invalid=762 0252: dt=36.288000, rms=0.544 (0.072%), neg=0, invalid=762 0253: dt=36.288000, rms=0.544 (0.069%), neg=0, invalid=762 0254: dt=36.288000, rms=0.543 (0.069%), neg=0, invalid=762 0255: dt=36.288000, rms=0.543 (0.068%), neg=0, invalid=762 0256: dt=36.288000, rms=0.543 (0.066%), neg=0, invalid=762 0257: dt=36.288000, rms=0.542 (0.064%), neg=0, invalid=762 0258: dt=36.288000, rms=0.542 (0.062%), neg=0, invalid=762 0259: dt=36.288000, rms=0.542 (0.061%), neg=0, invalid=762 0260: dt=36.288000, rms=0.541 (0.060%), neg=0, invalid=762 0261: dt=36.288000, rms=0.541 (0.059%), neg=0, invalid=762 0262: dt=36.288000, rms=0.541 (0.058%), neg=0, invalid=762 0263: dt=36.288000, rms=0.540 (0.058%), neg=0, invalid=762 0264: dt=36.288000, rms=0.540 (0.054%), neg=0, invalid=762 0265: dt=36.288000, rms=0.540 (0.052%), neg=0, invalid=762 0266: dt=36.288000, rms=0.539 (0.049%), neg=0, invalid=762 0267: dt=36.288000, rms=0.539 (0.048%), neg=0, invalid=762 0268: dt=36.288000, rms=0.539 (0.048%), neg=0, invalid=762 0269: dt=36.288000, rms=0.539 (0.047%), neg=0, invalid=762 0270: dt=36.288000, rms=0.538 (0.045%), neg=0, invalid=762 0271: dt=36.288000, rms=0.538 (0.044%), neg=0, invalid=762 0272: dt=36.288000, rms=0.538 (0.043%), neg=0, invalid=762 0273: dt=36.288000, rms=0.538 (0.042%), neg=0, invalid=762 0274: dt=36.288000, rms=0.538 (0.041%), neg=0, invalid=762 0275: dt=36.288000, rms=0.537 (0.039%), neg=0, invalid=762 0276: dt=36.288000, rms=0.537 (0.037%), neg=0, invalid=762 0277: dt=36.288000, rms=0.537 (0.037%), neg=0, invalid=762 0278: dt=36.288000, rms=0.537 (0.036%), neg=0, invalid=762 0279: dt=36.288000, rms=0.537 (0.035%), neg=0, invalid=762 0280: dt=36.288000, rms=0.536 (0.033%), neg=0, invalid=762 0281: dt=36.288000, rms=0.536 (0.034%), neg=0, invalid=762 0282: dt=36.288000, rms=0.536 (0.034%), neg=0, invalid=762 0283: dt=36.288000, rms=0.536 (0.033%), neg=0, invalid=762 0284: dt=36.288000, rms=0.536 (0.032%), neg=0, invalid=762 0285: dt=36.288000, rms=0.536 (0.033%), neg=0, invalid=762 0286: dt=36.288000, rms=0.535 (0.031%), neg=0, invalid=762 0287: dt=36.288000, rms=0.535 (0.031%), neg=0, invalid=762 0288: dt=36.288000, rms=0.535 (0.029%), neg=0, invalid=762 0289: dt=36.288000, rms=0.535 (0.031%), neg=0, invalid=762 0290: dt=36.288000, rms=0.535 (0.031%), neg=0, invalid=762 0291: dt=36.288000, rms=0.535 (0.030%), neg=0, invalid=762 0292: dt=36.288000, rms=0.534 (0.029%), neg=0, invalid=762 0293: dt=36.288000, rms=0.534 (0.029%), neg=0, invalid=762 0294: dt=36.288000, rms=0.534 (0.028%), neg=0, invalid=762 0295: dt=36.288000, rms=0.534 (0.028%), neg=0, invalid=762 0296: dt=36.288000, rms=0.534 (0.028%), neg=0, invalid=762 0297: dt=36.288000, rms=0.534 (0.026%), neg=0, invalid=762 0298: dt=36.288000, rms=0.534 (0.026%), neg=0, invalid=762 0299: dt=36.288000, rms=0.533 (0.027%), neg=0, invalid=762 0300: dt=36.288000, rms=0.533 (0.025%), neg=0, invalid=762 0301: dt=36.288000, rms=0.533 (0.025%), neg=0, invalid=762 0302: dt=36.288000, rms=0.533 (0.025%), neg=0, invalid=762 0303: dt=36.288000, rms=0.533 (0.024%), neg=0, invalid=762 0304: dt=145.152000, rms=0.533 (0.009%), neg=0, invalid=762 0305: dt=4.536000, rms=0.533 (0.001%), neg=0, invalid=762 0306: dt=2.268000, rms=0.533 (0.000%), neg=0, invalid=762 0307: dt=0.567000, rms=0.533 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.540, neg=0, invalid=762 0308: dt=44.800000, rms=0.537 (0.616%), neg=0, invalid=762 0309: dt=44.800000, rms=0.532 (0.893%), neg=0, invalid=762 0310: dt=77.001575, rms=0.529 (0.526%), neg=0, invalid=762 0311: dt=38.400000, rms=0.526 (0.678%), neg=0, invalid=762 0312: dt=30.923077, rms=0.524 (0.272%), neg=0, invalid=762 0313: dt=44.800000, rms=0.522 (0.362%), neg=0, invalid=762 0314: dt=32.000000, rms=0.521 (0.247%), neg=0, invalid=762 0315: dt=44.800000, rms=0.519 (0.272%), neg=0, invalid=762 0316: dt=11.200000, rms=0.519 (0.148%), neg=0, invalid=762 0317: dt=11.200000, rms=0.518 (0.105%), neg=0, invalid=762 0318: dt=2.000000, rms=0.518 (0.017%), neg=0, invalid=762 0319: dt=0.250000, rms=0.518 (0.001%), neg=0, invalid=762 0320: dt=0.062500, rms=0.518 (0.000%), neg=0, invalid=762 0321: dt=0.001953, rms=0.518 (0.000%), neg=0, invalid=762 0322: dt=0.000684, rms=0.518 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.519, neg=0, invalid=762 0323: dt=0.700000, rms=0.518 (0.150%), neg=0, invalid=762 0324: dt=0.600000, rms=0.518 (0.013%), neg=0, invalid=762 0325: dt=0.037500, rms=0.518 (0.001%), neg=0, invalid=762 0326: dt=0.018750, rms=0.518 (0.000%), neg=0, invalid=762 0327: dt=0.002344, rms=0.518 (0.000%), neg=0, invalid=762 0328: dt=0.000684, rms=0.518 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.536, neg=0, invalid=762 0329: dt=8.142574, rms=0.534 (0.519%), neg=0, invalid=762 0330: dt=3.456000, rms=0.533 (0.140%), neg=0, invalid=762 0331: dt=0.252000, rms=0.533 (0.010%), neg=0, invalid=762 0332: dt=0.063000, rms=0.533 (0.004%), neg=0, invalid=762 0333: dt=0.003938, rms=0.533 (0.000%), neg=0, invalid=762 0334: dt=0.001969, rms=0.533 (0.000%), neg=0, invalid=762 0335: dt=0.000984, rms=0.533 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.533, neg=0, invalid=762 0336: dt=12.363636, rms=0.531 (0.546%), neg=0, invalid=762 0337: dt=28.474576, rms=0.528 (0.497%), neg=0, invalid=762 0338: dt=16.128000, rms=0.526 (0.403%), neg=0, invalid=762 0339: dt=13.824000, rms=0.525 (0.129%), neg=0, invalid=762 0340: dt=22.117647, rms=0.524 (0.189%), neg=0, invalid=762 0341: dt=11.520000, rms=0.524 (0.069%), neg=0, invalid=762 0342: dt=16.128000, rms=0.523 (0.166%), neg=0, invalid=762 0343: dt=16.128000, rms=0.523 (0.034%), neg=0, invalid=762 0344: dt=16.128000, rms=0.522 (0.117%), neg=0, invalid=762 0345: dt=16.128000, rms=0.521 (0.151%), neg=0, invalid=762 0346: dt=16.128000, rms=0.521 (0.133%), neg=0, invalid=762 0347: dt=16.128000, rms=0.519 (0.246%), neg=0, invalid=762 0348: dt=16.128000, rms=0.519 (0.056%), neg=0, invalid=762 0349: dt=16.128000, rms=0.519 (0.034%), neg=0, invalid=762 0350: dt=16.128000, rms=0.518 (0.064%), neg=0, invalid=762 0351: dt=16.128000, rms=0.518 (0.128%), neg=0, invalid=762 0352: dt=16.128000, rms=0.517 (0.130%), neg=0, invalid=762 0353: dt=8.064000, rms=0.517 (0.032%), neg=0, invalid=762 0354: dt=8.064000, rms=0.517 (0.012%), neg=0, invalid=762 0355: dt=8.064000, rms=0.517 (0.023%), neg=0, invalid=762 0356: dt=8.064000, rms=0.517 (0.031%), neg=0, invalid=762 0357: dt=8.064000, rms=0.517 (-0.003%), neg=0, invalid=762 0358: dt=4.032000, rms=0.517 (0.002%), neg=0, invalid=762 0359: dt=4.032000, rms=0.517 (0.009%), neg=0, invalid=762 0360: dt=2.880000, rms=0.517 (0.002%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.531, neg=0, invalid=762 0361: dt=0.000000, rms=0.530 (0.116%), neg=0, invalid=762 0362: dt=0.000000, rms=0.530 (0.000%), neg=0, invalid=762 0363: dt=0.100000, rms=0.530 (-0.150%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.531, neg=0, invalid=762 0364: dt=0.000000, rms=0.530 (0.116%), neg=0, invalid=762 0365: dt=0.000000, rms=0.530 (0.000%), neg=0, invalid=762 0366: dt=0.100000, rms=0.530 (-0.138%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.508, neg=0, invalid=762 0367: dt=0.384000, rms=0.495 (2.500%), neg=0, invalid=762 0368: dt=0.448000, rms=0.490 (0.973%), neg=0, invalid=762 0369: dt=0.448000, rms=0.488 (0.416%), neg=0, invalid=762 0370: dt=0.112000, rms=0.488 (0.068%), neg=0, invalid=762 0371: dt=0.320000, rms=0.487 (0.177%), neg=0, invalid=762 0372: dt=0.384000, rms=0.486 (0.171%), neg=0, invalid=762 0373: dt=0.384000, rms=0.486 (0.131%), neg=0, invalid=762 0374: dt=0.384000, rms=0.485 (0.111%), neg=0, invalid=762 0375: dt=0.384000, rms=0.485 (0.085%), neg=0, invalid=762 0376: dt=0.384000, rms=0.484 (0.078%), neg=0, invalid=762 0377: dt=0.384000, rms=0.484 (0.058%), neg=0, invalid=762 0378: dt=0.384000, rms=0.484 (0.059%), neg=0, invalid=762 0379: dt=0.384000, rms=0.484 (0.044%), neg=0, invalid=762 0380: dt=0.384000, rms=0.483 (0.046%), neg=0, invalid=762 0381: dt=0.384000, rms=0.483 (0.069%), neg=0, invalid=762 0382: dt=0.384000, rms=0.483 (0.032%), neg=0, invalid=762 0383: dt=0.384000, rms=0.483 (0.052%), neg=0, invalid=762 0384: dt=0.384000, rms=0.482 (0.064%), neg=0, invalid=762 0385: dt=0.192000, rms=0.482 (0.009%), neg=0, invalid=762 0386: dt=0.192000, rms=0.482 (0.008%), neg=0, invalid=762 0387: dt=0.112000, rms=0.482 (0.005%), neg=0, invalid=762 0388: dt=0.112000, rms=0.482 (0.004%), neg=0, invalid=762 0389: dt=0.112000, rms=0.482 (0.006%), neg=0, invalid=762 0390: dt=0.112000, rms=0.482 (0.012%), neg=0, invalid=762 0391: dt=0.112000, rms=0.482 (0.011%), neg=0, invalid=762 0392: dt=0.112000, rms=0.482 (0.014%), neg=0, invalid=762 0393: dt=0.112000, rms=0.482 (0.017%), neg=0, invalid=762 0394: dt=0.112000, rms=0.482 (0.015%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.483, neg=0, invalid=762 0395: dt=0.240385, rms=0.480 (0.632%), neg=0, invalid=762 0396: dt=0.112000, rms=0.479 (0.112%), neg=0, invalid=762 0397: dt=0.320000, rms=0.478 (0.245%), neg=0, invalid=762 0398: dt=0.320000, rms=0.477 (0.075%), neg=0, invalid=762 0399: dt=0.320000, rms=0.477 (0.029%), neg=0, invalid=762 0400: dt=0.160000, rms=0.477 (0.003%), neg=0, invalid=762 0401: dt=0.160000, rms=0.477 (0.007%), neg=0, invalid=762 0402: dt=0.160000, rms=0.477 (0.001%), neg=0, invalid=762 0403: dt=0.160000, rms=0.477 (-0.001%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) ********************* ALLOWING NEGATIVE NODES IN DEFORMATION******************************** **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.476, neg=0, invalid=762 0404: dt=0.000000, rms=0.475 (0.150%), neg=0, invalid=762 0405: dt=0.000000, rms=0.475 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.476, neg=0, invalid=762 0406: dt=32.368000, rms=0.475 (0.151%), neg=0, invalid=762 0407: dt=92.480000, rms=0.475 (0.002%), neg=0, invalid=762 0408: dt=92.480000, rms=0.475 (0.015%), neg=0, invalid=762 0409: dt=92.480000, rms=0.475 (0.012%), neg=0, invalid=762 0410: dt=92.480000, rms=0.475 (0.007%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.476, neg=0, invalid=762 0411: dt=31.104000, rms=0.475 (0.215%), neg=0, invalid=762 0412: dt=31.104000, rms=0.474 (0.029%), neg=0, invalid=762 0413: dt=31.104000, rms=0.474 (0.013%), neg=0, invalid=762 0414: dt=31.104000, rms=0.474 (-0.025%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.475, neg=0, invalid=762 0415: dt=89.769912, rms=0.473 (0.520%), neg=0, invalid=762 0416: dt=70.956522, rms=0.472 (0.158%), neg=0, invalid=762 0417: dt=70.956522, rms=0.471 (0.092%), neg=0, invalid=762 0418: dt=70.956522, rms=0.471 (0.138%), neg=0, invalid=762 0419: dt=70.956522, rms=0.470 (0.206%), neg=0, invalid=762 0420: dt=70.956522, rms=0.469 (0.138%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0421: dt=70.956522, rms=0.469 (0.133%), neg=0, invalid=762 0422: dt=70.956522, rms=0.468 (0.093%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0423: dt=70.956522, rms=0.468 (0.124%), neg=0, invalid=762 0424: dt=70.956522, rms=0.467 (0.084%), neg=0, invalid=762 0425: dt=36.288000, rms=0.467 (0.015%), neg=0, invalid=762 0426: dt=36.288000, rms=0.467 (0.012%), neg=0, invalid=762 0427: dt=36.288000, rms=0.467 (0.021%), neg=0, invalid=762 0428: dt=36.288000, rms=0.467 (0.030%), neg=0, invalid=762 0429: dt=36.288000, rms=0.467 (0.035%), neg=0, invalid=762 0430: dt=36.288000, rms=0.466 (0.035%), neg=0, invalid=762 0431: dt=36.288000, rms=0.466 (0.037%), neg=0, invalid=762 0432: dt=36.288000, rms=0.466 (0.031%), neg=0, invalid=762 0433: dt=36.288000, rms=0.466 (0.032%), neg=0, invalid=762 0434: dt=36.288000, rms=0.466 (0.029%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.467, neg=0, invalid=762 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0435: dt=31.336788, rms=0.465 (0.444%), neg=0, invalid=762 iter 0, gcam->neg = 20 after 10 iterations, nbhd size=1, neg = 0 0436: dt=94.679943, rms=0.462 (0.597%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 2 iterations, nbhd size=0, neg = 0 0437: dt=32.000000, rms=0.461 (0.180%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 0438: dt=32.000000, rms=0.460 (0.216%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 9 iterations, nbhd size=1, neg = 0 0439: dt=32.000000, rms=0.459 (0.344%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 9 iterations, nbhd size=1, neg = 0 0440: dt=32.000000, rms=0.458 (0.246%), neg=0, invalid=762 iter 0, gcam->neg = 13 after 9 iterations, nbhd size=1, neg = 0 0441: dt=32.000000, rms=0.457 (0.227%), neg=0, invalid=762 iter 0, gcam->neg = 26 after 10 iterations, nbhd size=1, neg = 0 0442: dt=32.000000, rms=0.456 (0.215%), neg=0, invalid=762 iter 0, gcam->neg = 22 after 10 iterations, nbhd size=1, neg = 0 0443: dt=32.000000, rms=0.455 (0.167%), neg=0, invalid=762 iter 0, gcam->neg = 18 after 9 iterations, nbhd size=1, neg = 0 0444: dt=32.000000, rms=0.454 (0.193%), neg=0, invalid=762 iter 0, gcam->neg = 23 after 12 iterations, nbhd size=1, neg = 0 0445: dt=32.000000, rms=0.454 (0.096%), neg=0, invalid=762 iter 0, gcam->neg = 19 after 12 iterations, nbhd size=1, neg = 0 0446: dt=32.000000, rms=0.453 (0.147%), neg=0, invalid=762 iter 0, gcam->neg = 25 after 16 iterations, nbhd size=1, neg = 0 0447: dt=32.000000, rms=0.453 (0.084%), neg=0, invalid=762 iter 0, gcam->neg = 31 after 13 iterations, nbhd size=1, neg = 0 0448: dt=32.000000, rms=0.452 (0.143%), neg=0, invalid=762 iter 0, gcam->neg = 26 after 5 iterations, nbhd size=0, neg = 0 0449: dt=32.000000, rms=0.451 (0.087%), neg=0, invalid=762 iter 0, gcam->neg = 30 after 12 iterations, nbhd size=1, neg = 0 0450: dt=32.000000, rms=0.451 (0.048%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 10 iterations, nbhd size=1, neg = 0 0451: dt=25.600000, rms=0.451 (0.143%), neg=0, invalid=762 0452: dt=11.200000, rms=0.450 (0.037%), neg=0, invalid=762 0453: dt=11.200000, rms=0.450 (0.026%), neg=0, invalid=762 0454: dt=11.200000, rms=0.450 (0.030%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 3 iterations, nbhd size=0, neg = 0 0455: dt=11.200000, rms=0.450 (0.039%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0456: dt=11.200000, rms=0.450 (0.038%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0457: dt=11.200000, rms=0.450 (0.035%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.450, neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0458: dt=58.816901, rms=0.447 (0.873%), neg=0, invalid=762 0459: dt=32.000000, rms=0.445 (0.289%), neg=0, invalid=762 0460: dt=32.000000, rms=0.445 (0.104%), neg=0, invalid=762 0461: dt=32.000000, rms=0.445 (0.056%), neg=0, invalid=762 0462: dt=32.000000, rms=0.444 (0.172%), neg=0, invalid=762 0463: dt=32.000000, rms=0.443 (0.117%), neg=0, invalid=762 0464: dt=32.000000, rms=0.443 (0.129%), neg=0, invalid=762 0465: dt=32.000000, rms=0.443 (-0.027%), neg=0, invalid=762 0466: dt=11.200000, rms=0.443 (0.024%), neg=0, invalid=762 0467: dt=44.800000, rms=0.442 (0.043%), neg=0, invalid=762 0468: dt=32.000000, rms=0.442 (0.034%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.450, neg=0, invalid=762 0469: dt=1.333333, rms=0.450 (0.174%), neg=0, invalid=762 0470: dt=0.252000, rms=0.450 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.450, neg=0, invalid=762 0471: dt=3.400000, rms=0.449 (0.212%), neg=0, invalid=762 0472: dt=1.728000, rms=0.449 (0.012%), neg=0, invalid=762 0473: dt=1.728000, rms=0.449 (0.000%), neg=0, invalid=762 0474: dt=1.728000, rms=0.449 (-0.027%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.462, neg=0, invalid=762 0475: dt=1.024000, rms=0.460 (0.275%), neg=0, invalid=762 0476: dt=0.256000, rms=0.460 (0.008%), neg=0, invalid=762 0477: dt=0.256000, rms=0.460 (0.000%), neg=0, invalid=762 0478: dt=0.256000, rms=0.460 (-0.026%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.461, neg=0, invalid=762 0479: dt=1.536000, rms=0.459 (0.325%), neg=0, invalid=762 0480: dt=1.024000, rms=0.459 (0.034%), neg=0, invalid=762 0481: dt=1.024000, rms=0.459 (0.007%), neg=0, invalid=762 0482: dt=1.024000, rms=0.459 (-0.072%), 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=0.452, neg=0, invalid=762 iter 0, gcam->neg = 774 after 17 iterations, nbhd size=1, neg = 0 0483: dt=2.301864, rms=0.422 (6.518%), neg=0, invalid=762 0484: dt=0.096000, rms=0.422 (0.070%), neg=0, invalid=762 0485: dt=0.096000, rms=0.422 (-0.086%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.423, neg=0, invalid=762 0486: dt=0.064000, rms=0.422 (0.226%), neg=0, invalid=762 0487: dt=0.005000, rms=0.422 (0.004%), neg=0, invalid=762 0488: dt=0.005000, rms=0.422 (-0.000%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.407, neg=0, invalid=762 0489: dt=0.000000, rms=0.407 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.407, neg=0, invalid=762 0490: dt=92.480000, rms=0.407 (0.018%), neg=0, invalid=762 0491: dt=129.472000, rms=0.407 (0.011%), neg=0, invalid=762 0492: dt=129.472000, rms=0.407 (-0.001%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.407, neg=0, invalid=762 0493: dt=-0.002930, rms=0.407 (0.000%), neg=0, invalid=762 0494: dt=0.000000, rms=0.407 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.407, neg=0, invalid=762 0495: dt=103.680000, rms=0.407 (0.061%), neg=0, invalid=762 0496: dt=103.680000, rms=0.407 (0.051%), neg=0, invalid=762 0497: dt=103.680000, rms=0.407 (-0.015%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.408, neg=0, invalid=762 0498: dt=11.200000, rms=0.407 (0.136%), neg=0, invalid=762 0499: dt=11.200000, rms=0.407 (0.064%), neg=0, invalid=762 0500: dt=11.200000, rms=0.407 (0.035%), neg=0, invalid=762 0501: dt=11.200000, rms=0.407 (-0.012%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.407, neg=0, invalid=762 0502: dt=58.336283, rms=0.404 (0.630%), neg=0, invalid=762 0503: dt=32.000000, rms=0.403 (0.302%), neg=0, invalid=762 0504: dt=44.800000, rms=0.402 (0.174%), neg=0, invalid=762 0505: dt=44.800000, rms=0.402 (0.113%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0506: dt=44.800000, rms=0.401 (0.276%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 9 iterations, nbhd size=1, neg = 0 0507: dt=44.800000, rms=0.400 (0.206%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0508: dt=44.800000, rms=0.399 (0.260%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 10 iterations, nbhd size=1, neg = 0 0509: dt=44.800000, rms=0.398 (0.177%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 0510: dt=44.800000, rms=0.397 (0.208%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 3 iterations, nbhd size=0, neg = 0 0511: dt=44.800000, rms=0.397 (0.129%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 9 iterations, nbhd size=1, neg = 0 0512: dt=44.800000, rms=0.396 (0.083%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 11 iterations, nbhd size=1, neg = 0 0513: dt=44.800000, rms=0.396 (0.115%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 0 iterations, nbhd size=0, neg = 0 0514: dt=44.800000, rms=0.396 (0.085%), neg=0, invalid=762 0515: dt=11.200000, rms=0.396 (0.015%), neg=0, invalid=762 0516: dt=11.200000, rms=0.396 (0.005%), neg=0, invalid=762 0517: dt=11.200000, rms=0.396 (0.005%), neg=0, invalid=762 0518: dt=11.200000, rms=0.396 (0.004%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.401, neg=0, invalid=762 0519: dt=0.432000, rms=0.401 (0.001%), neg=0, invalid=762 0520: dt=0.063000, rms=0.401 (0.000%), neg=0, invalid=762 0521: dt=0.063000, rms=0.401 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.401, neg=0, invalid=762 0522: dt=2.666667, rms=0.400 (0.016%), neg=0, invalid=762 0523: dt=0.864000, rms=0.400 (0.001%), neg=0, invalid=762 0524: dt=0.864000, rms=0.400 (-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=0.410, neg=0, invalid=762 0525: dt=0.000000, rms=0.410 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.410, neg=0, invalid=762 0526: dt=0.112000, rms=0.410 (0.004%), neg=0, invalid=762 0527: dt=0.096000, rms=0.410 (0.001%), neg=0, invalid=762 0528: dt=0.096000, rms=0.410 (-0.001%), 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=0.395, neg=0, invalid=762 iter 0, gcam->neg = 614 after 14 iterations, nbhd size=1, neg = 0 0529: dt=1.280000, rms=0.386 (2.206%), neg=0, invalid=762 0530: dt=0.000020, rms=0.386 (0.000%), neg=0, invalid=762 0531: dt=0.000020, rms=0.386 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.386, neg=0, invalid=762 0532: dt=0.080000, rms=0.386 (0.035%), neg=0, invalid=762 0533: dt=0.028000, rms=0.386 (0.006%), neg=0, invalid=762 0534: dt=0.028000, rms=0.386 (0.003%), neg=0, invalid=762 0535: dt=0.028000, rms=0.386 (-0.005%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 1 hours, 33 minutes and 4 seconds. mri_ca_register utimesec 7487.817123 mri_ca_register stimesec 13.527544 mri_ca_register ru_maxrss 1332672 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 16108715 mri_ca_register ru_majflt 5 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 740 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 34112 mri_ca_register ru_nivcsw 2128 FSRUNTIME@ mri_ca_register 1.5510 hours 7 threads #-------------------------------------- #@# SubCort Seg Thu Mar 7 08:38:01 UTC 2019 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz sysname Linux hostname c14n09.farnam.hpc.yale.internal machine x86_64 setenv SUBJECTS_DIR /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer cd /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz == Number of threads available to mri_ca_label for OpenMP = 7 == relabeling unlikely voxels with window_size = 9 and prior threshold 0.30 using Gibbs prior factor = 0.500 renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes reading classifier array from /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca reading input volume from norm.mgz average std[0] = 7.3 reading transform from transforms/talairach.m3z setting orig areas to linear transform determinant scaled 6.06 Atlas used for the 3D morph was /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca average std = 7.3 using min determinant for regularization = 5.3 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.16259 (20) mri peak = 0.14728 (14) Left_Lateral_Ventricle (4): linear fit = 0.70 x + 0.0 (4676 voxels, overlap=0.444) Left_Lateral_Ventricle (4): linear fit = 0.70 x + 0.0 (4676 voxels, peak = 14), gca=14.1 gca peak = 0.17677 (13) mri peak = 0.13154 (16) Right_Lateral_Ventricle (43): linear fit = 1.11 x + 0.0 (5351 voxels, overlap=0.744) Right_Lateral_Ventricle (43): linear fit = 1.11 x + 0.0 (5351 voxels, peak = 14), gca=14.4 gca peak = 0.28129 (95) mri peak = 0.11909 (95) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (529 voxels, overlap=1.011) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (529 voxels, peak = 96), gca=96.4 gca peak = 0.16930 (96) mri peak = 0.13131 (98) Left_Pallidum (13): linear fit = 1.03 x + 0.0 (491 voxels, overlap=0.866) Left_Pallidum (13): linear fit = 1.03 x + 0.0 (491 voxels, peak = 99), gca=99.4 gca peak = 0.24553 (55) mri peak = 0.10494 (66) Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (1153 voxels, overlap=0.279) Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (1153 voxels, peak = 64), gca=63.5 gca peak = 0.30264 (59) mri peak = 0.08432 (63) Left_Hippocampus (17): linear fit = 1.11 x + 0.0 (1134 voxels, overlap=0.718) Left_Hippocampus (17): linear fit = 1.11 x + 0.0 (1134 voxels, peak = 65), gca=65.2 gca peak = 0.07580 (103) mri peak = 0.08785 (104) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (38049 voxels, overlap=0.693) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (38049 voxels, peak = 106), gca=105.6 gca peak = 0.07714 (104) mri peak = 0.12042 (107) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (40738 voxels, overlap=0.566) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (40738 voxels, peak = 107), gca=106.6 gca peak = 0.09712 (58) mri peak = 0.03479 (63) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (22041 voxels, overlap=0.946) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (22041 voxels, peak = 59), gca=59.4 gca peak = 0.11620 (58) mri peak = 0.03252 (66) Right_Cerebral_Cortex (42): linear fit = 1.10 x + 0.0 (22936 voxels, overlap=0.944) Right_Cerebral_Cortex (42): linear fit = 1.10 x + 0.0 (22936 voxels, peak = 64), gca=63.5 gca peak = 0.30970 (66) mri peak = 0.15625 (74) Right_Caudate (50): linear fit = 1.10 x + 0.0 (888 voxels, overlap=0.164) Right_Caudate (50): linear fit = 1.10 x + 0.0 (888 voxels, peak = 72), gca=72.3 gca peak = 0.15280 (69) mri peak = 0.12296 (78) Left_Caudate (11): linear fit = 1.04 x + 0.0 (797 voxels, overlap=0.675) Left_Caudate (11): linear fit = 1.04 x + 0.0 (797 voxels, peak = 72), gca=72.1 gca peak = 0.13902 (56) mri peak = 0.05753 (63) Left_Cerebellum_Cortex (8): linear fit = 1.13 x + 0.0 (24798 voxels, overlap=0.721) Left_Cerebellum_Cortex (8): linear fit = 1.13 x + 0.0 (24798 voxels, peak = 64), gca=63.6 gca peak = 0.14777 (55) mri peak = 0.05990 (64) Right_Cerebellum_Cortex (47): linear fit = 1.15 x + 0.0 (28423 voxels, overlap=0.587) Right_Cerebellum_Cortex (47): linear fit = 1.15 x + 0.0 (28423 voxels, peak = 64), gca=63.5 gca peak = 0.16765 (84) mri peak = 0.11662 (88) Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (5744 voxels, overlap=0.810) Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (5744 voxels, peak = 87), gca=86.9 gca peak = 0.18739 (84) mri peak = 0.12141 (87) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (5591 voxels, overlap=0.742) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (5591 voxels, peak = 87), gca=86.9 gca peak = 0.29869 (57) mri peak = 0.12321 (67) Left_Amygdala (18): linear fit = 1.12 x + 0.0 (453 voxels, overlap=0.049) Left_Amygdala (18): linear fit = 1.12 x + 0.0 (453 voxels, peak = 64), gca=63.6 gca peak = 0.33601 (57) mri peak = 0.12323 (63) Right_Amygdala (54): linear fit = 1.12 x + 0.0 (496 voxels, overlap=0.289) Right_Amygdala (54): linear fit = 1.12 x + 0.0 (496 voxels, peak = 64), gca=63.6 gca peak = 0.11131 (90) mri peak = 0.07426 (87) Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (4179 voxels, overlap=0.997) Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (4179 voxels, peak = 89), gca=88.7 gca peak = 0.11793 (83) mri peak = 0.08711 (84) Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (4051 voxels, overlap=0.978) Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (4051 voxels, peak = 85), gca=85.1 gca peak = 0.08324 (81) mri peak = 0.09508 (85) Left_Putamen (12): linear fit = 1.07 x + 0.0 (1494 voxels, overlap=0.632) Left_Putamen (12): linear fit = 1.07 x + 0.0 (1494 voxels, peak = 86), gca=86.3 gca peak = 0.10360 (77) mri peak = 0.08333 (78) Right_Putamen (51): linear fit = 1.03 x + 0.0 (1464 voxels, overlap=0.844) Right_Putamen (51): linear fit = 1.03 x + 0.0 (1464 voxels, peak = 80), gca=79.7 gca peak = 0.08424 (78) mri peak = 0.11696 (83) Brain_Stem (16): linear fit = 1.03 x + 0.0 (12040 voxels, overlap=0.476) Brain_Stem (16): linear fit = 1.03 x + 0.0 (12040 voxels, peak = 81), gca=80.7 gca peak = 0.12631 (89) mri peak = 0.08095 (91) Right_VentralDC (60): linear fit = 1.05 x + 0.0 (1326 voxels, overlap=0.562) Right_VentralDC (60): linear fit = 1.05 x + 0.0 (1326 voxels, peak = 94), gca=93.9 gca peak = 0.14500 (87) mri peak = 0.08014 (94) Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1221 voxels, overlap=0.583) Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1221 voxels, peak = 93), gca=92.7 gca peak = 0.14975 (24) mri peak = 0.19048 (18) gca peak = 0.19357 (14) mri peak = 0.14059 (16) Fourth_Ventricle (15): linear fit = 1.03 x + 0.0 (441 voxels, overlap=0.793) Fourth_Ventricle (15): linear fit = 1.03 x + 0.0 (441 voxels, peak = 14), gca=14.5 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 1.00000 (94) gca peak Third_Ventricle = 0.14975 (24) gca peak CSF = 0.23379 (36) gca peak Left_Accumbens_area = 0.70037 (62) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.24655 (23) gca peak Right_Accumbens_area = 0.45042 (65) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.65475 (32) gca peak WM_hypointensities = 0.07854 (76) gca peak non_WM_hypointensities = 0.08491 (43) gca peak Optic_Chiasm = 0.71127 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.10 x + 0.0 estimating mean wm scale to be 1.02 x + 0.0 estimating mean csf scale to be 0.95 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.19920 (14) mri peak = 0.14728 (14) Left_Lateral_Ventricle (4): linear fit = 1.03 x + 0.0 (4676 voxels, overlap=0.955) Left_Lateral_Ventricle (4): linear fit = 1.03 x + 0.0 (4676 voxels, peak = 14), gca=14.5 gca peak = 0.21141 (14) mri peak = 0.13154 (16) Right_Lateral_Ventricle (43): linear fit = 1.03 x + 0.0 (5351 voxels, overlap=0.658) Right_Lateral_Ventricle (43): linear fit = 1.03 x + 0.0 (5351 voxels, peak = 14), gca=14.5 gca peak = 0.25981 (97) mri peak = 0.11909 (95) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (529 voxels, overlap=1.011) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (529 voxels, peak = 97), gca=96.5 gca peak = 0.16005 (100) mri peak = 0.13131 (98) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (491 voxels, overlap=1.000) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (491 voxels, peak = 100), gca=100.5 gca peak = 0.24653 (64) mri peak = 0.10494 (66) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (1153 voxels, overlap=1.002) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (1153 voxels, peak = 63), gca=63.0 gca peak = 0.28515 (62) mri peak = 0.08432 (63) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (1134 voxels, overlap=1.010) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (1134 voxels, peak = 62), gca=62.0 gca peak = 0.07614 (105) mri peak = 0.08785 (104) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (38049 voxels, overlap=0.790) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (38049 voxels, peak = 104), gca=104.5 gca peak = 0.07686 (107) mri peak = 0.12042 (107) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (40738 voxels, overlap=0.677) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (40738 voxels, peak = 107), gca=107.0 gca peak = 0.09477 (59) mri peak = 0.03479 (63) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (22041 voxels, overlap=0.970) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (22041 voxels, peak = 60), gca=60.5 gca peak = 0.10586 (64) mri peak = 0.03252 (66) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (22936 voxels, overlap=0.981) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (22936 voxels, peak = 66), gca=65.6 gca peak = 0.25611 (73) mri peak = 0.15625 (74) Right_Caudate (50): linear fit = 1.00 x + 0.0 (888 voxels, overlap=1.002) Right_Caudate (50): linear fit = 1.00 x + 0.0 (888 voxels, peak = 73), gca=73.0 gca peak = 0.15386 (72) mri peak = 0.12296 (78) Left_Caudate (11): linear fit = 1.00 x + 0.0 (797 voxels, overlap=0.997) Left_Caudate (11): linear fit = 1.00 x + 0.0 (797 voxels, peak = 72), gca=72.0 gca peak = 0.12556 (63) mri peak = 0.05753 (63) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (24798 voxels, overlap=0.996) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (24798 voxels, peak = 63), gca=63.0 gca peak = 0.13035 (63) mri peak = 0.05990 (64) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (28423 voxels, overlap=0.994) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (28423 voxels, peak = 63), gca=63.0 gca peak = 0.15906 (87) mri peak = 0.11662 (88) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5744 voxels, overlap=0.926) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5744 voxels, peak = 87), gca=87.0 gca peak = 0.18381 (87) mri peak = 0.12141 (87) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5591 voxels, overlap=0.890) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5591 voxels, peak = 87), gca=86.6 gca peak = 0.24255 (65) mri peak = 0.12321 (67) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (453 voxels, overlap=1.015) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (453 voxels, peak = 66), gca=66.0 gca peak = 0.31457 (64) mri peak = 0.12323 (63) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (496 voxels, overlap=1.004) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (496 voxels, peak = 64), gca=64.0 gca peak = 0.09639 (87) mri peak = 0.07426 (87) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4179 voxels, overlap=0.993) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4179 voxels, peak = 87), gca=86.6 gca peak = 0.11296 (85) mri peak = 0.08711 (84) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4051 voxels, overlap=0.991) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4051 voxels, peak = 85), gca=84.6 gca peak = 0.08593 (80) mri peak = 0.09508 (85) Left_Putamen (12): linear fit = 1.01 x + 0.0 (1494 voxels, overlap=0.814) Left_Putamen (12): linear fit = 1.01 x + 0.0 (1494 voxels, peak = 81), gca=81.2 gca peak = 0.10883 (78) mri peak = 0.08333 (78) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1464 voxels, overlap=0.945) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1464 voxels, peak = 78), gca=78.0 gca peak = 0.08697 (81) mri peak = 0.11696 (83) Brain_Stem (16): linear fit = 1.01 x + 0.0 (12040 voxels, overlap=0.619) Brain_Stem (16): linear fit = 1.01 x + 0.0 (12040 voxels, peak = 82), gca=82.2 gca peak = 0.13365 (94) mri peak = 0.08095 (91) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (1326 voxels, overlap=0.791) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (1326 voxels, peak = 95), gca=95.4 gca peak = 0.16753 (91) mri peak = 0.08014 (94) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1221 voxels, overlap=0.876) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1221 voxels, peak = 91), gca=90.5 gca peak = 0.16744 (24) mri peak = 0.19048 (18) gca peak = 0.18343 (17) mri peak = 0.14059 (16) Fourth_Ventricle (15): linear fit = 1.00 x + 0.0 (441 voxels, overlap=0.778) Fourth_Ventricle (15): linear fit = 1.00 x + 0.0 (441 voxels, peak = 17), gca=17.0 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16057 (30) gca peak Left_Thalamus = 0.64095 (103) gca peak Third_Ventricle = 0.16744 (24) gca peak CSF = 0.22075 (34) gca peak Left_Accumbens_area = 0.73030 (65) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75962 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.18678 (27) gca peak Right_Accumbens_area = 0.29961 (71) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.65358 (30) gca peak WM_hypointensities = 0.07808 (78) gca peak non_WM_hypointensities = 0.07502 (56) gca peak Optic_Chiasm = 0.70630 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.01 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.02 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 56271 voxels changed in iteration 0 of unlikely voxel relabeling 226 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 37106 gm and wm labels changed (%25 to gray, %75 to white out of all changed labels) 341 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 61853 changed. image ll: -2.080, PF=0.500 pass 2: 17131 changed. image ll: -2.080, PF=0.500 pass 3: 5092 changed. pass 4: 1665 changed. 39229 voxels changed in iteration 0 of unlikely voxel relabeling 264 voxels changed in iteration 1 of unlikely voxel relabeling 7 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 6781 voxels changed in iteration 0 of unlikely voxel relabeling 65 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 5240 voxels changed in iteration 0 of unlikely voxel relabeling 37 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 4487 voxels changed in iteration 0 of unlikely voxel relabeling 40 voxels changed in iteration 1 of unlikely voxel relabeling 1 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling MRItoUCHAR: min=0, max=85 MRItoUCHAR: converting to UCHAR writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 2052.888863 mri_ca_label stimesec 3.462428 mri_ca_label ru_maxrss 2115100 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 4845759 mri_ca_label ru_majflt 5 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 850 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 883 mri_ca_label ru_nivcsw 182 auto-labeling took 33 minutes and 17 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/transforms/cc_up.lta sub-030 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/transforms/cc_up.lta reading aseg from /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/aseg.auto_noCCseg.mgz reading norm from /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/norm.mgz 29131 voxels in left wm, 67581 in right wm, xrange [121, 132] searching rotation angles z=[-8 6], y=[-9 5] searching scale 1 Z rot -8.0 searching scale 1 Z rot -7.7 searching scale 1 Z rot -7.5 searching scale 1 Z rot -7.2 searching scale 1 Z rot -7.0 searching scale 1 Z rot -6.7 searching scale 1 Z rot -6.5 searching scale 1 Z rot -6.2 searching scale 1 Z rot -6.0 searching scale 1 Z rot -5.7 searching scale 1 Z rot -5.5 searching scale 1 Z rot -5.2 searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.7 searching scale 1 Z rot -4.5 searching scale 1 Z rot -4.2 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.7 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 global minimum found at slice 128.0, rotations (-1.60, -1.24) final transformation (x=128.0, yr=-1.604, zr=-1.239): 0.99937 0.02161 -0.02799 1.28075; -0.02161 0.99977 0.00061 47.72025; 0.02799 0.00000 0.99961 17.45864; 0.00000 0.00000 0.00000 1.00000; updating x range to be [126, 131] in xformed coordinates best xformed slice 128 cc center is found at 128 83 107 eigenvectors: 0.00004 -0.00095 1.00000; -0.05469 -0.99850 -0.00095; 0.99850 -0.05469 -0.00009; error in mid anterior detected - correcting... writing aseg with callosum to /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/aseg.auto.mgz... corpus callosum segmentation took 0.7 minutes #-------------------------------------- #@# Merge ASeg Thu Mar 7 09:11:58 UTC 2019 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Thu Mar 7 09:11:58 UTC 2019 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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... 326 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 71 (71), valley at 23 (23) csf peak at 36, 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 71 (71), valley at 23 (23) csf peak at 36, setting threshold to 59 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 2 minutes and 3 seconds. #-------------------------------------------- #@# Mask BFS Thu Mar 7 09:14:02 UTC 2019 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1383556 voxels in mask (pct= 8.25) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Thu Mar 7 09:14:03 UTC 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 (104.0): 104.4 +- 4.9 [79.0 --> 125.0] GM (72.0) : 70.0 +- 10.1 [30.0 --> 95.0] setting bottom of white matter range to 80.1 setting top of gray matter range to 90.2 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 4063 sparsely connected voxels removed... thickening thin strands.... 20 segments, 2628 filled 26 bright non-wm voxels segmented. 2267 diagonally connected voxels added... white matter segmentation took 1.0 minutes writing output to wm.seg.mgz... assuming input volume is MGH (Van der Kouwe) MP-RAGE mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.39 minutes reading wm segmentation from wm.seg.mgz... 744 voxels added to wm to prevent paths from MTL structures to cortex 3224 additional wm voxels added 0 additional wm voxels added SEG EDIT: 65495 voxels turned on, 46025 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 0 new 0 115,126,128 old 0 new 0 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 20 found - 20 modified | TOTAL: 20 pass 2 (xy+): 0 found - 20 modified | TOTAL: 20 pass 1 (xy-): 15 found - 15 modified | TOTAL: 35 pass 2 (xy-): 0 found - 15 modified | TOTAL: 35 pass 1 (yz+): 18 found - 18 modified | TOTAL: 53 pass 2 (yz+): 0 found - 18 modified | TOTAL: 53 pass 1 (yz-): 18 found - 18 modified | TOTAL: 71 pass 2 (yz-): 0 found - 18 modified | TOTAL: 71 pass 1 (xz+): 15 found - 15 modified | TOTAL: 86 pass 2 (xz+): 0 found - 15 modified | TOTAL: 86 pass 1 (xz-): 13 found - 13 modified | TOTAL: 99 pass 2 (xz-): 0 found - 13 modified | TOTAL: 99 Iteration Number : 1 pass 1 (+++): 6 found - 6 modified | TOTAL: 6 pass 2 (+++): 0 found - 6 modified | TOTAL: 6 pass 1 (+++): 14 found - 14 modified | TOTAL: 20 pass 2 (+++): 0 found - 14 modified | TOTAL: 20 pass 1 (+++): 8 found - 8 modified | TOTAL: 28 pass 2 (+++): 0 found - 8 modified | TOTAL: 28 pass 1 (+++): 1 found - 1 modified | TOTAL: 29 pass 2 (+++): 0 found - 1 modified | TOTAL: 29 Iteration Number : 1 pass 1 (++): 63 found - 63 modified | TOTAL: 63 pass 2 (++): 0 found - 63 modified | TOTAL: 63 pass 1 (+-): 34 found - 34 modified | TOTAL: 97 pass 2 (+-): 0 found - 34 modified | TOTAL: 97 pass 1 (--): 73 found - 73 modified | TOTAL: 170 pass 2 (--): 0 found - 73 modified | TOTAL: 170 pass 1 (-+): 52 found - 52 modified | TOTAL: 222 pass 2 (-+): 0 found - 52 modified | TOTAL: 222 Iteration Number : 2 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 2 found - 2 modified | TOTAL: 5 pass 2 (xy-): 0 found - 2 modified | TOTAL: 5 pass 1 (yz+): 2 found - 2 modified | TOTAL: 7 pass 2 (yz+): 0 found - 2 modified | TOTAL: 7 pass 1 (yz-): 1 found - 1 modified | TOTAL: 8 pass 2 (yz-): 0 found - 1 modified | TOTAL: 8 pass 1 (xz+): 2 found - 2 modified | TOTAL: 10 pass 2 (xz+): 0 found - 2 modified | TOTAL: 10 pass 1 (xz-): 2 found - 2 modified | TOTAL: 12 pass 2 (xz-): 0 found - 2 modified | TOTAL: 12 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 4 Iteration Number : 2 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 1 found - 1 modified | TOTAL: 2 pass 2 (+-): 0 found - 1 modified | TOTAL: 2 pass 1 (--): 0 found - 0 modified | TOTAL: 2 pass 1 (-+): 1 found - 1 modified | TOTAL: 3 pass 2 (-+): 0 found - 1 modified | TOTAL: 3 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 370 (out of 557796: 0.066332) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Thu Mar 7 09:15:30 UTC 2019 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 1.12725 -0.00519 -0.02741 -14.77138; 0.00851 1.11452 0.17515 -14.55440; 0.02707 -0.12405 1.02986 -0.96066; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.12725 -0.00519 -0.02741 -14.77138; 0.00851 1.11452 0.17515 -14.55440; 0.02707 -0.12405 1.02986 -0.96066; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1556 (min = 350, max = 1400), aspect = 0.48 (min = 0.10, max = 0.75) need search nearby using seed (126, 106, 89), TAL = (2.0, -39.0, 22.0) talairach voxel to voxel transform 0.88653 0.00663 0.02247 13.21334; -0.00305 0.88055 -0.14984 12.62694; -0.02367 0.10589 0.95237 2.10643; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (126, 106, 89) --> (2.0, -39.0, 22.0) done. writing output to filled.mgz... filling took 0.5 minutes talairach cc position changed to (2.00, -39.00, 22.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, -39.00, 22.00) SRC: (111.66, 92.30, 95.54) search lh wm seed point around talairach space (-16.00, -39.00, 22.00), SRC: (143.58, 92.19, 94.68) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... Started at Thu Mar 7 07:00:29 UTC 2019 Ended at Thu Mar 7 09:15:59 UTC 2019 #@#%# recon-all-run-time-hours 2.258 recon-all -s sub-030 finished without error at Thu Mar 7 09:15:59 UTC 2019 New invocation of recon-all Thu Mar 7 11:05:16 UTC 2019 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030 /opt/freesurfer/bin/recon-all -autorecon3 -hemi lh -openmp 7 -subjid sub-030 -sd /home/mc2835/scratch60/RVLdata/fmriprep_output/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial subjid sub-030 setenv SUBJECTS_DIR /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /opt/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a Linux c14n09.farnam.hpc.yale.internal 3.10.0-693.37.4.el7.x86_64 #1 SMP Fri Aug 10 12:34:55 EDT 2018 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize unlimited memoryuse 65536000 kbytes vmemoryuse unlimited descriptors 51200 memorylocked unlimited maxproc 512036 maxlocks unlimited maxsignal 512036 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 131317832 20388484 76023304 654424 34906044 109524700 Swap: 16777212 151228 16625984 ######################################## 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: 2019/03/07-11:05:16-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:05:16-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:05:16-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-11:05:16-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:05:16-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:05:16-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-11:05:16-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-11:05:16-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-11:05:16-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-11:05:16-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-11:05:16-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-11:05:16-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:05:16-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:05:16-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-11:05:16-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:05:16-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:05:16-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:05:16-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:05:16-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:05:16-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:05:16-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-11:05:16-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:05:16-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:05:16-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:05:16-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-11:05:16-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:05:16-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-11:05:16-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:05:16-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:05:16-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:05:16-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:05:16-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:05:16-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:05:16-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:05:16-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:05:16-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:05:16-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:05:16-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:05:16-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /opt/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /opt/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #-------------------------------------------- #@# Cortical ribbon mask Thu Mar 7 11:05:16 UTC 2019 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri mris_volmask --aseg_name aseg.presurf --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon sub-030 SUBJECTS_DIR is /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer loading input data... computing distance to left white surface computing distance to left pial surface computing distance to right white surface computing distance to right pial surface hemi masks overlap voxels = 139 writing volume /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/ribbon.mgz mris_volmask took 6.78 minutes writing ribbon files #----------------------------------------- #@# Parcellation Stats lh Thu Mar 7 11:12:03 UTC 2019 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab sub-030 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/wm.mgz... reading input surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.white... reading input pial surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.pial... reading input white surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 217681 Total vertex volume 214128 (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) = 1538061 mm^3 (det: 1.266599 ) lhCtxGM: 213847.814 213400.000 diff= 447.8 pctdiff= 0.209 rhCtxGM: 213971.072 213772.000 diff= 199.1 pctdiff= 0.093 lhCtxWM: 231001.158 231265.500 diff= -264.3 pctdiff=-0.114 rhCtxWM: 233007.839 233280.500 diff= -272.7 pctdiff=-0.117 SubCortGMVol 51692.000 SupraTentVol 978048.883 (976068.000) diff=1980.883 pctdiff=0.203 SupraTentVolNotVent 945447.883 (943467.000) diff=1980.883 pctdiff=0.210 BrainSegVol 1113758.000 (1110375.000) diff=3383.000 pctdiff=0.304 BrainSegVolNotVent 1076419.000 (1076405.883) diff=13.117 pctdiff=0.001 BrainSegVolNotVent 1076419.000 CerebellumVol 132829.000 VentChorVol 32601.000 3rd4th5thCSF 4738.000 CSFVol 1355.000, OptChiasmVol 123.000 MaskVol 1386316.000 1167 825 1749 2.141 0.382 0.110 0.021 9 0.9 bankssts 1016 625 1490 2.321 0.627 0.149 0.018 19 0.7 caudalanteriorcingulate 2797 1908 5082 2.480 0.598 0.121 0.022 27 2.6 caudalmiddlefrontal 1969 1297 2543 1.818 0.539 0.155 0.030 32 2.3 cuneus 492 363 2171 4.020 0.701 0.133 0.031 6 0.6 entorhinal 4192 2985 8239 2.403 0.617 0.139 0.033 55 5.6 fusiform 6298 4315 9697 2.107 0.534 0.145 0.032 91 8.2 inferiorparietal 4849 3414 10511 2.488 0.646 0.158 0.047 102 10.1 inferiortemporal 1693 1096 2656 2.140 0.669 0.145 0.039 30 2.7 isthmuscingulate 8355 5411 11528 1.998 0.517 0.151 0.035 119 12.3 lateraloccipital 3849 2627 7172 2.572 0.644 0.141 0.035 53 5.6 lateralorbitofrontal 4146 2837 5635 1.903 0.530 0.151 0.033 60 5.7 lingual 3064 2129 5334 2.337 0.597 0.136 0.036 50 4.5 medialorbitofrontal 4545 3226 10311 2.573 0.649 0.150 0.034 72 6.8 middletemporal 994 654 1640 2.166 0.562 0.090 0.017 7 0.7 parahippocampal 2084 1352 3588 2.345 0.555 0.118 0.027 18 2.4 paracentral 2972 2035 5215 2.346 0.541 0.133 0.028 37 3.4 parsopercularis 1139 782 2804 2.742 0.592 0.171 0.051 23 2.6 parsorbitalis 2476 1687 4173 2.190 0.514 0.137 0.033 36 3.1 parstriangularis 1627 1094 1408 1.443 0.293 0.126 0.029 14 1.8 pericalcarine 6688 4326 8862 1.873 0.572 0.127 0.030 82 8.5 postcentral 2113 1434 3260 2.142 0.679 0.149 0.027 36 2.2 posteriorcingulate 7808 4972 13553 2.444 0.607 0.113 0.025 66 8.0 precentral 5290 3623 8332 2.213 0.476 0.144 0.035 68 7.5 precuneus 1392 936 2636 2.632 0.653 0.137 0.030 23 1.6 rostralanteriorcingulate 6809 4747 11934 2.259 0.492 0.144 0.036 102 10.3 rostralmiddlefrontal 10491 7041 20501 2.596 0.512 0.132 0.030 128 12.6 superiorfrontal 8103 5353 12588 2.070 0.604 0.136 0.029 100 9.5 superiorparietal 5291 3614 10240 2.531 0.677 0.120 0.025 54 5.4 superiortemporal 5571 3865 8987 2.178 0.501 0.147 0.040 80 9.4 supramarginal 350 239 804 2.544 0.545 0.182 0.070 11 0.9 frontalpole 772 555 2068 2.808 0.797 0.163 0.041 12 1.7 temporalpole 631 388 870 2.045 0.340 0.106 0.022 5 0.5 transversetemporal 3527 2367 6532 2.841 0.779 0.120 0.031 39 4.0 insula mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab sub-030 lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/wm.mgz... reading input surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.pial... reading input pial surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.pial... reading input white surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 217681 Total vertex volume 214128 (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) = 1538061 mm^3 (det: 1.266599 ) lhCtxGM: 213847.814 213400.000 diff= 447.8 pctdiff= 0.209 rhCtxGM: 213971.072 213772.000 diff= 199.1 pctdiff= 0.093 lhCtxWM: 231001.158 231265.500 diff= -264.3 pctdiff=-0.114 rhCtxWM: 233007.839 233280.500 diff= -272.7 pctdiff=-0.117 SubCortGMVol 51692.000 SupraTentVol 978048.883 (976068.000) diff=1980.883 pctdiff=0.203 SupraTentVolNotVent 945447.883 (943467.000) diff=1980.883 pctdiff=0.210 BrainSegVol 1113758.000 (1110375.000) diff=3383.000 pctdiff=0.304 BrainSegVolNotVent 1076419.000 (1076405.883) diff=13.117 pctdiff=0.001 BrainSegVolNotVent 1076419.000 CerebellumVol 132829.000 VentChorVol 32601.000 3rd4th5thCSF 4738.000 CSFVol 1355.000, OptChiasmVol 123.000 MaskVol 1386316.000 1167 845 1749 2.141 0.382 0.132 0.030 22 1.6 bankssts 1016 676 1490 2.321 0.627 0.134 0.033 26 1.2 caudalanteriorcingulate 2797 2189 5082 2.480 0.598 0.129 0.028 41 3.5 caudalmiddlefrontal 1969 1525 2543 1.818 0.539 0.131 0.036 26 2.6 cuneus 492 717 2171 4.020 0.701 0.203 0.040 7 0.9 entorhinal 4192 3720 8239 2.403 0.617 0.160 0.040 67 7.6 fusiform 6298 4972 9697 2.107 0.534 0.144 0.033 92 9.0 inferiorparietal 4849 4842 10511 2.488 0.646 0.183 0.043 82 10.3 inferiortemporal 1693 1364 2656 2.140 0.669 0.153 0.042 35 3.1 isthmuscingulate 8355 6242 11528 1.998 0.517 0.131 0.030 110 11.6 lateraloccipital 3849 2954 7172 2.572 0.644 0.135 0.033 55 5.4 lateralorbitofrontal 4146 3259 5635 1.903 0.530 0.138 0.035 63 6.5 lingual 3064 2471 5334 2.337 0.597 0.136 0.032 37 4.3 medialorbitofrontal 4545 4581 10311 2.573 0.649 0.176 0.039 64 8.3 middletemporal 994 885 1640 2.166 0.562 0.119 0.025 6 1.2 parahippocampal 2084 1729 3588 2.345 0.555 0.130 0.029 20 2.8 paracentral 2972 2456 5215 2.346 0.541 0.136 0.029 33 4.0 parsopercularis 1139 1200 2804 2.742 0.592 0.181 0.042 14 2.3 parsorbitalis 2476 2080 4173 2.190 0.514 0.157 0.033 32 3.6 parstriangularis 1627 944 1408 1.443 0.293 0.115 0.028 19 2.0 pericalcarine 6688 5143 8862 1.873 0.572 0.129 0.029 66 8.4 postcentral 2113 1570 3260 2.142 0.679 0.142 0.030 36 2.8 posteriorcingulate 7808 5872 13553 2.444 0.607 0.116 0.026 74 9.0 precentral 5290 3918 8332 2.213 0.476 0.139 0.034 74 8.0 precuneus 1392 1168 2636 2.632 0.653 0.151 0.032 33 1.9 rostralanteriorcingulate 6809 5709 11934 2.259 0.492 0.157 0.037 125 11.6 rostralmiddlefrontal 10491 8509 20501 2.596 0.512 0.138 0.030 137 13.4 superiorfrontal 8103 6529 12588 2.070 0.604 0.142 0.031 110 11.8 superiorparietal 5291 4362 10240 2.531 0.677 0.140 0.033 77 7.5 superiortemporal 5571 4348 8987 2.178 0.501 0.150 0.036 88 9.4 supramarginal 350 393 804 2.544 0.545 0.210 0.046 4 0.8 frontalpole 772 864 2068 2.808 0.797 0.203 0.044 15 1.8 temporalpole 631 505 870 2.045 0.340 0.112 0.025 6 0.6 transversetemporal 3527 2087 6532 2.841 0.779 0.111 0.031 48 4.2 insula #----------------------------------------- #@# Cortical Parc 2 lh Thu Mar 7 11:12:48 UTC 2019 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-030 lh ../surf/lh.sphere.reg /opt/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 /opt/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... 36 labels changed using aseg relabeling using gibbs priors... 000: 8888 changed, 132838 examined... 001: 2084 changed, 34624 examined... 002: 565 changed, 10862 examined... 003: 250 changed, 3240 examined... 004: 135 changed, 1460 examined... 005: 60 changed, 735 examined... 006: 40 changed, 350 examined... 007: 20 changed, 209 examined... 008: 8 changed, 98 examined... 009: 1 changed, 37 examined... 010: 0 changed, 10 examined... 7 labels changed using aseg 000: 248 total segments, 160 labels (1960 vertices) changed 001: 94 total segments, 6 labels (24 vertices) changed 002: 88 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 35 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 846 vertices marked for relabeling... 846 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 13 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Thu Mar 7 11:13:02 UTC 2019 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab sub-030 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/wm.mgz... reading input surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.white... reading input pial surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.pial... reading input white surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 217681 Total vertex volume 214128 (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) = 1538061 mm^3 (det: 1.266599 ) lhCtxGM: 213847.814 213400.000 diff= 447.8 pctdiff= 0.209 rhCtxGM: 213971.072 213772.000 diff= 199.1 pctdiff= 0.093 lhCtxWM: 231001.158 231265.500 diff= -264.3 pctdiff=-0.114 rhCtxWM: 233007.839 233280.500 diff= -272.7 pctdiff=-0.117 SubCortGMVol 51692.000 SupraTentVol 978048.883 (976068.000) diff=1980.883 pctdiff=0.203 SupraTentVolNotVent 945447.883 (943467.000) diff=1980.883 pctdiff=0.210 BrainSegVol 1113758.000 (1110375.000) diff=3383.000 pctdiff=0.304 BrainSegVolNotVent 1076419.000 (1076405.883) diff=13.117 pctdiff=0.001 BrainSegVolNotVent 1076419.000 CerebellumVol 132829.000 VentChorVol 32601.000 3rd4th5thCSF 4738.000 CSFVol 1355.000, OptChiasmVol 123.000 MaskVol 1386316.000 1148 828 2083 2.305 0.455 0.149 0.042 20 2.4 G&S_frontomargin 1605 1088 2468 2.021 0.539 0.153 0.032 22 2.2 G&S_occipital_inf 1747 1092 3282 2.361 0.599 0.121 0.029 16 2.2 G&S_paracentral 1511 1042 2721 2.306 0.434 0.134 0.029 19 1.7 G&S_subcentral 529 382 1297 2.632 0.421 0.178 0.050 11 1.1 G&S_transv_frontopol 2703 1827 4606 2.459 0.474 0.134 0.027 38 2.8 G&S_cingul-Ant 1360 923 2217 2.430 0.570 0.127 0.020 15 1.1 G&S_cingul-Mid-Ant 1547 1075 2749 2.397 0.503 0.135 0.024 19 1.5 G&S_cingul-Mid-Post 836 581 1798 2.467 0.585 0.168 0.042 16 1.5 G_cingul-Post-dorsal 369 233 706 2.438 0.756 0.156 0.057 8 0.7 G_cingul-Post-ventral 1770 1177 2810 1.917 0.750 0.161 0.033 31 2.2 G_cuneus 1722 1171 3570 2.476 0.493 0.149 0.035 30 2.5 G_front_inf-Opercular 678 414 1438 2.462 0.517 0.141 0.037 15 1.2 G_front_inf-Orbital 1627 1127 3130 2.316 0.496 0.159 0.039 30 2.5 G_front_inf-Triangul 3520 2381 7791 2.550 0.572 0.152 0.036 61 5.4 G_front_middle 7190 4652 15269 2.705 0.518 0.140 0.034 102 9.9 G_front_sup 667 440 1363 3.004 0.796 0.129 0.040 8 0.9 G_Ins_lg&S_cent_ins 809 521 2198 3.315 0.832 0.134 0.034 13 1.0 G_insular_short 2380 1542 4096 2.227 0.565 0.162 0.039 43 3.8 G_occipital_middle 1612 1039 2510 2.088 0.639 0.147 0.034 22 2.1 G_occipital_sup 1798 1261 4079 2.492 0.598 0.147 0.040 32 2.9 G_oc-temp_lat-fusifor 2992 2003 4186 1.859 0.566 0.163 0.040 51 4.9 G_oc-temp_med-Lingual 1147 752 3097 2.998 1.023 0.115 0.026 12 1.2 G_oc-temp_med-Parahip 2667 1798 6041 2.637 0.673 0.161 0.046 50 5.1 G_orbital 2456 1658 4502 2.263 0.588 0.158 0.039 43 3.9 G_pariet_inf-Angular 3002 2098 5625 2.196 0.538 0.156 0.048 55 6.4 G_pariet_inf-Supramar 3280 2148 5684 2.165 0.602 0.142 0.033 47 4.3 G_parietal_sup 2681 1624 3932 1.959 0.669 0.141 0.041 44 4.7 G_postcentral 2758 1618 6132 2.739 0.686 0.113 0.028 29 3.2 G_precentral 2704 1810 5245 2.312 0.565 0.158 0.042 46 4.6 G_precuneus 1250 850 2541 2.358 0.540 0.169 0.053 32 2.8 G_rectus 644 457 1290 2.846 0.865 0.121 0.045 10 0.9 G_subcallosal 476 284 765 2.179 0.297 0.107 0.024 4 0.4 G_temp_sup-G_T_transv 1779 1237 4609 2.729 0.607 0.154 0.041 33 2.8 G_temp_sup-Lateral 761 522 1823 2.945 0.811 0.093 0.017 4 0.4 G_temp_sup-Plan_polar 710 492 1335 2.342 0.450 0.102 0.020 5 0.6 G_temp_sup-Plan_tempo 2801 1933 6703 2.560 0.632 0.166 0.053 73 6.7 G_temporal_inf 2560 1815 6765 2.693 0.627 0.157 0.038 50 4.2 G_temporal_middle 255 166 368 2.201 0.329 0.113 0.027 2 0.2 Lat_Fis-ant-Horizont 377 273 456 2.021 0.501 0.112 0.020 2 0.3 Lat_Fis-ant-Vertical 1086 724 1226 2.160 0.469 0.129 0.026 9 1.2 Lat_Fis-post 2613 1580 3361 1.936 0.537 0.147 0.036 36 3.9 Pole_occipital 1509 1167 5071 3.112 0.835 0.178 0.059 30 4.2 Pole_temporal 2200 1482 2204 1.738 0.555 0.126 0.027 19 2.3 S_calcarine 3258 2200 3521 1.834 0.516 0.107 0.021 21 2.9 S_central 1013 722 1360 2.098 0.364 0.138 0.031 11 1.2 S_cingul-Marginalis 545 370 814 2.663 0.594 0.099 0.016 2 0.4 S_circular_insula_ant 1453 986 2079 2.549 0.661 0.097 0.017 12 1.1 S_circular_insula_inf 1861 1272 2466 2.348 0.548 0.106 0.021 9 1.5 S_circular_insula_sup 775 578 1411 2.409 0.544 0.131 0.025 9 0.8 S_collat_transv_ant 548 354 482 1.879 0.406 0.160 0.035 8 0.8 S_collat_transv_post 2469 1714 3329 2.013 0.401 0.128 0.028 25 2.9 S_front_inf 931 667 1305 2.009 0.420 0.128 0.030 9 1.0 S_front_middle 2114 1515 3299 2.393 0.425 0.103 0.018 12 1.5 S_front_sup 179 133 281 2.266 0.584 0.146 0.030 2 0.2 S_interm_prim-Jensen 2457 1688 2871 1.893 0.329 0.119 0.019 21 1.9 S_intrapariet&P_trans 994 689 1044 1.799 0.342 0.145 0.038 11 1.6 S_oc_middle&Lunatus 1039 715 1338 1.955 0.347 0.133 0.028 10 1.2 S_oc_sup&transversal 842 598 1104 2.034 0.358 0.134 0.026 9 0.9 S_occipital_ant 849 592 1265 2.323 0.423 0.136 0.033 9 1.1 S_oc-temp_lat 1982 1400 2524 2.003 0.455 0.113 0.018 14 1.5 S_oc-temp_med&Lingual 464 333 629 2.027 0.343 0.106 0.016 2 0.3 S_orbital_lateral 701 483 862 2.159 0.460 0.117 0.016 7 0.4 S_orbital_med-olfact 1180 837 2305 2.762 0.655 0.145 0.041 15 2.0 S_orbital-H_Shaped 1641 1089 2011 2.076 0.518 0.122 0.025 15 1.6 S_parieto_occipital 1458 885 1142 1.622 0.626 0.128 0.018 27 0.9 S_pericallosal 3320 2247 3765 1.829 0.371 0.125 0.026 31 3.6 S_postcentral 1830 1250 2571 2.317 0.485 0.117 0.023 14 1.6 S_precentral-inf-part 1412 960 1918 2.209 0.428 0.108 0.019 10 1.2 S_precentral-sup-part 585 409 756 2.233 0.503 0.121 0.021 5 0.6 S_suborbital 1218 859 1730 2.139 0.345 0.151 0.037 15 1.7 S_subparietal 1623 1154 2317 2.145 0.466 0.138 0.024 17 1.8 S_temporal_inf 5589 3878 8077 2.199 0.511 0.124 0.024 52 5.3 S_temporal_sup 397 268 415 1.905 0.387 0.130 0.015 4 0.3 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Thu Mar 7 11:13:23 UTC 2019 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-030 lh ../surf/lh.sphere.reg /opt/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 /opt/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... 1209 labels changed using aseg relabeling using gibbs priors... 000: 1970 changed, 132838 examined... 001: 491 changed, 9099 examined... 002: 128 changed, 2695 examined... 003: 70 changed, 715 examined... 004: 44 changed, 401 examined... 005: 24 changed, 240 examined... 006: 18 changed, 146 examined... 007: 14 changed, 98 examined... 008: 10 changed, 83 examined... 009: 9 changed, 52 examined... 010: 4 changed, 46 examined... 011: 2 changed, 20 examined... 012: 4 changed, 14 examined... 013: 4 changed, 20 examined... 014: 5 changed, 18 examined... 015: 4 changed, 23 examined... 016: 7 changed, 23 examined... 017: 4 changed, 29 examined... 018: 0 changed, 23 examined... 367 labels changed using aseg 000: 46 total segments, 13 labels (160 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 4 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 652 vertices marked for relabeling... 652 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 11 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Thu Mar 7 11:13:34 UTC 2019 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas.stats -b -a ../label/lh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab sub-030 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/wm.mgz... reading input surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.white... reading input pial surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.pial... reading input white surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 217681 Total vertex volume 214128 (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) = 1538061 mm^3 (det: 1.266599 ) lhCtxGM: 213847.814 213400.000 diff= 447.8 pctdiff= 0.209 rhCtxGM: 213971.072 213772.000 diff= 199.1 pctdiff= 0.093 lhCtxWM: 231001.158 231265.500 diff= -264.3 pctdiff=-0.114 rhCtxWM: 233007.839 233280.500 diff= -272.7 pctdiff=-0.117 SubCortGMVol 51692.000 SupraTentVol 978048.883 (976068.000) diff=1980.883 pctdiff=0.203 SupraTentVolNotVent 945447.883 (943467.000) diff=1980.883 pctdiff=0.210 BrainSegVol 1113758.000 (1110375.000) diff=3383.000 pctdiff=0.304 BrainSegVolNotVent 1076419.000 (1076405.883) diff=13.117 pctdiff=0.001 BrainSegVolNotVent 1076419.000 CerebellumVol 132829.000 VentChorVol 32601.000 3rd4th5thCSF 4738.000 CSFVol 1355.000, OptChiasmVol 123.000 MaskVol 1386316.000 1914 1200 3126 2.421 0.580 0.136 0.020 29 1.5 caudalanteriorcingulate 3038 2065 5488 2.469 0.588 0.122 0.024 30 3.2 caudalmiddlefrontal 2615 1724 3750 1.889 0.664 0.147 0.030 38 3.0 cuneus 469 333 1928 3.925 0.801 0.125 0.030 5 0.5 entorhinal 3795 2662 6860 2.324 0.562 0.137 0.031 49 4.7 fusiform 6359 4341 9896 2.112 0.538 0.145 0.032 92 8.1 inferiorparietal 4904 3501 11082 2.529 0.674 0.158 0.047 102 10.5 inferiortemporal 1672 1086 2647 2.161 0.665 0.146 0.040 30 2.7 isthmuscingulate 8300 5378 11634 2.006 0.518 0.150 0.035 117 12.0 lateraloccipital 4139 2860 8152 2.652 0.692 0.148 0.039 63 6.7 lateralorbitofrontal 4297 2933 5753 1.894 0.526 0.153 0.034 63 6.1 lingual 2448 1692 4371 2.327 0.626 0.141 0.041 45 4.2 medialorbitofrontal 5959 4251 12865 2.504 0.633 0.151 0.035 93 9.1 middletemporal 1023 672 1690 2.173 0.581 0.091 0.017 7 0.7 parahippocampal 2492 1616 4230 2.386 0.543 0.118 0.027 21 2.8 paracentral 2804 1907 4896 2.365 0.530 0.135 0.030 37 3.4 parsopercularis 1190 787 2409 2.537 0.557 0.137 0.033 18 1.6 parsorbitalis 3111 2163 5234 2.157 0.520 0.143 0.033 45 4.2 parstriangularis 1650 1111 1418 1.442 0.289 0.125 0.029 13 1.9 pericalcarine 7531 4898 10059 1.894 0.585 0.129 0.031 92 9.8 postcentral 2347 1584 3730 2.186 0.680 0.151 0.028 39 2.7 posteriorcingulate 7666 4890 13309 2.446 0.602 0.113 0.025 64 7.7 precentral 5213 3579 8486 2.243 0.493 0.148 0.036 71 7.5 precuneus 2004 1355 3774 2.575 0.596 0.136 0.029 31 2.2 rostralanteriorcingulate 4760 3278 8645 2.323 0.508 0.141 0.036 66 6.9 rostralmiddlefrontal 10578 7211 20498 2.537 0.541 0.136 0.032 141 13.7 superiorfrontal 6506 4309 9792 2.045 0.542 0.131 0.028 77 7.2 superiorparietal 6898 4717 13579 2.559 0.712 0.122 0.027 72 7.5 superiortemporal 5192 3581 8199 2.163 0.498 0.145 0.039 74 8.7 supramarginal 637 391 875 2.044 0.339 0.107 0.022 5 0.5 transversetemporal 3052 2053 5753 2.802 0.718 0.117 0.027 33 3.2 insula #----------------------------------------- #@# WM/GM Contrast lh Thu Mar 7 11:13:56 UTC 2019 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/scripts pctsurfcon --s sub-030 --lh-only Log file is /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/scripts/pctsurfcon.log Thu Mar 7 11:13:56 UTC 2019 setenv SUBJECTS_DIR /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer cd /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/scripts /opt/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux c14n09.farnam.hpc.yale.internal 3.10.0-693.37.4.el7.x86_64 #1 SMP Fri Aug 10 12:34:55 EDT 2018 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /opt/freesurfer mri_vol2surf --mov /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/tmp.pctsurfcon.3381/lh.wm.mgh --regheader sub-030 --cortex srcvol = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/orig.mgz as target reference. -------- original matrix ----------- -1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/label/lh.cortex.label Reading surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 = 73352 Masking with /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/label/lh.cortex.label Writing to /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/tmp.pctsurfcon.3381/lh.wm.mgh Dim: 132838 1 1 mri_vol2surf --mov /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/tmp.pctsurfcon.3381/lh.gm.mgh --projfrac 0.3 --regheader sub-030 --cortex srcvol = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/orig.mgz as target reference. -------- original matrix ----------- -1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/label/lh.cortex.label Reading surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.white Done reading source surface Reading thickness /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 = 88341 Masking with /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/label/lh.cortex.label Writing to /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/tmp.pctsurfcon.3381/lh.gm.mgh Dim: 132838 1 1 mri_concat /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/tmp.pctsurfcon.3381/lh.wm.mgh /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/tmp.pctsurfcon.3381/lh.gm.mgh --paired-diff-norm --mul 100 --o /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.w-g.pct.mgh mri_segstats --in /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.w-g.pct.mgh --annot sub-030 lh aparc --sum /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.w-g.pct.mgh --annot sub-030 lh aparc --sum /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/stats/lh.w-g.pct.stats --snr sysname Linux hostname c14n09.farnam.hpc.yale.internal machine x86_64 user mc2835 UseRobust 0 Constructing seg from annotation Reading annotation /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.w-g.pct.mgh Vertex Area is 0.674257 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 #----------------------------------------- #@# Relabel Hypointensities Thu Mar 7 11:14:00 UTC 2019 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 1847 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 3498 voxels changed to hypointensity... 5356 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg aparc Thu Mar 7 11:14:15 UTC 2019 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030 mri_aparc2aseg --s sub-030 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer subject sub-030 outvol /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.white Reading lh pial surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.pial Loading lh annotations from /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.white Reading rh pial surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.pial Loading rh annotations from /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 6.06 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 107 rescaling Left_Cerebral_Cortex from 61 --> 60 rescaling Left_Lateral_Ventricle from 13 --> 14 rescaling Left_Inf_Lat_Vent from 34 --> 30 rescaling Left_Cerebellum_White_Matter from 86 --> 87 rescaling Left_Cerebellum_Cortex from 60 --> 63 rescaling Left_Thalamus from 94 --> 104 rescaling Left_Thalamus_Proper from 84 --> 87 rescaling Left_Caudate from 75 --> 72 rescaling Left_Putamen from 80 --> 81 rescaling Left_Pallidum from 98 --> 100 rescaling Third_Ventricle from 25 --> 25 rescaling Fourth_Ventricle from 22 --> 17 rescaling Brain_Stem from 81 --> 82 rescaling Left_Hippocampus from 57 --> 62 rescaling Left_Amygdala from 56 --> 66 rescaling CSF from 32 --> 35 rescaling Left_Accumbens_area from 62 --> 65 rescaling Left_VentralDC from 87 --> 91 rescaling Right_Cerebral_White_Matter from 105 --> 104 rescaling Right_Cerebral_Cortex from 58 --> 66 rescaling Right_Lateral_Ventricle from 13 --> 14 rescaling Right_Inf_Lat_Vent from 25 --> 27 rescaling Right_Cerebellum_White_Matter from 87 --> 87 rescaling Right_Cerebellum_Cortex from 59 --> 63 rescaling Right_Thalamus_Proper from 85 --> 85 rescaling Right_Caudate from 62 --> 73 rescaling Right_Putamen from 80 --> 78 rescaling Right_Pallidum from 97 --> 97 rescaling Right_Hippocampus from 53 --> 63 rescaling Right_Amygdala from 55 --> 64 rescaling Right_Accumbens_area from 65 --> 71 rescaling Right_VentralDC from 86 --> 95 rescaling Fifth_Ventricle from 40 --> 31 rescaling WM_hypointensities from 78 --> 78 rescaling non_WM_hypointensities from 40 --> 56 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 = 425812 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 262 changed. pass 2: 21 changed. pass 3: 13 changed. pass 4: 4 changed. pass 5: 0 changed. nchanged = 0 Writing output aseg to /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/aparc+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg a2009s Thu Mar 7 11:17:40 UTC 2019 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030 INFO: skipping a2009s aparc2aseg #----------------------------------------- #@# AParc-to-ASeg DKTatlas Thu Mar 7 11:17:40 UTC 2019 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030 INFO: skipping DKTatlas aparc2aseg #----------------------------------------- #@# APas-to-ASeg Thu Mar 7 11:17:40 UTC 2019 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri apas2aseg --i aparc+aseg.mgz --o aseg.mgz Thu Mar 7 11:17:40 UTC 2019 setenv SUBJECTS_DIR /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer cd /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri /opt/freesurfer/bin/apas2aseg --i aparc+aseg.mgz --o aseg.mgz freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a $Id: apas2aseg,v 1.2 2016/02/12 21:43:14 zkaufman Exp $ Linux c14n09.farnam.hpc.yale.internal 3.10.0-693.37.4.el7.x86_64 #1 SMP Fri Aug 10 12:34:55 EDT 2018 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 c14n09.farnam.hpc.yale.internal machine x86_64 user mc2835 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 Mar 7 11:17:40 UTC 2019 Ended at Thu Mar 7 11:17:43 UTC 2019 Apas2aseg-Run-Time-Sec 3 apas2aseg Done #-------------------------------------------- #@# ASeg Stats Thu Mar 7 11:17:43 UTC 2019 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /opt/freesurfer/ASegStatsLUT.txt --subject sub-030 $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /opt/freesurfer/ASegStatsLUT.txt --subject sub-030 sysname Linux hostname c14n09.farnam.hpc.yale.internal machine x86_64 user mc2835 UseRobust 0 atlas_icv (eTIV) = 1538061 mm^3 (det: 1.266599 ) Computing euler number orig.nofix lheno = -54, rheno = -34 orig.nofix lhholes = 28, rhholes = 18 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 213847.814 213400.000 diff= 447.8 pctdiff= 0.209 rhCtxGM: 213971.072 213772.000 diff= 199.1 pctdiff= 0.093 lhCtxWM: 231001.158 231265.500 diff= -264.3 pctdiff=-0.114 rhCtxWM: 233007.839 233280.500 diff= -272.7 pctdiff=-0.117 SubCortGMVol 51692.000 SupraTentVol 978048.883 (976068.000) diff=1980.883 pctdiff=0.203 SupraTentVolNotVent 945447.883 (943467.000) diff=1980.883 pctdiff=0.210 BrainSegVol 1113758.000 (1110375.000) diff=3383.000 pctdiff=0.304 BrainSegVolNotVent 1076419.000 (1076405.883) diff=13.117 pctdiff=0.001 BrainSegVolNotVent 1076419.000 CerebellumVol 132829.000 VentChorVol 32601.000 3rd4th5thCSF 4738.000 CSFVol 1355.000, OptChiasmVol 123.000 MaskVol 1386316.000 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 Mar 7 11:18:11 UTC 2019 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030 mri_aparc2aseg --s sub-030 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer subject sub-030 outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/aparc+aseg.mgz Reading lh white surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.white Reading lh pial surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.pial Loading lh annotations from /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.white Reading rh pial surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.pial Loading rh annotations from /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/ribbon.mgz Loading filled from /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/ribbon.mgz Ripping vertices labeled as unkown Ripped 8278 vertices from left hemi Ripped 7985 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/aseg.mgz Loading Ctx Seg File /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 = 888513 Used brute-force search on 230 voxels Fixing Parahip LH WM Found 7 clusters 0 k 1.000000 1 k 5.000000 2 k 1.000000 3 k 4.000000 4 k 2.000000 5 k 1.000000 6 k 1291.000000 Fixing Parahip RH WM Found 4 clusters 0 k 1.000000 1 k 2.000000 2 k 1495.000000 3 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 sub-030 --surf-wm-vol --ctab /opt/freesurfer/WMParcStatsLUT.txt --etiv $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject sub-030 --surf-wm-vol --ctab /opt/freesurfer/WMParcStatsLUT.txt --etiv sysname Linux hostname c14n09.farnam.hpc.yale.internal machine x86_64 user mc2835 UseRobust 0 atlas_icv (eTIV) = 1538061 mm^3 (det: 1.266599 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 213847.814 213400.000 diff= 447.8 pctdiff= 0.209 rhCtxGM: 213971.072 213772.000 diff= 199.1 pctdiff= 0.093 lhCtxWM: 231001.158 231265.500 diff= -264.3 pctdiff=-0.114 rhCtxWM: 233007.839 233280.500 diff= -272.7 pctdiff=-0.117 SubCortGMVol 51692.000 SupraTentVol 978048.883 (976068.000) diff=1980.883 pctdiff=0.203 SupraTentVolNotVent 945447.883 (943467.000) diff=1980.883 pctdiff=0.210 BrainSegVol 1113758.000 (1110375.000) diff=3383.000 pctdiff=0.304 BrainSegVolNotVent 1076419.000 (1076405.883) diff=13.117 pctdiff=0.001 BrainSegVolNotVent 1076419.000 CerebellumVol 132829.000 VentChorVol 32601.000 3rd4th5thCSF 4738.000 CSFVol 1355.000, OptChiasmVol 123.000 MaskVol 1386316.000 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/label #-------------------------------------------- #@# BA_exvivo Labels lh Thu Mar 7 11:21:35 UTC 2019 mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.BA1_exvivo.label --trgsubject sub-030 --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 132838 Number of reverse mapping hits = 360 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4489 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.BA2_exvivo.label --trgsubject sub-030 --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.BA2_exvivo.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 132838 Number of reverse mapping hits = 723 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8632 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.BA3a_exvivo.label --trgsubject sub-030 --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 132838 Number of reverse mapping hits = 168 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4245 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.BA3b_exvivo.label --trgsubject sub-030 --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 132838 Number of reverse mapping hits = 378 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6361 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.BA4a_exvivo.label --trgsubject sub-030 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 132838 Number of reverse mapping hits = 368 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 6152 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.BA4p_exvivo.label --trgsubject sub-030 --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 132838 Number of reverse mapping hits = 186 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4256 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.BA6_exvivo.label --trgsubject sub-030 --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.BA6_exvivo.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 132838 Number of reverse mapping hits = 1074 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 14663 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.BA44_exvivo.label --trgsubject sub-030 --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.BA44_exvivo.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 132838 Number of reverse mapping hits = 569 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4750 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.BA45_exvivo.label --trgsubject sub-030 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.BA45_exvivo.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 132838 Number of reverse mapping hits = 1183 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 4605 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.V1_exvivo.label --trgsubject sub-030 --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.V1_exvivo.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 132838 Number of reverse mapping hits = 1151 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 5792 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.V2_exvivo.label --trgsubject sub-030 --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.V2_exvivo.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 132838 Number of reverse mapping hits = 2809 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 10923 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.MT_exvivo.label --trgsubject sub-030 --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.MT_exvivo.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 132838 Number of reverse mapping hits = 437 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2455 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject sub-030 --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1290 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 132838 Number of reverse mapping hits = 60 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1350 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject sub-030 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 132838 Number of reverse mapping hits = 60 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1259 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject sub-030 --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 132838 Number of reverse mapping hits = 106 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1120 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject sub-030 --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 132838 Number of reverse mapping hits = 240 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2332 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject sub-030 --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 132838 Number of reverse mapping hits = 40 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1544 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject sub-030 --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 132838 Number of reverse mapping hits = 142 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2138 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject sub-030 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 132838 Number of reverse mapping hits = 128 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2447 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject sub-030 --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 132838 Number of reverse mapping hits = 88 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1637 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject sub-030 --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 132838 Number of reverse mapping hits = 547 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 7582 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject sub-030 --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 132838 Number of reverse mapping hits = 271 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 2183 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject sub-030 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 132838 Number of reverse mapping hits = 516 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1667 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject sub-030 --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 132838 Number of reverse mapping hits = 716 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 4121 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject sub-030 --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 132838 Number of reverse mapping hits = 1330 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 4664 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject sub-030 --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 132838 Number of reverse mapping hits = 119 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 632 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject sub-030 --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 470 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 132838 Number of reverse mapping hits = 32 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 502 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject sub-030 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/lh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 450 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 132838 Number of reverse mapping hits = 9 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 459 mri_label2label: Done mris_label2annot --s sub-030 --hemi lh --ctab /opt/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 /opt/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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/label cmdline mris_label2annot --s sub-030 --hemi lh --ctab /opt/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 c14n09.farnam.hpc.yale.internal machine x86_64 user mc2835 subject sub-030 hemi lh SUBJECTS_DIR /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer ColorTable /opt/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 90034 unhit vertices Writing annot to /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/label/lh.BA_exvivo.annot mris_label2annot --s sub-030 --hemi lh --ctab /opt/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 /opt/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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/label cmdline mris_label2annot --s sub-030 --hemi lh --ctab /opt/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 c14n09.farnam.hpc.yale.internal machine x86_64 user mc2835 subject sub-030 hemi lh SUBJECTS_DIR /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer ColorTable /opt/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 107680 unhit vertices Writing annot to /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/label/lh.BA_exvivo.thresh.annot mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.stats -b -a ./lh.BA_exvivo.annot -c ./BA_exvivo.ctab sub-030 lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/wm.mgz... reading input surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.white... reading input pial surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.pial... reading input white surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 217681 Total vertex volume 214128 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /opt/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) = 1538061 mm^3 (det: 1.266599 ) lhCtxGM: 213847.814 213400.000 diff= 447.8 pctdiff= 0.209 rhCtxGM: 213971.072 213772.000 diff= 199.1 pctdiff= 0.093 lhCtxWM: 231001.158 231265.500 diff= -264.3 pctdiff=-0.114 rhCtxWM: 233007.839 233280.500 diff= -272.7 pctdiff=-0.117 SubCortGMVol 51692.000 SupraTentVol 978048.883 (976068.000) diff=1980.883 pctdiff=0.203 SupraTentVolNotVent 945447.883 (943467.000) diff=1980.883 pctdiff=0.210 BrainSegVol 1113758.000 (1110375.000) diff=3383.000 pctdiff=0.304 BrainSegVolNotVent 1076419.000 (1076405.883) diff=13.117 pctdiff=0.001 BrainSegVolNotVent 1076419.000 CerebellumVol 132829.000 VentChorVol 32601.000 3rd4th5thCSF 4738.000 CSFVol 1355.000, OptChiasmVol 123.000 MaskVol 1386316.000 1225 720 1977 2.172 0.598 0.152 0.047 25 2.4 BA1_exvivo 4354 2904 5778 1.924 0.499 0.126 0.029 46 5.2 BA2_exvivo 1064 737 1083 1.760 0.419 0.139 0.029 10 1.3 BA3a_exvivo 2429 1606 3019 1.682 0.527 0.122 0.026 27 2.7 BA3b_exvivo 1679 1067 3196 2.505 0.606 0.106 0.024 10 1.9 BA4a_exvivo 1379 886 2017 2.299 0.409 0.086 0.019 6 1.0 BA4p_exvivo 9375 5994 18449 2.625 0.579 0.122 0.028 102 10.5 BA6_exvivo 2648 1832 4448 2.305 0.457 0.128 0.028 30 3.1 BA44_exvivo 3743 2613 6443 2.195 0.515 0.147 0.035 58 5.4 BA45_exvivo 3258 2133 3508 1.627 0.485 0.133 0.030 35 4.0 V1_exvivo 8424 5476 11129 1.932 0.541 0.158 0.038 132 12.7 V2_exvivo 2083 1450 3524 2.188 0.521 0.156 0.033 31 3.1 MT_exvivo 537 359 1697 3.350 1.054 0.141 0.042 8 0.9 perirhinal_exvivo 606 435 1574 2.851 1.006 0.100 0.019 5 0.4 entorhinal_exvivo mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab sub-030 lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/wm.mgz... reading input surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.white... reading input pial surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.pial... reading input white surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 217681 Total vertex volume 214128 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /opt/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) = 1538061 mm^3 (det: 1.266599 ) lhCtxGM: 213847.814 213400.000 diff= 447.8 pctdiff= 0.209 rhCtxGM: 213971.072 213772.000 diff= 199.1 pctdiff= 0.093 lhCtxWM: 231001.158 231265.500 diff= -264.3 pctdiff=-0.114 rhCtxWM: 233007.839 233280.500 diff= -272.7 pctdiff=-0.117 SubCortGMVol 51692.000 SupraTentVol 978048.883 (976068.000) diff=1980.883 pctdiff=0.203 SupraTentVolNotVent 945447.883 (943467.000) diff=1980.883 pctdiff=0.210 BrainSegVol 1113758.000 (1110375.000) diff=3383.000 pctdiff=0.304 BrainSegVolNotVent 1076419.000 (1076405.883) diff=13.117 pctdiff=0.001 BrainSegVolNotVent 1076419.000 CerebellumVol 132829.000 VentChorVol 32601.000 3rd4th5thCSF 4738.000 CSFVol 1355.000, OptChiasmVol 123.000 MaskVol 1386316.000 793 451 1285 2.265 0.706 0.152 0.046 16 1.3 BA1_exvivo 1765 1168 2291 1.846 0.513 0.121 0.027 18 2.1 BA2_exvivo 893 622 831 1.715 0.358 0.139 0.031 8 1.1 BA3a_exvivo 1516 1017 1464 1.436 0.326 0.107 0.021 13 1.3 BA3b_exvivo 1611 1005 3027 2.551 0.550 0.095 0.023 9 1.5 BA4a_exvivo 1142 744 1619 2.238 0.403 0.096 0.020 6 1.0 BA4p_exvivo 5309 3299 10437 2.664 0.613 0.120 0.027 53 5.6 BA6_exvivo 1744 1207 2910 2.324 0.441 0.125 0.027 19 2.0 BA44_exvivo 1566 1109 3264 2.396 0.541 0.161 0.041 29 2.4 BA45_exvivo 3446 2279 3886 1.648 0.499 0.134 0.030 37 4.2 V1_exvivo 4247 2738 5198 1.862 0.556 0.164 0.038 73 6.5 V2_exvivo 546 384 971 2.188 0.504 0.154 0.032 8 0.8 MT_exvivo 280 193 1122 3.771 0.869 0.138 0.031 4 0.4 perirhinal_exvivo 300 205 757 3.079 0.773 0.092 0.018 2 0.2 entorhinal_exvivo Started at Thu Mar 7 11:05:16 UTC 2019 Ended at Thu Mar 7 11:24:55 UTC 2019 #@#%# recon-all-run-time-hours 0.327 recon-all -s sub-030 finished without error at Thu Mar 7 11:24:55 UTC 2019 New invocation of recon-all Thu Mar 7 11:24:55 UTC 2019 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030 /opt/freesurfer/bin/recon-all -autorecon3 -hemi rh -openmp 7 -subjid sub-030 -sd /home/mc2835/scratch60/RVLdata/fmriprep_output/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortribbon -nohyporelabel -noapas2aseg -nosegstats -nowmparc subjid sub-030 setenv SUBJECTS_DIR /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /opt/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a Linux c14n09.farnam.hpc.yale.internal 3.10.0-693.37.4.el7.x86_64 #1 SMP Fri Aug 10 12:34:55 EDT 2018 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize unlimited memoryuse 65536000 kbytes vmemoryuse unlimited descriptors 51200 memorylocked unlimited maxproc 512036 maxlocks unlimited maxsignal 512036 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 131317832 20567324 75745696 654424 35004812 109346056 Swap: 16777212 151228 16625984 ######################################## 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: 2019/03/07-11:24:55-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:24:55-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:24:55-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-11:24:55-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:24:55-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:24:55-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-11:24:55-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-11:24:55-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-11:24:55-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-11:24:55-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-11:24:55-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-11:24:55-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:24:55-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:24:55-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-11:24:55-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:24:55-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:24:55-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:24:55-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:24:55-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:24:55-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:24:55-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-11:24:55-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:24:55-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:24:55-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:24:55-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-11:24:55-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:24:55-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-11:24:55-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:24:55-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:24:55-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:24:55-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:24:55-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:24:55-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:24:55-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:24:55-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:24:55-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:24:55-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:24:55-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:24:56-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /opt/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /opt/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #----------------------------------------- #@# Parcellation Stats rh Thu Mar 7 11:24:56 UTC 2019 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab sub-030 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/wm.mgz... reading input surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.white... reading input pial surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.pial... reading input white surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 218308 Total vertex volume 214705 (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) = 1538061 mm^3 (det: 1.266599 ) lhCtxGM: 213847.814 213400.000 diff= 447.8 pctdiff= 0.209 rhCtxGM: 213971.072 213772.000 diff= 199.1 pctdiff= 0.093 lhCtxWM: 231001.158 231265.500 diff= -264.3 pctdiff=-0.114 rhCtxWM: 233007.839 233280.500 diff= -272.7 pctdiff=-0.117 SubCortGMVol 51692.000 SupraTentVol 978048.883 (976068.000) diff=1980.883 pctdiff=0.203 SupraTentVolNotVent 945447.883 (943467.000) diff=1980.883 pctdiff=0.210 BrainSegVol 1113758.000 (1110375.000) diff=3383.000 pctdiff=0.304 BrainSegVolNotVent 1076419.000 (1076405.883) diff=13.117 pctdiff=0.001 BrainSegVolNotVent 1076419.000 CerebellumVol 132829.000 VentChorVol 32601.000 3rd4th5thCSF 4738.000 CSFVol 1355.000, OptChiasmVol 123.000 MaskVol 1386316.000 1124 793 1904 2.510 0.409 0.111 0.021 8 1.0 bankssts 1374 873 2128 2.160 0.614 0.143 0.019 26 1.0 caudalanteriorcingulate 2699 1842 4774 2.409 0.450 0.125 0.028 27 3.0 caudalmiddlefrontal 2310 1506 2510 1.699 0.410 0.156 0.037 35 3.6 cuneus 547 398 2178 3.569 0.960 0.137 0.034 10 0.9 entorhinal 4410 3011 8501 2.622 0.630 0.136 0.030 59 5.3 fusiform 7816 5351 12472 2.192 0.470 0.135 0.029 102 9.0 inferiorparietal 5419 3712 11485 2.626 0.747 0.148 0.039 94 9.2 inferiortemporal 1131 720 1942 2.586 0.666 0.144 0.032 21 1.3 isthmuscingulate 8027 5188 11552 2.049 0.571 0.154 0.037 118 12.0 lateraloccipital 3726 2593 6431 2.310 0.651 0.153 0.041 64 6.2 lateralorbitofrontal 3965 2712 5330 1.881 0.614 0.153 0.036 55 6.1 lingual 3177 2137 5475 2.263 0.606 0.134 0.038 60 5.3 medialorbitofrontal 5031 3525 10339 2.499 0.548 0.140 0.032 78 6.7 middletemporal 1051 655 1694 2.250 0.626 0.089 0.015 7 0.5 parahippocampal 2376 1579 3780 2.307 0.516 0.114 0.020 18 1.9 paracentral 1749 1195 3095 2.357 0.454 0.127 0.027 21 1.9 parsopercularis 1120 807 2516 2.614 0.649 0.167 0.045 25 1.9 parsorbitalis 2240 1519 3685 2.234 0.503 0.143 0.031 36 2.6 parstriangularis 1981 1339 1608 1.409 0.344 0.139 0.037 23 3.0 pericalcarine 6622 4199 8732 1.863 0.599 0.118 0.029 76 8.5 postcentral 1809 1219 2907 2.187 0.672 0.153 0.029 34 2.1 posteriorcingulate 7860 5081 12878 2.326 0.573 0.116 0.026 75 8.6 precentral 5321 3651 9069 2.361 0.553 0.139 0.032 66 7.0 precuneus 1249 831 2495 2.619 0.679 0.143 0.032 22 1.8 rostralanteriorcingulate 8565 5759 13262 2.063 0.486 0.146 0.038 134 13.4 rostralmiddlefrontal 9675 6471 18815 2.600 0.601 0.131 0.031 112 12.2 superiorfrontal 9352 6094 12940 1.979 0.489 0.134 0.031 121 11.8 superiorparietal 5052 3483 9358 2.411 0.595 0.118 0.022 55 4.6 superiortemporal 5820 3945 9030 2.231 0.539 0.145 0.035 90 8.3 supramarginal 567 402 1440 2.744 0.616 0.216 0.073 18 1.9 frontalpole 580 424 2155 3.623 0.582 0.162 0.047 10 1.2 temporalpole 515 300 667 2.152 0.429 0.142 0.036 8 0.7 transversetemporal 4072 2693 7495 2.736 0.881 0.125 0.034 48 5.2 insula mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab sub-030 rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/wm.mgz... reading input surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.pial... reading input pial surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.pial... reading input white surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 218308 Total vertex volume 214705 (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) = 1538061 mm^3 (det: 1.266599 ) lhCtxGM: 213847.814 213400.000 diff= 447.8 pctdiff= 0.209 rhCtxGM: 213971.072 213772.000 diff= 199.1 pctdiff= 0.093 lhCtxWM: 231001.158 231265.500 diff= -264.3 pctdiff=-0.114 rhCtxWM: 233007.839 233280.500 diff= -272.7 pctdiff=-0.117 SubCortGMVol 51692.000 SupraTentVol 978048.883 (976068.000) diff=1980.883 pctdiff=0.203 SupraTentVolNotVent 945447.883 (943467.000) diff=1980.883 pctdiff=0.210 BrainSegVol 1113758.000 (1110375.000) diff=3383.000 pctdiff=0.304 BrainSegVolNotVent 1076419.000 (1076405.883) diff=13.117 pctdiff=0.001 BrainSegVolNotVent 1076419.000 CerebellumVol 132829.000 VentChorVol 32601.000 3rd4th5thCSF 4738.000 CSFVol 1355.000, OptChiasmVol 123.000 MaskVol 1386316.000 1124 741 1904 2.510 0.409 0.118 0.030 12 1.4 bankssts 1374 1044 2128 2.160 0.614 0.132 0.023 20 1.3 caudalanteriorcingulate 2699 2098 4774 2.409 0.450 0.127 0.026 33 3.1 caudalmiddlefrontal 2310 1619 2510 1.699 0.410 0.124 0.031 30 3.3 cuneus 547 808 2178 3.569 0.960 0.200 0.038 6 1.1 entorhinal 4410 3435 8501 2.622 0.630 0.139 0.039 85 7.5 fusiform 7816 6026 12472 2.192 0.470 0.136 0.029 94 10.2 inferiorparietal 5419 4896 11485 2.626 0.747 0.151 0.034 101 8.7 inferiortemporal 1131 896 1942 2.586 0.666 0.146 0.036 36 1.6 isthmuscingulate 8027 5909 11552 2.049 0.571 0.132 0.032 103 11.5 lateraloccipital 3726 2968 6431 2.310 0.651 0.156 0.039 69 6.7 lateralorbitofrontal 3965 3145 5330 1.881 0.614 0.135 0.034 56 6.1 lingual 3177 2684 5475 2.263 0.606 0.148 0.033 42 4.5 medialorbitofrontal 5031 4701 10339 2.499 0.548 0.153 0.031 63 7.1 middletemporal 1051 874 1694 2.250 0.626 0.115 0.024 8 1.1 parahippocampal 2376 1716 3780 2.307 0.516 0.118 0.025 32 2.7 paracentral 1749 1400 3095 2.357 0.454 0.135 0.029 20 2.1 parsopercularis 1120 1087 2516 2.614 0.649 0.169 0.039 14 1.9 parsorbitalis 2240 1817 3685 2.234 0.503 0.148 0.027 30 2.7 parstriangularis 1981 1134 1608 1.409 0.344 0.108 0.031 24 2.5 pericalcarine 6622 5047 8732 1.863 0.599 0.120 0.026 58 7.1 postcentral 1809 1428 2907 2.187 0.672 0.146 0.033 35 2.6 posteriorcingulate 7860 5779 12878 2.326 0.573 0.118 0.025 90 8.8 precentral 5321 4020 9069 2.361 0.553 0.135 0.033 75 7.7 precuneus 1249 1144 2495 2.619 0.679 0.167 0.036 18 2.0 rostralanteriorcingulate 8565 6984 13262 2.063 0.486 0.158 0.035 122 13.5 rostralmiddlefrontal 9675 7757 18815 2.600 0.601 0.139 0.032 116 13.4 superiorfrontal 9352 7009 12940 1.979 0.489 0.132 0.029 111 12.1 superiorparietal 5052 4220 9358 2.411 0.595 0.135 0.025 51 5.8 superiortemporal 5820 4265 9030 2.231 0.539 0.138 0.036 91 8.6 supramarginal 567 638 1440 2.744 0.616 0.215 0.048 8 1.4 frontalpole 580 750 2155 3.623 0.582 0.181 0.035 7 1.0 temporalpole 515 329 667 2.152 0.429 0.102 0.021 3 0.4 transversetemporal 4072 2550 7495 2.736 0.881 0.123 0.037 101 6.5 insula #----------------------------------------- #@# Cortical Parc 2 rh Thu Mar 7 11:25:42 UTC 2019 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-030 rh ../surf/rh.sphere.reg /opt/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 /opt/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... 68 labels changed using aseg relabeling using gibbs priors... 000: 8949 changed, 136317 examined... 001: 2071 changed, 35499 examined... 002: 596 changed, 10860 examined... 003: 230 changed, 3460 examined... 004: 116 changed, 1268 examined... 005: 37 changed, 602 examined... 006: 29 changed, 236 examined... 007: 15 changed, 154 examined... 008: 6 changed, 78 examined... 009: 5 changed, 35 examined... 010: 2 changed, 25 examined... 011: 2 changed, 12 examined... 012: 0 changed, 17 examined... 66 labels changed using aseg 000: 261 total segments, 170 labels (1746 vertices) changed 001: 99 total segments, 10 labels (32 vertices) changed 002: 90 total segments, 1 labels (1 vertices) changed 003: 89 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 40 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1361 vertices marked for relabeling... 1361 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 14 seconds. #----------------------------------------- #@# Parcellation Stats 2 rh Thu Mar 7 11:25:56 UTC 2019 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab sub-030 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/wm.mgz... reading input surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.white... reading input pial surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.pial... reading input white surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 218308 Total vertex volume 214705 (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) = 1538061 mm^3 (det: 1.266599 ) lhCtxGM: 213847.814 213400.000 diff= 447.8 pctdiff= 0.209 rhCtxGM: 213971.072 213772.000 diff= 199.1 pctdiff= 0.093 lhCtxWM: 231001.158 231265.500 diff= -264.3 pctdiff=-0.114 rhCtxWM: 233007.839 233280.500 diff= -272.7 pctdiff=-0.117 SubCortGMVol 51692.000 SupraTentVol 978048.883 (976068.000) diff=1980.883 pctdiff=0.203 SupraTentVolNotVent 945447.883 (943467.000) diff=1980.883 pctdiff=0.210 BrainSegVol 1113758.000 (1110375.000) diff=3383.000 pctdiff=0.304 BrainSegVolNotVent 1076419.000 (1076405.883) diff=13.117 pctdiff=0.001 BrainSegVolNotVent 1076419.000 CerebellumVol 132829.000 VentChorVol 32601.000 3rd4th5thCSF 4738.000 CSFVol 1355.000, OptChiasmVol 123.000 MaskVol 1386316.000 937 624 1540 2.165 0.664 0.159 0.042 18 1.6 G&S_frontomargin 1399 948 2417 2.352 0.540 0.150 0.036 19 1.9 G&S_occipital_inf 1581 1005 2647 2.242 0.613 0.127 0.029 16 1.9 G&S_paracentral 1290 870 2421 2.451 0.392 0.142 0.032 16 1.8 G&S_subcentral 1292 936 2833 2.336 0.591 0.189 0.065 28 3.9 G&S_transv_frontopol 3306 2205 5606 2.429 0.507 0.130 0.028 46 3.8 G&S_cingul-Ant 1518 1043 2614 2.387 0.493 0.134 0.021 21 1.3 G&S_cingul-Mid-Ant 1436 995 2452 2.374 0.469 0.127 0.026 17 1.4 G&S_cingul-Mid-Post 581 390 1365 2.800 0.518 0.179 0.042 12 1.0 G_cingul-Post-dorsal 313 176 575 2.707 0.624 0.117 0.038 4 0.4 G_cingul-Post-ventral 2071 1367 2303 1.655 0.450 0.155 0.036 31 3.2 G_cuneus 1230 849 2693 2.498 0.433 0.132 0.028 18 1.4 G_front_inf-Opercular 550 357 1061 2.516 0.632 0.174 0.042 14 0.9 G_front_inf-Orbital 803 542 1521 2.255 0.427 0.149 0.040 18 1.2 G_front_inf-Triangul 4200 2712 7737 2.284 0.513 0.153 0.039 79 6.6 G_front_middle 6286 4098 14594 2.852 0.536 0.143 0.037 93 9.9 G_front_sup 601 422 1443 3.157 0.699 0.130 0.027 8 0.5 G_Ins_lg&S_cent_ins 789 488 2194 3.266 0.879 0.146 0.042 13 1.4 G_insular_short 2376 1533 4602 2.411 0.516 0.151 0.035 38 3.4 G_occipital_middle 1571 1030 2356 2.042 0.553 0.145 0.034 21 2.0 G_occipital_sup 1959 1287 4386 2.683 0.632 0.145 0.035 35 2.7 G_oc-temp_lat-fusifor 2193 1537 3220 1.784 0.598 0.155 0.040 30 3.7 G_oc-temp_med-Lingual 1299 812 3574 2.995 1.006 0.118 0.032 15 1.5 G_oc-temp_med-Parahip 2826 1930 6246 2.541 0.717 0.169 0.052 67 5.9 G_orbital 3477 2343 6665 2.301 0.480 0.154 0.036 66 5.2 G_pariet_inf-Angular 2585 1748 4669 2.347 0.574 0.149 0.038 45 3.9 G_pariet_inf-Supramar 2874 1798 4883 2.135 0.518 0.142 0.041 49 5.1 G_parietal_sup 2443 1426 3557 1.915 0.671 0.126 0.041 40 4.6 G_postcentral 2985 1805 6073 2.534 0.598 0.122 0.036 37 4.4 G_precentral 2853 1920 5827 2.436 0.549 0.156 0.038 49 4.7 G_precuneus 983 628 1934 2.128 0.600 0.151 0.067 30 3.0 G_rectus 823 509 1179 2.206 1.115 0.099 0.036 9 1.0 G_subcallosal 420 233 618 2.284 0.534 0.134 0.035 7 0.5 G_temp_sup-G_T_transv 1666 1189 4131 2.592 0.589 0.151 0.037 31 2.6 G_temp_sup-Lateral 695 502 1547 2.903 0.796 0.139 0.044 11 1.1 G_temp_sup-Plan_polar 887 601 1419 2.125 0.496 0.129 0.024 13 0.8 G_temp_sup-Plan_tempo 2926 1991 7183 2.737 0.763 0.161 0.050 65 6.4 G_temporal_inf 2915 2088 7061 2.607 0.524 0.159 0.040 62 4.9 G_temporal_middle 374 265 559 2.248 0.414 0.153 0.029 5 0.5 Lat_Fis-ant-Horizont 222 163 343 2.473 0.551 0.124 0.019 2 0.2 Lat_Fis-ant-Vertical 1461 976 1721 2.206 0.543 0.113 0.021 11 1.2 Lat_Fis-post 4105 2628 4987 1.737 0.528 0.157 0.040 64 6.9 Pole_occipital 1855 1291 5050 2.915 0.847 0.151 0.043 32 3.5 Pole_temporal 2093 1415 2054 1.780 0.651 0.143 0.036 27 3.2 S_calcarine 3322 2247 3438 1.739 0.517 0.102 0.018 21 2.4 S_central 1153 820 1535 2.038 0.472 0.105 0.017 7 0.7 S_cingul-Marginalis 812 542 1039 2.402 0.453 0.130 0.035 8 1.3 S_circular_insula_ant 1153 773 1503 2.265 0.577 0.082 0.010 4 0.5 S_circular_insula_inf 1290 887 1814 2.401 0.480 0.107 0.019 7 1.0 S_circular_insula_sup 832 591 1785 3.139 0.762 0.136 0.032 10 1.0 S_collat_transv_ant 387 253 447 2.056 0.598 0.150 0.029 5 0.5 S_collat_transv_post 1936 1324 2413 1.945 0.379 0.128 0.023 19 1.9 S_front_inf 2208 1539 2742 1.964 0.374 0.124 0.027 19 2.3 S_front_middle 2144 1526 3329 2.173 0.453 0.108 0.018 15 1.5 S_front_sup 655 453 746 2.038 0.394 0.129 0.028 6 0.7 S_interm_prim-Jensen 4318 2906 4874 1.843 0.360 0.115 0.020 37 3.5 S_intrapariet&P_trans 958 623 946 1.824 0.335 0.143 0.030 11 1.3 S_oc_middle&Lunatus 1492 1003 1634 1.836 0.323 0.133 0.025 17 1.4 S_oc_sup&transversal 613 417 999 2.404 0.557 0.141 0.029 8 0.7 S_occipital_ant 1295 883 1802 2.326 0.435 0.122 0.022 11 1.2 S_oc-temp_lat 2183 1529 2804 2.166 0.477 0.120 0.024 19 2.0 S_oc-temp_med&Lingual 281 205 317 1.615 0.285 0.113 0.019 2 0.2 S_orbital_lateral 771 575 996 1.979 0.527 0.111 0.013 5 0.4 S_orbital_med-olfact 1267 913 2066 2.190 0.557 0.155 0.037 19 2.1 S_orbital-H_Shaped 1942 1310 2382 2.112 0.541 0.126 0.026 18 2.1 S_parieto_occipital 1460 873 1297 2.057 0.914 0.149 0.020 33 0.9 S_pericallosal 3095 2050 3410 1.909 0.439 0.134 0.028 35 3.6 S_postcentral 1573 1046 1974 2.105 0.393 0.115 0.021 13 1.4 S_precentral-inf-part 1452 1007 2105 2.384 0.399 0.103 0.015 8 1.0 S_precentral-sup-part 430 308 597 2.107 0.704 0.129 0.023 4 0.3 S_suborbital 1053 728 1500 2.258 0.392 0.130 0.026 9 1.1 S_subparietal 1437 1010 1844 2.175 0.462 0.122 0.017 12 1.1 S_temporal_inf 5517 3807 8151 2.330 0.434 0.113 0.021 39 4.7 S_temporal_sup 266 186 361 2.521 0.426 0.132 0.014 3 0.2 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 rh Thu Mar 7 11:26:19 UTC 2019 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-030 rh ../surf/rh.sphere.reg /opt/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 /opt/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... 1313 labels changed using aseg relabeling using gibbs priors... 000: 2086 changed, 136317 examined... 001: 474 changed, 9466 examined... 002: 141 changed, 2667 examined... 003: 59 changed, 797 examined... 004: 39 changed, 368 examined... 005: 28 changed, 242 examined... 006: 24 changed, 156 examined... 007: 11 changed, 134 examined... 008: 7 changed, 60 examined... 009: 6 changed, 35 examined... 010: 9 changed, 30 examined... 011: 5 changed, 42 examined... 012: 8 changed, 34 examined... 013: 8 changed, 39 examined... 014: 3 changed, 44 examined... 015: 3 changed, 20 examined... 016: 1 changed, 14 examined... 017: 0 changed, 7 examined... 389 labels changed using aseg 000: 55 total segments, 22 labels (129 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 7 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1145 vertices marked for relabeling... 1145 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 11 seconds. #----------------------------------------- #@# Parcellation Stats 3 rh Thu Mar 7 11:26:31 UTC 2019 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab sub-030 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/wm.mgz... reading input surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.white... reading input pial surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.pial... reading input white surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 218308 Total vertex volume 214705 (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) = 1538061 mm^3 (det: 1.266599 ) lhCtxGM: 213847.814 213400.000 diff= 447.8 pctdiff= 0.209 rhCtxGM: 213971.072 213772.000 diff= 199.1 pctdiff= 0.093 lhCtxWM: 231001.158 231265.500 diff= -264.3 pctdiff=-0.114 rhCtxWM: 233007.839 233280.500 diff= -272.7 pctdiff=-0.117 SubCortGMVol 51692.000 SupraTentVol 978048.883 (976068.000) diff=1980.883 pctdiff=0.203 SupraTentVolNotVent 945447.883 (943467.000) diff=1980.883 pctdiff=0.210 BrainSegVol 1113758.000 (1110375.000) diff=3383.000 pctdiff=0.304 BrainSegVolNotVent 1076419.000 (1076405.883) diff=13.117 pctdiff=0.001 BrainSegVolNotVent 1076419.000 CerebellumVol 132829.000 VentChorVol 32601.000 3rd4th5thCSF 4738.000 CSFVol 1355.000, OptChiasmVol 123.000 MaskVol 1386316.000 1483 945 2292 2.160 0.611 0.143 0.019 28 1.0 caudalanteriorcingulate 2867 1952 4970 2.391 0.451 0.126 0.028 29 3.2 caudalmiddlefrontal 2663 1757 3057 1.736 0.445 0.155 0.037 39 4.2 cuneus 517 377 2119 3.612 0.969 0.141 0.033 10 0.9 entorhinal 4124 2802 7858 2.620 0.634 0.136 0.031 55 4.8 fusiform 7893 5386 12655 2.204 0.472 0.139 0.030 108 9.6 inferiorparietal 5718 3926 12243 2.638 0.741 0.149 0.039 100 10.0 inferiortemporal 1138 723 1964 2.595 0.666 0.142 0.032 20 1.3 isthmuscingulate 8155 5259 11747 2.043 0.583 0.153 0.037 121 12.1 lateraloccipital 4455 3048 7629 2.291 0.690 0.157 0.045 83 8.2 lateralorbitofrontal 3832 2626 5149 1.879 0.607 0.155 0.037 54 6.0 lingual 2677 1777 4538 2.151 0.783 0.126 0.042 50 4.4 medialorbitofrontal 6015 4211 11888 2.492 0.532 0.138 0.031 86 7.8 middletemporal 1084 685 1767 2.248 0.603 0.088 0.014 7 0.5 parahippocampal 2482 1656 4069 2.337 0.534 0.115 0.021 19 2.2 paracentral 1943 1340 3424 2.367 0.477 0.130 0.028 24 2.1 parsopercularis 1155 802 2124 2.377 0.585 0.147 0.032 19 1.6 parsorbitalis 2152 1472 3539 2.201 0.507 0.145 0.032 37 2.8 parstriangularis 1906 1293 1564 1.404 0.348 0.135 0.034 21 2.6 pericalcarine 7311 4633 9766 1.895 0.621 0.119 0.029 84 9.3 postcentral 1884 1263 2986 2.212 0.655 0.151 0.030 34 2.2 posteriorcingulate 7499 4853 12261 2.318 0.550 0.116 0.026 72 8.3 precentral 5588 3815 9523 2.356 0.556 0.142 0.033 72 7.7 precuneus 1648 1081 3017 2.575 0.665 0.139 0.030 26 2.2 rostralanteriorcingulate 6049 4053 9420 2.096 0.511 0.146 0.035 95 8.7 rostralmiddlefrontal 12664 8526 24500 2.526 0.615 0.136 0.034 166 17.9 superiorfrontal 7954 5170 10722 1.943 0.441 0.130 0.029 100 9.7 superiorparietal 6498 4509 13007 2.543 0.688 0.123 0.027 76 6.8 superiortemporal 5445 3699 8204 2.209 0.547 0.142 0.033 80 7.3 supramarginal 521 303 673 2.128 0.416 0.136 0.034 7 0.7 transversetemporal 3024 2069 6031 2.864 0.725 0.126 0.028 32 3.5 insula #----------------------------------------- #@# WM/GM Contrast rh Thu Mar 7 11:26:54 UTC 2019 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/scripts pctsurfcon --s sub-030 --rh-only Log file is /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/scripts/pctsurfcon.log Thu Mar 7 11:26:54 UTC 2019 setenv SUBJECTS_DIR /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer cd /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/scripts /opt/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux c14n09.farnam.hpc.yale.internal 3.10.0-693.37.4.el7.x86_64 #1 SMP Fri Aug 10 12:34:55 EDT 2018 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /opt/freesurfer mri_vol2surf --mov /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/tmp.pctsurfcon.5441/rh.wm.mgh --regheader sub-030 --cortex srcvol = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/orig.mgz as target reference. -------- original matrix ----------- -1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/label/rh.cortex.label Reading surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 = 75155 Masking with /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/label/rh.cortex.label Writing to /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/tmp.pctsurfcon.5441/rh.wm.mgh Dim: 136317 1 1 mri_vol2surf --mov /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/tmp.pctsurfcon.5441/rh.gm.mgh --projfrac 0.3 --regheader sub-030 --cortex srcvol = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/orig.mgz as target reference. -------- original matrix ----------- -1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/label/rh.cortex.label Reading surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.white Done reading source surface Reading thickness /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 = 90380 Masking with /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/label/rh.cortex.label Writing to /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/tmp.pctsurfcon.5441/rh.gm.mgh Dim: 136317 1 1 mri_concat /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/tmp.pctsurfcon.5441/rh.wm.mgh /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/tmp.pctsurfcon.5441/rh.gm.mgh --paired-diff-norm --mul 100 --o /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.w-g.pct.mgh mri_segstats --in /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.w-g.pct.mgh --annot sub-030 rh aparc --sum /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.w-g.pct.mgh --annot sub-030 rh aparc --sum /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/stats/rh.w-g.pct.stats --snr sysname Linux hostname c14n09.farnam.hpc.yale.internal machine x86_64 user mc2835 UseRobust 0 Constructing seg from annotation Reading annotation /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.w-g.pct.mgh Vertex Area is 0.668912 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 #----------------------------------------- #@# AParc-to-ASeg aparc Thu Mar 7 11:26:58 UTC 2019 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030 mri_aparc2aseg --s sub-030 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer subject sub-030 outvol /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.white Reading lh pial surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.pial Loading lh annotations from /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.white Reading rh pial surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.pial Loading rh annotations from /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 6.06 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 107 rescaling Left_Cerebral_Cortex from 61 --> 60 rescaling Left_Lateral_Ventricle from 13 --> 14 rescaling Left_Inf_Lat_Vent from 34 --> 30 rescaling Left_Cerebellum_White_Matter from 86 --> 87 rescaling Left_Cerebellum_Cortex from 60 --> 63 rescaling Left_Thalamus from 94 --> 104 rescaling Left_Thalamus_Proper from 84 --> 87 rescaling Left_Caudate from 75 --> 72 rescaling Left_Putamen from 80 --> 81 rescaling Left_Pallidum from 98 --> 100 rescaling Third_Ventricle from 25 --> 25 rescaling Fourth_Ventricle from 22 --> 17 rescaling Brain_Stem from 81 --> 82 rescaling Left_Hippocampus from 57 --> 62 rescaling Left_Amygdala from 56 --> 66 rescaling CSF from 32 --> 35 rescaling Left_Accumbens_area from 62 --> 65 rescaling Left_VentralDC from 87 --> 91 rescaling Right_Cerebral_White_Matter from 105 --> 104 rescaling Right_Cerebral_Cortex from 58 --> 66 rescaling Right_Lateral_Ventricle from 13 --> 14 rescaling Right_Inf_Lat_Vent from 25 --> 27 rescaling Right_Cerebellum_White_Matter from 87 --> 87 rescaling Right_Cerebellum_Cortex from 59 --> 63 rescaling Right_Thalamus_Proper from 85 --> 85 rescaling Right_Caudate from 62 --> 73 rescaling Right_Putamen from 80 --> 78 rescaling Right_Pallidum from 97 --> 97 rescaling Right_Hippocampus from 53 --> 63 rescaling Right_Amygdala from 55 --> 64 rescaling Right_Accumbens_area from 65 --> 71 rescaling Right_VentralDC from 86 --> 95 rescaling Fifth_Ventricle from 40 --> 31 rescaling WM_hypointensities from 78 --> 78 rescaling non_WM_hypointensities from 40 --> 56 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 = 425812 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 262 changed. pass 2: 21 changed. pass 3: 13 changed. pass 4: 4 changed. pass 5: 0 changed. nchanged = 0 Writing output aseg to /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/aparc+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg a2009s Thu Mar 7 11:30:22 UTC 2019 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030 mri_aparc2aseg --s sub-030 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --a2009s relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer subject sub-030 outvol /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.white Reading lh pial surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.pial Loading lh annotations from /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/label/lh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Reading rh white surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.white Reading rh pial surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.pial Loading rh annotations from /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 6.06 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 107 rescaling Left_Cerebral_Cortex from 61 --> 60 rescaling Left_Lateral_Ventricle from 13 --> 14 rescaling Left_Inf_Lat_Vent from 34 --> 30 rescaling Left_Cerebellum_White_Matter from 86 --> 87 rescaling Left_Cerebellum_Cortex from 60 --> 63 rescaling Left_Thalamus from 94 --> 104 rescaling Left_Thalamus_Proper from 84 --> 87 rescaling Left_Caudate from 75 --> 72 rescaling Left_Putamen from 80 --> 81 rescaling Left_Pallidum from 98 --> 100 rescaling Third_Ventricle from 25 --> 25 rescaling Fourth_Ventricle from 22 --> 17 rescaling Brain_Stem from 81 --> 82 rescaling Left_Hippocampus from 57 --> 62 rescaling Left_Amygdala from 56 --> 66 rescaling CSF from 32 --> 35 rescaling Left_Accumbens_area from 62 --> 65 rescaling Left_VentralDC from 87 --> 91 rescaling Right_Cerebral_White_Matter from 105 --> 104 rescaling Right_Cerebral_Cortex from 58 --> 66 rescaling Right_Lateral_Ventricle from 13 --> 14 rescaling Right_Inf_Lat_Vent from 25 --> 27 rescaling Right_Cerebellum_White_Matter from 87 --> 87 rescaling Right_Cerebellum_Cortex from 59 --> 63 rescaling Right_Thalamus_Proper from 85 --> 85 rescaling Right_Caudate from 62 --> 73 rescaling Right_Putamen from 80 --> 78 rescaling Right_Pallidum from 97 --> 97 rescaling Right_Hippocampus from 53 --> 63 rescaling Right_Amygdala from 55 --> 64 rescaling Right_Accumbens_area from 65 --> 71 rescaling Right_VentralDC from 86 --> 95 rescaling Fifth_Ventricle from 40 --> 31 rescaling WM_hypointensities from 78 --> 78 rescaling non_WM_hypointensities from 40 --> 56 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 = 425843 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 262 changed. pass 2: 21 changed. pass 3: 13 changed. pass 4: 4 changed. pass 5: 0 changed. nchanged = 0 Writing output aseg to /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg DKTatlas Thu Mar 7 11:33:46 UTC 2019 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030 mri_aparc2aseg --s sub-030 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --annot aparc.DKTatlas --o mri/aparc.DKTatlas+aseg.mgz relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer subject sub-030 outvol mri/aparc.DKTatlas+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.white Reading lh pial surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/lh.pial Loading lh annotations from /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.white Reading rh pial surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.pial Loading rh annotations from /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 6.06 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 107 rescaling Left_Cerebral_Cortex from 61 --> 60 rescaling Left_Lateral_Ventricle from 13 --> 14 rescaling Left_Inf_Lat_Vent from 34 --> 30 rescaling Left_Cerebellum_White_Matter from 86 --> 87 rescaling Left_Cerebellum_Cortex from 60 --> 63 rescaling Left_Thalamus from 94 --> 104 rescaling Left_Thalamus_Proper from 84 --> 87 rescaling Left_Caudate from 75 --> 72 rescaling Left_Putamen from 80 --> 81 rescaling Left_Pallidum from 98 --> 100 rescaling Third_Ventricle from 25 --> 25 rescaling Fourth_Ventricle from 22 --> 17 rescaling Brain_Stem from 81 --> 82 rescaling Left_Hippocampus from 57 --> 62 rescaling Left_Amygdala from 56 --> 66 rescaling CSF from 32 --> 35 rescaling Left_Accumbens_area from 62 --> 65 rescaling Left_VentralDC from 87 --> 91 rescaling Right_Cerebral_White_Matter from 105 --> 104 rescaling Right_Cerebral_Cortex from 58 --> 66 rescaling Right_Lateral_Ventricle from 13 --> 14 rescaling Right_Inf_Lat_Vent from 25 --> 27 rescaling Right_Cerebellum_White_Matter from 87 --> 87 rescaling Right_Cerebellum_Cortex from 59 --> 63 rescaling Right_Thalamus_Proper from 85 --> 85 rescaling Right_Caudate from 62 --> 73 rescaling Right_Putamen from 80 --> 78 rescaling Right_Pallidum from 97 --> 97 rescaling Right_Hippocampus from 53 --> 63 rescaling Right_Amygdala from 55 --> 64 rescaling Right_Accumbens_area from 65 --> 71 rescaling Right_VentralDC from 86 --> 95 rescaling Fifth_Ventricle from 40 --> 31 rescaling WM_hypointensities from 78 --> 78 rescaling non_WM_hypointensities from 40 --> 56 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 = 425843 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 262 changed. pass 2: 21 changed. pass 3: 13 changed. pass 4: 4 changed. pass 5: 0 changed. nchanged = 0 Writing output aseg to mri/aparc.DKTatlas+aseg.mgz /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/label #-------------------------------------------- #@# BA_exvivo Labels rh Thu Mar 7 11:37:08 UTC 2019 mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.BA1_exvivo.label --trgsubject sub-030 --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.BA1_exvivo.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 136317 Number of reverse mapping hits = 396 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4358 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.BA2_exvivo.label --trgsubject sub-030 --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.BA2_exvivo.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 136317 Number of reverse mapping hits = 557 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 7244 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.BA3a_exvivo.label --trgsubject sub-030 --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 136317 Number of reverse mapping hits = 141 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4121 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.BA3b_exvivo.label --trgsubject sub-030 --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 136317 Number of reverse mapping hits = 273 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 4795 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.BA4a_exvivo.label --trgsubject sub-030 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 136317 Number of reverse mapping hits = 397 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 6144 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.BA4p_exvivo.label --trgsubject sub-030 --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 136317 Number of reverse mapping hits = 221 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4694 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.BA6_exvivo.label --trgsubject sub-030 --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.BA6_exvivo.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 136317 Number of reverse mapping hits = 837 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 13093 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.BA44_exvivo.label --trgsubject sub-030 --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.BA44_exvivo.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 136317 Number of reverse mapping hits = 451 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 7363 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.BA45_exvivo.label --trgsubject sub-030 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.BA45_exvivo.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 136317 Number of reverse mapping hits = 734 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 6089 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.V1_exvivo.label --trgsubject sub-030 --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.V1_exvivo.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 136317 Number of reverse mapping hits = 1326 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 6053 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.V2_exvivo.label --trgsubject sub-030 --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.V2_exvivo.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 136317 Number of reverse mapping hits = 2471 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 10487 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.MT_exvivo.label --trgsubject sub-030 --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.MT_exvivo.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 136317 Number of reverse mapping hits = 453 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2385 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject sub-030 --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1038 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 136317 Number of reverse mapping hits = 51 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1089 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject sub-030 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 136317 Number of reverse mapping hits = 24 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 776 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject sub-030 --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 136317 Number of reverse mapping hits = 156 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 1032 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject sub-030 --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 136317 Number of reverse mapping hits = 204 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2892 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject sub-030 --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 136317 Number of reverse mapping hits = 55 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1753 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject sub-030 --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 136317 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject sub-030 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 136317 Number of reverse mapping hits = 103 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1491 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject sub-030 --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 136317 Number of reverse mapping hits = 98 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1587 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject sub-030 --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 136317 Number of reverse mapping hits = 417 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 7376 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject sub-030 --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 136317 Number of reverse mapping hits = 81 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1093 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject sub-030 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 136317 Number of reverse mapping hits = 106 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1284 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject sub-030 --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 136317 Number of reverse mapping hits = 842 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 4074 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject sub-030 --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 136317 Number of reverse mapping hits = 1086 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 4523 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject sub-030 --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 136317 Number of reverse mapping hits = 55 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 323 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject sub-030 --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 694 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 136317 Number of reverse mapping hits = 32 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 726 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject sub-030 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/label/rh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-030 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 291 points in source label. Starting surface-based mapping Reading source registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.white Reading target registration /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 136317 Number of reverse mapping hits = 3 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 294 mri_label2label: Done mris_label2annot --s sub-030 --hemi rh --ctab /opt/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 /opt/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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/label cmdline mris_label2annot --s sub-030 --hemi rh --ctab /opt/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 c14n09.farnam.hpc.yale.internal machine x86_64 user mc2835 subject sub-030 hemi rh SUBJECTS_DIR /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer ColorTable /opt/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 95601 unhit vertices Writing annot to /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/label/rh.BA_exvivo.annot mris_label2annot --s sub-030 --hemi rh --ctab /opt/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 /opt/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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/label cmdline mris_label2annot --s sub-030 --hemi rh --ctab /opt/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 c14n09.farnam.hpc.yale.internal machine x86_64 user mc2835 subject sub-030 hemi rh SUBJECTS_DIR /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer ColorTable /opt/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 113312 unhit vertices Writing annot to /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/label/rh.BA_exvivo.thresh.annot mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.stats -b -a ./rh.BA_exvivo.annot -c ./BA_exvivo.ctab sub-030 rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/wm.mgz... reading input surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.white... reading input pial surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.pial... reading input white surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 218308 Total vertex volume 214705 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /opt/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) = 1538061 mm^3 (det: 1.266599 ) lhCtxGM: 213847.814 213400.000 diff= 447.8 pctdiff= 0.209 rhCtxGM: 213971.072 213772.000 diff= 199.1 pctdiff= 0.093 lhCtxWM: 231001.158 231265.500 diff= -264.3 pctdiff=-0.114 rhCtxWM: 233007.839 233280.500 diff= -272.7 pctdiff=-0.117 SubCortGMVol 51692.000 SupraTentVol 978048.883 (976068.000) diff=1980.883 pctdiff=0.203 SupraTentVolNotVent 945447.883 (943467.000) diff=1980.883 pctdiff=0.210 BrainSegVol 1113758.000 (1110375.000) diff=3383.000 pctdiff=0.304 BrainSegVolNotVent 1076419.000 (1076405.883) diff=13.117 pctdiff=0.001 BrainSegVolNotVent 1076419.000 CerebellumVol 132829.000 VentChorVol 32601.000 3rd4th5thCSF 4738.000 CSFVol 1355.000, OptChiasmVol 123.000 MaskVol 1386316.000 1096 623 1758 2.025 0.739 0.154 0.064 26 3.4 BA1_exvivo 3675 2340 4459 1.894 0.486 0.117 0.026 37 3.9 BA2_exvivo 1159 765 942 1.608 0.387 0.142 0.028 14 1.2 BA3a_exvivo 2026 1351 2481 1.628 0.511 0.108 0.020 16 1.9 BA3b_exvivo 1658 1063 2986 2.450 0.515 0.094 0.020 10 1.4 BA4a_exvivo 1389 911 1970 2.185 0.466 0.093 0.018 7 1.1 BA4p_exvivo 7898 5146 15922 2.670 0.585 0.123 0.029 82 9.2 BA6_exvivo 3407 2305 5371 2.219 0.451 0.125 0.024 40 3.4 BA44_exvivo 3966 2730 7153 2.294 0.536 0.151 0.034 73 5.4 BA45_exvivo 3709 2518 4364 1.622 0.564 0.142 0.034 45 5.4 V1_exvivo 7793 5080 9431 1.819 0.541 0.160 0.041 123 13.0 V2_exvivo 2088 1398 3326 2.273 0.470 0.150 0.034 28 2.8 MT_exvivo 548 368 1931 3.485 1.017 0.136 0.030 10 0.7 perirhinal_exvivo 304 228 588 2.357 0.555 0.083 0.012 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 sub-030 rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri/wm.mgz... reading input surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.white... reading input pial surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.pial... reading input white surface /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 218308 Total vertex volume 214705 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /opt/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) = 1538061 mm^3 (det: 1.266599 ) lhCtxGM: 213847.814 213400.000 diff= 447.8 pctdiff= 0.209 rhCtxGM: 213971.072 213772.000 diff= 199.1 pctdiff= 0.093 lhCtxWM: 231001.158 231265.500 diff= -264.3 pctdiff=-0.114 rhCtxWM: 233007.839 233280.500 diff= -272.7 pctdiff=-0.117 SubCortGMVol 51692.000 SupraTentVol 978048.883 (976068.000) diff=1980.883 pctdiff=0.203 SupraTentVolNotVent 945447.883 (943467.000) diff=1980.883 pctdiff=0.210 BrainSegVol 1113758.000 (1110375.000) diff=3383.000 pctdiff=0.304 BrainSegVolNotVent 1076419.000 (1076405.883) diff=13.117 pctdiff=0.001 BrainSegVolNotVent 1076419.000 CerebellumVol 132829.000 VentChorVol 32601.000 3rd4th5thCSF 4738.000 CSFVol 1355.000, OptChiasmVol 123.000 MaskVol 1386316.000 762 430 1064 1.745 0.668 0.154 0.074 21 3.0 BA1_exvivo 2154 1337 2775 1.922 0.597 0.102 0.020 19 1.8 BA2_exvivo 1059 706 805 1.594 0.358 0.148 0.029 12 1.2 BA3a_exvivo 1606 1071 1593 1.460 0.354 0.096 0.015 10 1.1 BA3b_exvivo 1049 638 1763 2.563 0.535 0.109 0.026 8 1.2 BA4a_exvivo 1167 759 1631 2.160 0.481 0.085 0.017 5 0.8 BA4p_exvivo 5058 3306 10559 2.713 0.606 0.120 0.028 48 5.6 BA6_exvivo 815 574 1518 2.337 0.481 0.127 0.027 11 0.9 BA44_exvivo 937 631 1771 2.400 0.449 0.147 0.031 18 1.1 BA45_exvivo 3537 2393 4017 1.609 0.566 0.140 0.034 41 5.3 V1_exvivo 4053 2711 4610 1.668 0.472 0.163 0.041 65 7.2 V2_exvivo 285 197 611 2.519 0.591 0.168 0.038 5 0.3 MT_exvivo 332 222 1241 3.567 0.960 0.141 0.032 7 0.6 perirhinal_exvivo 191 156 568 2.617 0.577 0.097 0.017 2 0.1 entorhinal_exvivo Started at Thu Mar 7 11:24:55 UTC 2019 Ended at Thu Mar 7 11:40:31 UTC 2019 #@#%# recon-all-run-time-hours 0.260 recon-all -s sub-030 finished without error at Thu Mar 7 11:40:31 UTC 2019 New invocation of recon-all Thu Mar 7 11:40:32 UTC 2019 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030 /opt/freesurfer/bin/recon-all -autorecon3 -hemi lh -openmp 7 -subjid sub-030 -sd /home/mc2835/scratch60/RVLdata/fmriprep_output/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nocortribbon -nohyporelabel -noaparc2aseg -nosegstats -nowmparc -nobalabels subjid sub-030 setenv SUBJECTS_DIR /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /opt/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a Linux c14n09.farnam.hpc.yale.internal 3.10.0-693.37.4.el7.x86_64 #1 SMP Fri Aug 10 12:34:55 EDT 2018 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize unlimited memoryuse 65536000 kbytes vmemoryuse unlimited descriptors 51200 memorylocked unlimited maxproc 512036 maxlocks unlimited maxsignal 512036 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 131317832 22384588 73862412 654424 35070832 107528456 Swap: 16777212 151228 16625984 ######################################## 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: 2019/03/07-11:40:32-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:40:32-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:40:32-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-11:40:32-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:40:32-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:40:32-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-11:40:32-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-11:40:32-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-11:40:32-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-11:40:32-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-11:40:32-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-11:40:32-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:40:32-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:40:32-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-11:40:32-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:40:32-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:40:32-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:40:32-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:40:32-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:40:32-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:40:32-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-11:40:32-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:40:32-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:40:32-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:40:32-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-11:40:32-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:40:32-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/07-11:40:32-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:40:32-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:40:32-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:40:32-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:40:32-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:40:32-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:40:32-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:40:32-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:40:32-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:40:32-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:40:32-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/07-11:40:32-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: mc2835 Machine: c14n09.farnam.hpc.yale.internal Platform: Linux PlatformVersion: 3.10.0-693.37.4.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /opt/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /opt/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #----------------------------------------- #@# APas-to-ASeg Thu Mar 7 11:40:33 UTC 2019 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri apas2aseg --i aparc+aseg.mgz --o aseg.mgz Thu Mar 7 11:40:33 UTC 2019 setenv SUBJECTS_DIR /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer cd /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/mri /opt/freesurfer/bin/apas2aseg --i aparc+aseg.mgz --o aseg.mgz freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a $Id: apas2aseg,v 1.2 2016/02/12 21:43:14 zkaufman Exp $ Linux c14n09.farnam.hpc.yale.internal 3.10.0-693.37.4.el7.x86_64 #1 SMP Fri Aug 10 12:34:55 EDT 2018 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 /gpfs/ysm/scratch60/mc2835/RVLdata/fmriprep_output/freesurfer/sub-030/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 c14n09.farnam.hpc.yale.internal machine x86_64 user mc2835 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 Mar 7 11:40:33 UTC 2019 Ended at Thu Mar 7 11:40:35 UTC 2019 Apas2aseg-Run-Time-Sec 2 apas2aseg Done Started at Thu Mar 7 11:40:32 UTC 2019 Ended at Thu Mar 7 11:40:35 UTC 2019 #@#%# recon-all-run-time-hours 0.001 recon-all -s sub-030 finished without error at Thu Mar 7 11:40:36 UTC 2019